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2004
Westhof E
How to silence silencing Journal Article
In: Chem Biol, vol. 11, no. 2, pp. 158-160, 2004, ISBN: 15123277, (1074-5521 Journal Article).
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {How to silence silencing},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15123277},
isbn = {15123277},
year = {2004},
date = {2004-01-01},
journal = {Chem Biol},
volume = {11},
number = {2},
pages = {158-160},
abstract = {Two recent reports describe the stunning crystal structures of complexes between a viral protein that suppresses RNA silencing and a 21 nucleotide small interfering (si)RNA.},
note = {1074-5521
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Two recent reports describe the stunning crystal structures of complexes between a viral protein that suppresses RNA silencing and a 21 nucleotide small interfering (si)RNA.
Keiper S, Bebenroth D, Seelig B, Westhof E, Jaschke A
Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket Journal Article
In: Chem Biol, vol. 11, no. 9, pp. 1217-1227, 2004, ISBN: 15380182, (1074-5521 Journal Article).
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket},
author = {S Keiper and D Bebenroth and B Seelig and E Westhof and A Jaschke},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15380182},
isbn = {15380182},
year = {2004},
date = {2004-01-01},
journal = {Chem Biol},
volume = {11},
number = {9},
pages = {1217-1227},
abstract = {Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.},
note = {1074-5521
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.
Francois B, Szychowski J, Adhikari S S, Pachamuthu K, Swayze E E, Griffey R H, Migawa M T, Westhof E, Hanessian S
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site Journal Article
In: Angew Chem Int Ed Engl, vol. 43, no. 48, pp. 6735-6738, 2004, ISBN: 15593140, (0570-0833 Journal Article).
Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site},
author = {B Francois and J Szychowski and S S Adhikari and K Pachamuthu and E E Swayze and R H Griffey and M T Migawa and E Westhof and S Hanessian},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15593140},
isbn = {15593140},
year = {2004},
date = {2004-01-01},
journal = {Angew Chem Int Ed Engl},
volume = {43},
number = {48},
pages = {6735-6738},
note = {0570-0833
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Hays F A, Westhof E, Ho P S
Halogen bonds in biological molecules Journal Article
In: Proc Natl Acad Sci U S A, vol. 101, no. 48, pp. 16789-16794, 2004, ISBN: 15557000, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Halogen bonds in biological molecules},
author = {P Auffinger and F A Hays and E Westhof and P S Ho},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15557000},
isbn = {15557000},
year = {2004},
date = {2004-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {101},
number = {48},
pages = {16789-16794},
abstract = {Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short CX.OY interaction (CX is a carbon-bonded chlorine, bromine, or iodine, and OY is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X.O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl.O, 3.37A for Br.O, and 3.50 A for I.O) and can conform to the geometry seen in small molecules, with the CX.O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X.OY angle approximately 120 degrees. Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.},
note = {0027-8424
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short CX.OY interaction (CX is a carbon-bonded chlorine, bromine, or iodine, and OY is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X.O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl.O, 3.37A for Br.O, and 3.50 A for I.O) and can conform to the geometry seen in small molecules, with the CX.O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X.OY angle approximately 120 degrees. Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.
Auffinger P, Bielecki L, Westhof E
Anion binding to nucleic acids Journal Article
In: Structure, vol. 12, no. 3, pp. 379-388, 2004, ISBN: 15016354, (0969-2126 Journal Article).
Abstract | Links | BibTeX | Tags: Anions/chemistry/*metabolism Computer Simulation Databases, Molecular Nucleic Acids/chemistry/*metabolism Support, Non-U.S. Gov't X-Ray Diffraction, Nucleic Acid Models, Unité ARN, WESTHOF
@article{,
title = {Anion binding to nucleic acids},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15016354},
isbn = {15016354},
year = {2004},
date = {2004-01-01},
journal = {Structure},
volume = {12},
number = {3},
pages = {379-388},
abstract = {Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.},
note = {0969-2126
Journal Article},
keywords = {Anions/chemistry/*metabolism Computer Simulation Databases, Molecular Nucleic Acids/chemistry/*metabolism Support, Non-U.S. Gov't X-Ray Diffraction, Nucleic Acid Models, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.
Rangan P, Masquida B, Westhof E, Woodson S A
Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA Journal Article
In: J Mol Biol, vol. 339, no. 1, pp. 41-51, 2004, ISBN: 15123419, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15123419},
isbn = {15123419},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {339},
number = {1},
pages = {41-51},
abstract = {Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA(ile) from the bacterium Azoarcus was probed by ribonuclease T(1) and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3'-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg(2+) and the concentration of urea, and RNase T(1) experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5' and 3' ends of unspliced pre-tRNA.},
note = {0022-2836
Journal Article},
keywords = {Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA(ile) from the bacterium Azoarcus was probed by ribonuclease T(1) and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3'-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg(2+) and the concentration of urea, and RNase T(1) experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5' and 3' ends of unspliced pre-tRNA.
Malnou C E, Werner A, Borman A M, Westhof E, Kean K M
Effects of vaccine strain mutations in domain V of the internal ribosome entry segment compared in the wild type poliovirus type 1 context Journal Article
In: J Biol Chem, vol. 279, no. 11, pp. 10261-10269, 2004, ISBN: 14672927, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Blotting, Genetic, Messenger/metabolism Ribosomes/*genetics Support, Non-U.S. Gov't Translation, Tertiary RNA/chemistry RNA, Unité ARN, Viral Electrophoresis, Western DNA, WESTHOF
@article{,
title = {Effects of vaccine strain mutations in domain V of the internal ribosome entry segment compared in the wild type poliovirus type 1 context},
author = {C E Malnou and A Werner and A M Borman and E Westhof and K M Kean},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14672927},
isbn = {14672927},
year = {2004},
date = {2004-01-01},
journal = {J Biol Chem},
volume = {279},
number = {11},
pages = {10261-10269},
abstract = {Initiation of poliovirus (PV) protein synthesis is governed by an internal ribosome entry segment structured into several domains including domain V, which is accepted to be important in PV neurovirulence because it harbors an attenuating mutation in each of the vaccine strains developed by A. Sabin. To better understand how these single point mutations exert their effects, we placed each of them into the same genomic context, that of PV type 1. Only the mutation equivalent to the Sabin type 3 strain mutation resulted in significantly reduced viral growth both in HeLa and neuroblastoma cells. This correlated with poor translation efficiency in vitro and could be explained by a structural perturbation of the domain V of the internal ribosome entry segment, as evidenced by RNA melting experiments. We demonstrated that reduced cell death observed during infection by this mutant is due to the absence of inhibition of host cell translation. We confirmed that this shut-off is correlated principally with cleavage of eIF4GII and not eIF4GI and that this cleavage is significantly impaired in the case of the defective mutant. These data support the previously reported conclusion that the 2A protease has markedly different affinities for the two eIF4G isoforms.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence Blotting, Genetic, Messenger/metabolism Ribosomes/*genetics Support, Non-U.S. Gov't Translation, Tertiary RNA/chemistry RNA, Unité ARN, Viral Electrophoresis, Western DNA, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Initiation of poliovirus (PV) protein synthesis is governed by an internal ribosome entry segment structured into several domains including domain V, which is accepted to be important in PV neurovirulence because it harbors an attenuating mutation in each of the vaccine strains developed by A. Sabin. To better understand how these single point mutations exert their effects, we placed each of them into the same genomic context, that of PV type 1. Only the mutation equivalent to the Sabin type 3 strain mutation resulted in significantly reduced viral growth both in HeLa and neuroblastoma cells. This correlated with poor translation efficiency in vitro and could be explained by a structural perturbation of the domain V of the internal ribosome entry segment, as evidenced by RNA melting experiments. We demonstrated that reduced cell death observed during infection by this mutant is due to the absence of inhibition of host cell translation. We confirmed that this shut-off is correlated principally with cleavage of eIF4GII and not eIF4GI and that this cleavage is significantly impaired in the case of the defective mutant. These data support the previously reported conclusion that the 2A protease has markedly different affinities for the two eIF4G isoforms.
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, Montigny J De, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich J M, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, Daruvar A De, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud J M, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard G F, Straub M L, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet J L
Genome evolution in yeasts Journal Article
In: Nature, vol. 430, no. 6995, pp. 35-44, 2004, ISBN: 15229592, (1476-4687 Journal Article).
Abstract | Links | BibTeX | Tags: Chromosomes, Fungal Molecular Sequence Data RNA, Fungal/*genetics *Genome, Fungal/genetics Conserved Sequence/genetics *Evolution, Molecular Gene Duplication Genes, Non-U.S. Gov't Synteny/genetics Tandem Repeat Sequences/genetics Yeasts/*classification/*genetics, Ribosomal/genetics RNA, Transfer/genetics Saccharomyces cerevisiae Proteins/genetics Support, Unité ARN, WESTHOF
@article{,
title = {Genome evolution in yeasts},
author = {B Dujon and D Sherman and G Fischer and P Durrens and S Casaregola and I Lafontaine and J De Montigny and C Marck and C Neuveglise and E Talla and N Goffard and L Frangeul and M Aigle and V Anthouard and A Babour and V Barbe and S Barnay and S Blanchin and J M Beckerich and E Beyne and C Bleykasten and A Boisrame and J Boyer and L Cattolico and F Confanioleri and A De Daruvar and L Despons and E Fabre and C Fairhead and H Ferry-Dumazet and A Groppi and F Hantraye and C Hennequin and N Jauniaux and P Joyet and R Kachouri and A Kerrest and R Koszul and M Lemaire and I Lesur and L Ma and H Muller and J M Nicaud and M Nikolski and S Oztas and O Ozier-Kalogeropoulos and S Pellenz and S Potier and G F Richard and M L Straub and A Suleau and D Swennen and F Tekaia and M Wesolowski-Louvel and E Westhof and B Wirth and M Zeniou-Meyer and I Zivanovic and M Bolotin-Fukuhara and A Thierry and C Bouchier and B Caudron and C Scarpelli and C Gaillardin and J Weissenbach and P Wincker and J L Souciet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15229592},
isbn = {15229592},
year = {2004},
date = {2004-01-01},
journal = {Nature},
volume = {430},
number = {6995},
pages = {35-44},
abstract = {Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.},
note = {1476-4687
Journal Article},
keywords = {Chromosomes, Fungal Molecular Sequence Data RNA, Fungal/*genetics *Genome, Fungal/genetics Conserved Sequence/genetics *Evolution, Molecular Gene Duplication Genes, Non-U.S. Gov't Synteny/genetics Tandem Repeat Sequences/genetics Yeasts/*classification/*genetics, Ribosomal/genetics RNA, Transfer/genetics Saccharomyces cerevisiae Proteins/genetics Support, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Serra M J, Smolter P E, Westhof E
Pronounced instability of tandem IU base pairs in RNA Journal Article
In: Nucleic Acids Res, vol. 32, no. 5, pp. 1824-1828, 2004, ISBN: 15037659, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Base Pairing Inosine/*chemistry Magnesium/chemistry Nucleic Acid Conformation RNA/*chemistry RNA Stability Support, Non-P.H.S. Thermodynamics Uracil/*chemistry, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Pronounced instability of tandem IU base pairs in RNA},
author = {M J Serra and P E Smolter and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15037659},
isbn = {15037659},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {5},
pages = {1824-1828},
abstract = {Optical melting was used to determine the stabilities of three series of RNA oligomers containing tandem XU base pairs, GGCXUGCC (5'XU3'), GGCUXGCC (5'UX3') and GGCXXGGC/CCGUUCCG (5'XX3'), where X is either A, G or I (inosine). The helices containing tandem AU base pairs were the most stable in the first two series (5'XU3' and 5'UX3'), with an average melting temperature approximately 11 degrees C higher than the helices with tandem 5'GU3' base pairs and 25 degrees C higher than the helices with tandem 5'IU3' base pairs. For the third series (5'XX3'), the helix containing tandem GG is the most stable, with an average melting temperature approximately 2 degrees C higher than the helix with tandem AA base pairs and approximately 24 degrees C higher than the helix with tandem II base pairs. The thermodynamic stability of the oligomers with tandem IU base pairs was also investigated as a function of magnesium ion concentration. As with normal A-U or G-U tandem duplexes, the data could best be interpreted as non-specific binding of magnesium ions to the inosine-containing RNA oligonucleotides.},
note = {1362-4962
Journal Article},
keywords = {Base Pairing Inosine/*chemistry Magnesium/chemistry Nucleic Acid Conformation RNA/*chemistry RNA Stability Support, Non-P.H.S. Thermodynamics Uracil/*chemistry, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Optical melting was used to determine the stabilities of three series of RNA oligomers containing tandem XU base pairs, GGCXUGCC (5'XU3'), GGCUXGCC (5'UX3') and GGCXXGGC/CCGUUCCG (5'XX3'), where X is either A, G or I (inosine). The helices containing tandem AU base pairs were the most stable in the first two series (5'XU3' and 5'UX3'), with an average melting temperature approximately 11 degrees C higher than the helices with tandem 5'GU3' base pairs and 25 degrees C higher than the helices with tandem 5'IU3' base pairs. For the third series (5'XX3'), the helix containing tandem GG is the most stable, with an average melting temperature approximately 2 degrees C higher than the helix with tandem AA base pairs and approximately 24 degrees C higher than the helix with tandem II base pairs. The thermodynamic stability of the oligomers with tandem IU base pairs was also investigated as a function of magnesium ion concentration. As with normal A-U or G-U tandem duplexes, the data could best be interpreted as non-specific binding of magnesium ions to the inosine-containing RNA oligonucleotides.
Zhang H, Kolb F A, Jaskiewicz L, Westhof E, Filipowicz W
Single processing center models for human Dicer and bacterial RNase III Journal Article
In: Cell, vol. 118, no. 1, pp. 57-68, 2004, ISBN: 15242644, (0092-8674 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF
@article{,
title = {Single processing center models for human Dicer and bacterial RNase III},
author = {H Zhang and F A Kolb and L Jaskiewicz and E Westhof and W Filipowicz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15242644},
isbn = {15242644},
year = {2004},
date = {2004-01-01},
journal = {Cell},
volume = {118},
number = {1},
pages = {57-68},
abstract = {Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins. Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer. Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed. We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing. Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs. Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins. Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer. Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed. We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing. Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs. Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.
Westhof E, Massire C
Structural biology. Evolution of RNA architecture Journal Article
In: Science, vol. 306, no. 5693, pp. 62-63, 2004, ISBN: 15459373, (1095-9203 Comment Journal Article).
Links | BibTeX | Tags: Adenine/chemistry Base Pairing Computational Biology Crystallography, Bacterial/*chemistry/metabolism RNA, Molecular Nucleic Acid Conformation RNA Precursors/metabolism RNA, Transfer/metabolism Ribonuclease P/*chemistry/metabolism Thermus thermophilus/*chemistry/enzymology, Unité ARN, WESTHOF, X-Ray Evolution
@article{,
title = {Structural biology. Evolution of RNA architecture},
author = {E Westhof and C Massire},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15459373},
isbn = {15459373},
year = {2004},
date = {2004-01-01},
journal = {Science},
volume = {306},
number = {5693},
pages = {62-63},
note = {1095-9203
Comment
Journal Article},
keywords = {Adenine/chemistry Base Pairing Computational Biology Crystallography, Bacterial/*chemistry/metabolism RNA, Molecular Nucleic Acid Conformation RNA Precursors/metabolism RNA, Transfer/metabolism Ribonuclease P/*chemistry/metabolism Thermus thermophilus/*chemistry/enzymology, Unité ARN, WESTHOF, X-Ray Evolution},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Bielecki L, Westhof E
Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations Journal Article
In: J Mol Biol, vol. 335, no. 2, pp. 555-571, 2004, ISBN: 14672663, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/metabolism Support, Bacterial/chemistry RNA, Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation Potassium/chemistry/*metabolism Protein Binding/genetics RNA, Non-U.S. Gov't Water/chemistry/metabolism, Ribosomal, Unité ARN, WESTHOF, WESTHOF Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models
@article{,
title = {Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14672663},
isbn = {14672663},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {335},
number = {2},
pages = {555-571},
abstract = {Potassium binding to the 5S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg2+. A clear pattern of seven deep groove K+ binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G.A pair) were found to accommodate K+ ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg2+ binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson-Crick pairs that has certainly to be stabilized by specific Mg2+ ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K+ concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K+ binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.},
note = {0022-2836
Journal Article},
keywords = {5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/metabolism Support, Bacterial/chemistry RNA, Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation Potassium/chemistry/*metabolism Protein Binding/genetics RNA, Non-U.S. Gov't Water/chemistry/metabolism, Ribosomal, Unité ARN, WESTHOF, WESTHOF Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Potassium binding to the 5S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg2+. A clear pattern of seven deep groove K+ binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G.A pair) were found to accommodate K+ ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg2+ binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson-Crick pairs that has certainly to be stabilized by specific Mg2+ ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K+ concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K+ binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.
2003
Leontis N B, Westhof E
Analysis of RNA motifs Journal Article
In: Curr Opin Struct Biol, vol. 13, no. 3, pp. 300-308, 2003, ISBN: 12831880, (0959-440x Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: *Base Pairing Binding Sites Magnetic Resonance Imaging *Nucleic Acid Conformation RNA/*chemistry RNA, Chloroplast/chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Analysis of RNA motifs},
author = {N B Leontis and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12831880},
isbn = {12831880},
year = {2003},
date = {2003-01-01},
journal = {Curr Opin Struct Biol},
volume = {13},
number = {3},
pages = {300-308},
abstract = {RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices as seen in two-dimensional representations of RNA structure. RNA motifs mediate the specific interactions that induce the compact folding of complex RNAs. RNA motifs also constitute specific protein or ligand binding sites. A given motif is characterized by all the sequences that fold into essentially identical three-dimensional structures with the same ordered array of isosteric non-Watson-Crick base pairs. It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically.},
note = {0959-440x
Journal Article
Review
Review, Tutorial},
keywords = {*Base Pairing Binding Sites Magnetic Resonance Imaging *Nucleic Acid Conformation RNA/*chemistry RNA, Chloroplast/chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices as seen in two-dimensional representations of RNA structure. RNA motifs mediate the specific interactions that induce the compact folding of complex RNAs. RNA motifs also constitute specific protein or ligand binding sites. A given motif is characterized by all the sequences that fold into essentially identical three-dimensional structures with the same ordered array of isosteric non-Watson-Crick base pairs. It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically.
Rangan P, Masquida B, Westhof E, Woodson S A
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme Journal Article
In: Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1574-1579, 2003, ISBN: 12574513, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12574513},
isbn = {12574513},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {4},
pages = {1574-1579},
abstract = {Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.},
note = {0027-8424
Journal Article},
keywords = {Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.
Vicens Q, Westhof E
Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide Journal Article
In: J Mol Biol, vol. 326, no. 4, pp. 1175-1188, 2003, ISBN: 12589761, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes
@article{,
title = {Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12589761},
isbn = {12589761},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {326},
number = {4},
pages = {1175-1188},
abstract = {Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes},
pubstate = {published},
tppubtype = {article}
}
Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.
Tsai H Y, Masquida B, Biswas R, Westhof E, Gopalan V
Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme Journal Article
In: J Mol Biol, vol. 325, no. 4, pp. 661-675, 2003, ISBN: 12507471, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Sequence Base Sequence Catalytic Domain Computer Simulation Cysteine/chemistry DNA Footprinting DNA, Bacterial/chemistry/genetics/metabolism RNA, Bacterial/genetics Edetic Acid Endoribonucleases/*chemistry/genetics/metabolism Escherichia coli/*enzymology/genetics Evolution, Catalytic/*chemistry/genetics/metabolism Ribonuclease P Support, Molecular Ferrous Compounds Holoenzymes/chemistry/genetics/metabolism Hydroxyl Radical/chemistry Models, Molecular Molecular Sequence Data Mutagenesis, Non-P.H.S. Support, P.H.S., Site-Directed Nucleic Acid Conformation Protein Subunits RNA, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme},
author = {H Y Tsai and B Masquida and R Biswas and E Westhof and V Gopalan},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12507471},
isbn = {12507471},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {325},
number = {4},
pages = {661-675},
abstract = {Bacterial ribonuclease P (RNase P), an enzyme involved in tRNA maturation, consists of a catalytic RNA subunit and a protein cofactor. Comparative phylogenetic analysis and molecular modeling have been employed to derive secondary and tertiary structure models of the RNA subunits from Escherichia coli (type A) and Bacillus subtilis (type B) RNase P. The tertiary structure of the protein subunit of B.subtilis and Staphylococcus aureus RNase P has recently been determined. However, an understanding of the structure of the RNase P holoenzyme (i.e. the ribonucleoprotein complex) is lacking. We have now used an EDTA-Fe-based footprinting approach to generate information about RNA-protein contact sites in E.coli RNase P. The footprinting data, together with results from other biochemical and biophysical studies, have furnished distance constraints, which in turn have enabled us to build three-dimensional models of both type A and B versions of the bacterial RNase P holoenzyme in the absence and presence of its precursor tRNA substrate. These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Catalytic Domain Computer Simulation Cysteine/chemistry DNA Footprinting DNA, Bacterial/chemistry/genetics/metabolism RNA, Bacterial/genetics Edetic Acid Endoribonucleases/*chemistry/genetics/metabolism Escherichia coli/*enzymology/genetics Evolution, Catalytic/*chemistry/genetics/metabolism Ribonuclease P Support, Molecular Ferrous Compounds Holoenzymes/chemistry/genetics/metabolism Hydroxyl Radical/chemistry Models, Molecular Molecular Sequence Data Mutagenesis, Non-P.H.S. Support, P.H.S., Site-Directed Nucleic Acid Conformation Protein Subunits RNA, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Bacterial ribonuclease P (RNase P), an enzyme involved in tRNA maturation, consists of a catalytic RNA subunit and a protein cofactor. Comparative phylogenetic analysis and molecular modeling have been employed to derive secondary and tertiary structure models of the RNA subunits from Escherichia coli (type A) and Bacillus subtilis (type B) RNase P. The tertiary structure of the protein subunit of B.subtilis and Staphylococcus aureus RNase P has recently been determined. However, an understanding of the structure of the RNase P holoenzyme (i.e. the ribonucleoprotein complex) is lacking. We have now used an EDTA-Fe-based footprinting approach to generate information about RNA-protein contact sites in E.coli RNase P. The footprinting data, together with results from other biochemical and biophysical studies, have furnished distance constraints, which in turn have enabled us to build three-dimensional models of both type A and B versions of the bacterial RNase P holoenzyme in the absence and presence of its precursor tRNA substrate. These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex.
Vicens Q, Westhof E
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures Journal Article
In: Biopolymers, vol. 70, no. 1, pp. 42-57, 2003, ISBN: 12925992, (0006-3525 Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Binding Sites Crystallography, Chemical Models, Microbial Enzymes/*chemistry Models, Molecular Protein Binding RNA/chemistry RNA, Ribosomal/*chemistry Ribosomes/chemistry, Unité ARN, WESTHOF, X-Ray/*methods *Drug Resistance
@article{,
title = {Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12925992},
isbn = {12925992},
year = {2003},
date = {2003-01-01},
journal = {Biopolymers},
volume = {70},
number = {1},
pages = {42-57},
abstract = {The potential of RNA molecules to be used as therapeutic targets by small inhibitors is now well established. In this fascinating wide-open field, aminoglycoside antibiotics constitute the most studied family of RNA binding drugs. Within the last three years, several x-ray crystal structures were solved for aminoglycosides complexed to one of their main natural targets in the bacterial cell, the decoding aminoacyl-tRNA site (A site). Other crystallographic structures have revealed the binding modes of aminoglycosides to the three existing types of resistance-associated enzymes. The present review summarizes the various aspects of the molecular recognition of aminoglycosides by these natural RNA or protein receptors. The analysis and the comparisons of the detailed interactions offer insights that are helpful in designing new generations of antibiotics.},
note = {0006-3525
Journal Article
Review
Review, Tutorial},
keywords = {Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Binding Sites Crystallography, Chemical Models, Microbial Enzymes/*chemistry Models, Molecular Protein Binding RNA/chemistry RNA, Ribosomal/*chemistry Ribosomes/chemistry, Unité ARN, WESTHOF, X-Ray/*methods *Drug Resistance},
pubstate = {published},
tppubtype = {article}
}
The potential of RNA molecules to be used as therapeutic targets by small inhibitors is now well established. In this fascinating wide-open field, aminoglycoside antibiotics constitute the most studied family of RNA binding drugs. Within the last three years, several x-ray crystal structures were solved for aminoglycosides complexed to one of their main natural targets in the bacterial cell, the decoding aminoacyl-tRNA site (A site). Other crystallographic structures have revealed the binding modes of aminoglycosides to the three existing types of resistance-associated enzymes. The present review summarizes the various aspects of the molecular recognition of aminoglycosides by these natural RNA or protein receptors. The analysis and the comparisons of the detailed interactions offer insights that are helpful in designing new generations of antibiotics.
Vicens Q, Westhof E
RNA as a drug target: the case of aminoglycosides Journal Article
In: Chembiochem, vol. 4, no. 10, pp. 1018-1023, 2003, ISBN: 14523919, (1439-4227 Journal Article Review Review, Tutorial).
Links | BibTeX | Tags: 16S/*chemistry/drug effects/metabolism Substrate Specificity Technology, Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Drug Delivery Systems Models, Catalytic/chemistry/metabolism RNA, Molecular RNA/chemistry/metabolism RNA, Pharmaceutical Water/chemistry, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {RNA as a drug target: the case of aminoglycosides},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14523919},
isbn = {14523919},
year = {2003},
date = {2003-01-01},
journal = {Chembiochem},
volume = {4},
number = {10},
pages = {1018-1023},
note = {1439-4227
Journal Article
Review
Review, Tutorial},
keywords = {16S/*chemistry/drug effects/metabolism Substrate Specificity Technology, Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Drug Delivery Systems Models, Catalytic/chemistry/metabolism RNA, Molecular RNA/chemistry/metabolism RNA, Pharmaceutical Water/chemistry, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Khvorova A, Lescoute A, Westhof E, Jayasena S D
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity Journal Article
In: Nat Struct Biol, vol. 10, no. 9, pp. 708-712, 2003, ISBN: 12881719, (1072-8368 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Motifs Base Sequence Catalysis Dose-Response Relationship, Catalytic/*chemistry Sequence Homology, Drug Genes, Nucleic Acid Time Factors, Reporter Genetic Vectors Kinetics Magnesium/chemistry Molecular Sequence Data Mutation Nucleic Acid Conformation Plasmids/metabolism Protein Binding Protein Conformation RNA/metabolism RNA, Unité ARN, WESTHOF
@article{,
title = {Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity},
author = {A Khvorova and A Lescoute and E Westhof and S D Jayasena},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12881719},
isbn = {12881719},
year = {2003},
date = {2003-01-01},
journal = {Nat Struct Biol},
volume = {10},
number = {9},
pages = {708-712},
abstract = {The hammerhead ribozyme (HHRz) is a small, naturally occurring ribozyme that site-specifically cleaves RNA and has long been considered a potentially useful tool for gene silencing. The minimal conserved HHRz motif derived from natural sequences consists of three helices that intersect at a highly conserved catalytic core of 11 nucleotides. The presence of this motif is sufficient to support cleavage at high Mg2+ concentrations, but not at the low Mg2+ concentrations characteristic of intracellular environments. Here we demonstrate that natural HHRzs require the presence of additional nonconserved sequence elements outside of the conserved catalytic core to enable intracellular activity. These elements may stabilize the HHRz in a catalytically active conformation via tertiary interactions. HHRzs stabilized by these interactions cleave efficiently at physiological Mg2+ concentrations and are functional in vivo. The proposed role of these tertiary interacting motifs is supported by mutational, functional, structural and molecular modeling analysis of natural HHRzs.},
note = {1072-8368
Journal Article},
keywords = {Amino Acid Motifs Base Sequence Catalysis Dose-Response Relationship, Catalytic/*chemistry Sequence Homology, Drug Genes, Nucleic Acid Time Factors, Reporter Genetic Vectors Kinetics Magnesium/chemistry Molecular Sequence Data Mutation Nucleic Acid Conformation Plasmids/metabolism Protein Binding Protein Conformation RNA/metabolism RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The hammerhead ribozyme (HHRz) is a small, naturally occurring ribozyme that site-specifically cleaves RNA and has long been considered a potentially useful tool for gene silencing. The minimal conserved HHRz motif derived from natural sequences consists of three helices that intersect at a highly conserved catalytic core of 11 nucleotides. The presence of this motif is sufficient to support cleavage at high Mg2+ concentrations, but not at the low Mg2+ concentrations characteristic of intracellular environments. Here we demonstrate that natural HHRzs require the presence of additional nonconserved sequence elements outside of the conserved catalytic core to enable intracellular activity. These elements may stabilize the HHRz in a catalytically active conformation via tertiary interactions. HHRzs stabilized by these interactions cleave efficiently at physiological Mg2+ concentrations and are functional in vivo. The proposed role of these tertiary interacting motifs is supported by mutational, functional, structural and molecular modeling analysis of natural HHRzs.
Auffinger P, Bielecki L, Westhof E
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations Journal Article
In: Chem Biol, vol. 10, no. 6, pp. 551-561, 2003, ISBN: 12837388, (1074-5521 Journal Article).
Abstract | Links | BibTeX | Tags: 5S/*chemistry/metabolism Support, Bacterial/*chemistry RNA, Binding Sites Cations, Divalent Computer Simulation Crystallization Electrostatics Hydrogen Bonding Magnesium/*chemistry/metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't Thermodynamics Water/chemistry, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12837388},
isbn = {12837388},
year = {2003},
date = {2003-01-01},
journal = {Chem Biol},
volume = {10},
number = {6},
pages = {551-561},
abstract = {Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.},
note = {1074-5521
Journal Article},
keywords = {5S/*chemistry/metabolism Support, Bacterial/*chemistry RNA, Binding Sites Cations, Divalent Computer Simulation Crystallization Electrostatics Hydrogen Bonding Magnesium/*chemistry/metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't Thermodynamics Water/chemistry, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.
Caillet J, Nogueira T, Masquida B, Winter F, Graffe M, Dock-Bregeon A C, Torres-Larios A, Sankaranarayanan R, Westhof E, Ehresmann B, Ehresmann C, Romby P, Springer M
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression Journal Article
In: Mol Microbiol, vol. 47, no. 4, pp. 961-974, 2003, ISBN: 12581352, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF
@article{,
title = {The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression},
author = {J Caillet and T Nogueira and B Masquida and F Winter and M Graffe and A C Dock-Bregeon and A Torres-Larios and R Sankaranarayanan and E Westhof and B Ehresmann and C Ehresmann and P Romby and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12581352},
isbn = {12581352},
year = {2003},
date = {2003-01-01},
journal = {Mol Microbiol},
volume = {47},
number = {4},
pages = {961-974},
abstract = {In addition to its role in tRNA aminoacylation, Escherichia coli threonyl-tRNA synthetase is a regulatory protein which binds a site, called the operator, located in the leader of its own mRNA and inhibits translational initiation by competing with ribosome binding. This work shows that the two essential steps of regulation, operator recognition and inhibition of ribosome binding, are performed by different domains of the protein. The catalytic and the C-terminal domain of the protein are involved in binding the two anticodon arm-like structures in the operator whereas the N-terminal domain of the enzyme is responsible for the competition with the ribosome. This is the first demonstration of a modular structure for a translational repressor and is reminiscent of that of transcriptional regulators. The mimicry between the operator and tRNA, suspected on the basis of previous experiments, is further supported by the fact that identical regions of the synthetase recognize both the operator and the tRNA anticodon arm. Based on these results, and recent structural data, we have constructed a computer-derived molecular model for the operator-threonyl-tRNA synthetase complex, which sheds light on several essential aspects of the regulatory mechanism.},
note = {0950-382x
Journal Article},
keywords = {Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
In addition to its role in tRNA aminoacylation, Escherichia coli threonyl-tRNA synthetase is a regulatory protein which binds a site, called the operator, located in the leader of its own mRNA and inhibits translational initiation by competing with ribosome binding. This work shows that the two essential steps of regulation, operator recognition and inhibition of ribosome binding, are performed by different domains of the protein. The catalytic and the C-terminal domain of the protein are involved in binding the two anticodon arm-like structures in the operator whereas the N-terminal domain of the enzyme is responsible for the competition with the ribosome. This is the first demonstration of a modular structure for a translational repressor and is reminiscent of that of transcriptional regulators. The mimicry between the operator and tRNA, suspected on the basis of previous experiments, is further supported by the fact that identical regions of the synthetase recognize both the operator and the tRNA anticodon arm. Based on these results, and recent structural data, we have constructed a computer-derived molecular model for the operator-threonyl-tRNA synthetase complex, which sheds light on several essential aspects of the regulatory mechanism.
Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E
Tools for the automatic identification and classification of RNA base pairs Journal Article
In: Nucleic Acids Res, vol. 31, no. 13, pp. 3450-3460, 2003, ISBN: 12824344, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Tools for the automatic identification and classification of RNA base pairs},
author = {H Yang and F Jossinet and N Leontis and L Chen and J Westbrook and H Berman and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824344},
isbn = {12824344},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {13},
pages = {3450-3460},
abstract = {Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.},
note = {1362-4962
Journal Article},
keywords = {Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.
Pfister P, Hobbie S, Vicens Q, Bottger E C, Westhof E
In: Chembiochem, vol. 4, no. 10, pp. 1078-1088, 2003, ISBN: 14523926, (1439-4227 Journal Article).
Abstract | Links | BibTeX | Tags: Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models
@article{,
title = {The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures},
author = {P Pfister and S Hobbie and Q Vicens and E C Bottger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14523926},
isbn = {14523926},
year = {2003},
date = {2003-01-01},
journal = {Chembiochem},
volume = {4},
number = {10},
pages = {1078-1088},
abstract = {Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the non-Watson-Crick U1406.U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6' (either hydroxy or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409-G1491 to A1409-U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6'-NH3+ aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406.U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406.U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies.},
note = {1439-4227
Journal Article},
keywords = {Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models},
pubstate = {published},
tppubtype = {article}
}
Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the non-Watson-Crick U1406.U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6' (either hydroxy or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409-G1491 to A1409-U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6'-NH3+ aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406.U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406.U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies.
2002
Walter F, Putz J, Giege R, Westhof E
Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation Journal Article
In: EMBO J, vol. 21, no. 4, pp. 760-768, 2002, ISBN: 11847123, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Base Sequence Carbohydrate Sequence Fluorescence Polarization Molecular Sequence Data *Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism Saccharomyces cerevisiae/*genetics Support, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tobramycin/*metabolism, Transfer, Unité ARN, WESTHOF
@article{,
title = {Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation},
author = {F Walter and J Putz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11847123},
isbn = {11847123},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {4},
pages = {760-768},
abstract = {Aminoglycosides inhibit translation in bacteria by binding to the A site in the ribosome. Here, it is shown that, in yeast, aminoglycosides can also interfere with other processes of translation in vitro. Steady-state aminoacylation kinetics of unmodified yeast tRNA(Asp) transcript indicate that the complex between tRNA(Asp) and tobramycin is a competitive inhibitor of the aspartylation reaction with an inhibition constant (K(I)) of 36 nM. Addition of an excess of heterologous tRNAs did not reverse the charging of tRNA(Asp), indicating a specific inhibition of the aspartylation reaction. Although magnesium ions compete with the inhibitory effect, the formation of the aspartate adenylate in the ATP-PP(i) exchange reaction by aspartyl-tRNA synthetase in the absence of the tRNA is not inhibited. Ultraviolet absorbance melting experiments indicate that tobramycin interacts with and destabilizes the native L-shaped tertiary structure of tRNA(Asp). Fluorescence anisotropy using fluorescein-labelled tobramycin reveals a stoichiometry of one molecule bound to tRNA(Asp) with a K(D) of 267 nM. The results indicate that aminoglycosides are biologically effective when their binding induces a shift in a conformational equilibrium of the RNA.},
note = {0261-4189
Journal Article},
keywords = {Acylation Base Sequence Carbohydrate Sequence Fluorescence Polarization Molecular Sequence Data *Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism Saccharomyces cerevisiae/*genetics Support, Fungal/chemistry/*metabolism RNA, Non-U.S. Gov't Tobramycin/*metabolism, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Aminoglycosides inhibit translation in bacteria by binding to the A site in the ribosome. Here, it is shown that, in yeast, aminoglycosides can also interfere with other processes of translation in vitro. Steady-state aminoacylation kinetics of unmodified yeast tRNA(Asp) transcript indicate that the complex between tRNA(Asp) and tobramycin is a competitive inhibitor of the aspartylation reaction with an inhibition constant (K(I)) of 36 nM. Addition of an excess of heterologous tRNAs did not reverse the charging of tRNA(Asp), indicating a specific inhibition of the aspartylation reaction. Although magnesium ions compete with the inhibitory effect, the formation of the aspartate adenylate in the ATP-PP(i) exchange reaction by aspartyl-tRNA synthetase in the absence of the tRNA is not inhibited. Ultraviolet absorbance melting experiments indicate that tobramycin interacts with and destabilizes the native L-shaped tertiary structure of tRNA(Asp). Fluorescence anisotropy using fluorescein-labelled tobramycin reveals a stoichiometry of one molecule bound to tRNA(Asp) with a K(D) of 267 nM. The results indicate that aminoglycosides are biologically effective when their binding induces a shift in a conformational equilibrium of the RNA.
van Buuren B N, Hermann T, Wijmenga S S, Westhof E
Brownian-dynamics simulations of metal-ion binding to four-way junctions Journal Article
In: Nucleic Acids Res, vol. 30, no. 2, pp. 507-514, 2002, ISBN: 11788713, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Base Pair Mismatch Base Sequence Binding Sites Cations/*metabolism *Computer Simulation DNA/*chemistry/genetics/*metabolism Diffusion Electrostatics Metals/*metabolism Models, Biomolecular *Nucleic Acid Conformation Nucleic Acid Hybridization RNA/chemistry/genetics/metabolism Recombination, Genetic/*genetics Support, Molecular Nuclear Magnetic Resonance, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Brownian-dynamics simulations of metal-ion binding to four-way junctions},
author = {B N van Buuren and T Hermann and S S Wijmenga and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11788713},
isbn = {11788713},
year = {2002},
date = {2002-01-01},
journal = {Nucleic Acids Res},
volume = {30},
number = {2},
pages = {507-514},
abstract = {Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.},
note = {1362-4962
Journal Article},
keywords = {Base Pair Mismatch Base Sequence Binding Sites Cations/*metabolism *Computer Simulation DNA/*chemistry/genetics/*metabolism Diffusion Electrostatics Metals/*metabolism Models, Biomolecular *Nucleic Acid Conformation Nucleic Acid Hybridization RNA/chemistry/genetics/metabolism Recombination, Genetic/*genetics Support, Molecular Nuclear Magnetic Resonance, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.
Vicens Q, Westhof E
Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site Journal Article
In: Chem Biol, vol. 9, no. 6, pp. 747-755, 2002, ISBN: 12079787, (1074-5521 Journal Article).
Abstract | Links | BibTeX | Tags: 16S/*chemistry Support, Anti-Bacterial Agents/*chemistry Binding Sites Crystallography Escherichia coli/metabolism Models, Molecular Oligonucleotides/*chemistry Paromomycin/chemistry Protein Structure, Non-U.S. Gov't Tobramycin/*chemistry, Ribosomal, Secondary Protein Structure, Tertiary RNA, Unité ARN, WESTHOF
@article{,
title = {Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12079787},
isbn = {12079787},
year = {2002},
date = {2002-01-01},
journal = {Chem Biol},
volume = {9},
number = {6},
pages = {747-755},
abstract = {Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin. The three aminosugar rings making up tobramycin interact with the deep-groove atoms directly or via water molecules and stabilize a fully bulged-out conformation of adenines A(1492) and A(1493). The comparison between this structure and the one previously solved in the presence of paromomycin confirms the importance of the functional groups on the common neamine part of these two antibiotics for binding to RNA. Furthermore, the analysis of the present structure provides a molecular explanation to some of the resistance mechanisms that have spread among bacteria and rendered aminoglycoside antibiotics inefficient.},
note = {1074-5521
Journal Article},
keywords = {16S/*chemistry Support, Anti-Bacterial Agents/*chemistry Binding Sites Crystallography Escherichia coli/metabolism Models, Molecular Oligonucleotides/*chemistry Paromomycin/chemistry Protein Structure, Non-U.S. Gov't Tobramycin/*chemistry, Ribosomal, Secondary Protein Structure, Tertiary RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin. The three aminosugar rings making up tobramycin interact with the deep-groove atoms directly or via water molecules and stabilize a fully bulged-out conformation of adenines A(1492) and A(1493). The comparison between this structure and the one previously solved in the presence of paromomycin confirms the importance of the functional groups on the common neamine part of these two antibiotics for binding to RNA. Furthermore, the analysis of the present structure provides a molecular explanation to some of the resistance mechanisms that have spread among bacteria and rendered aminoglycoside antibiotics inefficient.
Serra M J, Baird J D, Dale T, Fey B L, Retatagos K, Westhof E
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures Journal Article
In: RNA, vol. 8, no. 3, pp. 307-323, 2002, ISBN: 12003491, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Base Pairing Heat Hydrogen Bonding Magnesium/*pharmacology Models, Molecular Nucleic Acid Conformation RNA/*metabolism RNA Stability/*drug effects Support, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Effects of magnesium ions on the stabilization of RNA oligomers of defined structures},
author = {M J Serra and J D Baird and T Dale and B L Fey and K Retatagos and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12003491},
isbn = {12003491},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {3},
pages = {307-323},
abstract = {Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated.},
note = {1355-8382
Journal Article},
keywords = {Base Pairing Heat Hydrogen Bonding Magnesium/*pharmacology Models, Molecular Nucleic Acid Conformation RNA/*metabolism RNA Stability/*drug effects Support, Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Thermodynamics, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated.
Westhof E
Foreword Journal Article
In: Biochimie, vol. 84, no. 8, pp. 687-689, 2002.
Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Foreword},
author = {E Westhof},
url = {http://www.sciencedirect.com/science/article/pii/S0300908402014645},
doi = {10.1016/S0300-9084(02)01464-5},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {8},
pages = {687-689},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Westhof E
Group I introns and RNA folding Journal Article
In: Biochem Soc Trans, vol. 30, no. Pt 6, pp. 1149-1152, 2002, ISBN: 12440993, (0300-5127 Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: Base Sequence *Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA Splicing RNA, Catalytic, Unité ARN, WESTHOF
@article{,
title = {Group I introns and RNA folding},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12440993},
isbn = {12440993},
year = {2002},
date = {2002-01-01},
journal = {Biochem Soc Trans},
volume = {30},
number = {Pt 6},
pages = {1149-1152},
abstract = {Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine cofactors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.},
note = {0300-5127
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence *Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA Splicing RNA, Catalytic, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine cofactors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.
Auffinger P, Westhof E
Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study Journal Article
In: Biophys Chem, vol. 95, no. 3, pp. 203-210, 2002, ISBN: 12062380, (0301-4622 Journal Article).
Abstract | Links | BibTeX | Tags: Computer Simulation Entropy Models, Double-Stranded/*chemistry Solvents/chemistry/metabolism Temperature Thermodynamics Water/*chemistry/metabolism, Molecular Molecular Structure Motion Nucleic Acid Conformation RNA, Unité ARN, WESTHOF
@article{,
title = {Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12062380},
isbn = {12062380},
year = {2002},
date = {2002-01-01},
journal = {Biophys Chem},
volume = {95},
number = {3},
pages = {203-210},
abstract = {From three 2.4-ns molecular dynamics simulations of the r(CpG)(12) duplex conducted at 5, 25 and 37 degrees C, a strong temperature dependence of the dynamics of the water molecules and ions located in the first nucleic acid coordination shell is observed. At 5 degrees C, the highest residence times of bound water molecules exceed 1 ns while, at 37 degrees C, they decrease to 0.5 ns in agreement with available NMR data. Similar temperature dependencies are observed for the potassium ions bound to the duplex. In this temperature range, the structure of the RNA helix remains essentially unchanged. Thus, the observed alterations correspond to a 'premelting' of the solvent structure around the duplex. It is proposed that, before the nucleic acid structure melts, the entropy of the solvent increases to a point where it is no longer compensated by the enthalpic contribution of solute-solute and solute-solvent interactions. At this stage, the weakest structural elements start to melt. In other terms, the experimentally observed melting processes are preceded by a melting of the more labile solvent structure.},
note = {0301-4622
Journal Article},
keywords = {Computer Simulation Entropy Models, Double-Stranded/*chemistry Solvents/chemistry/metabolism Temperature Thermodynamics Water/*chemistry/metabolism, Molecular Molecular Structure Motion Nucleic Acid Conformation RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
From three 2.4-ns molecular dynamics simulations of the r(CpG)(12) duplex conducted at 5, 25 and 37 degrees C, a strong temperature dependence of the dynamics of the water molecules and ions located in the first nucleic acid coordination shell is observed. At 5 degrees C, the highest residence times of bound water molecules exceed 1 ns while, at 37 degrees C, they decrease to 0.5 ns in agreement with available NMR data. Similar temperature dependencies are observed for the potassium ions bound to the duplex. In this temperature range, the structure of the RNA helix remains essentially unchanged. Thus, the observed alterations correspond to a 'premelting' of the solvent structure around the duplex. It is proposed that, before the nucleic acid structure melts, the entropy of the solvent increases to a point where it is no longer compensated by the enthalpic contribution of solute-solute and solute-solvent interactions. At this stage, the weakest structural elements start to melt. In other terms, the experimentally observed melting processes are preceded by a melting of the more labile solvent structure.
Waldsich C, Masquida B, Westhof E, Schroeder R
Monitoring intermediate folding states of the td group I intron in vivo Journal Article
In: EMBO J, vol. 21, no. 19, pp. 5281-5291, 2002, ISBN: 12356744, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial/chemistry/genetics Escherichia coli/genetics Introns/*physiology Models, Base Sequence DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Support, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Monitoring intermediate folding states of the td group I intron in vivo},
author = {C Waldsich and B Masquida and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12356744},
isbn = {12356744},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {19},
pages = {5281-5291},
abstract = {Group I introns consist of two major structural domains, the P4-P6 and P3-P9 domains, which assemble through interactions with peripheral extensions to fold into an active ribozyme. To assess group I intron folding in vivo, we probed the structure of td wild-type and mutant introns using dimethyl sulfate. The results suggest that the majority of the intron population is in the native state in accordance with the current structural model, which was refined to include two novel tertiary contacts. The importance of the loop E motif in the P7.1-P7.2 extension in assisting ribozyme folding was deduced from modeling and mutational analyses. Destabilization of stem P6 results in a deficiency in tertiary structure formation in both major domains, while weakening of stem P7 only interferes with folding of the P3-P9 domain. The different impact of mutations on the tertiary structure suggests that they interfere with folding at different stages. These results provide a first insight into the structure of folding intermediates and suggest a putative order of events in a hierarchical folding pathway in vivo.},
note = {0261-4189
Journal Article},
keywords = {Bacterial/chemistry/genetics Escherichia coli/genetics Introns/*physiology Models, Base Sequence DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Support, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Group I introns consist of two major structural domains, the P4-P6 and P3-P9 domains, which assemble through interactions with peripheral extensions to fold into an active ribozyme. To assess group I intron folding in vivo, we probed the structure of td wild-type and mutant introns using dimethyl sulfate. The results suggest that the majority of the intron population is in the native state in accordance with the current structural model, which was refined to include two novel tertiary contacts. The importance of the loop E motif in the P7.1-P7.2 extension in assisting ribozyme folding was deduced from modeling and mutational analyses. Destabilization of stem P6 results in a deficiency in tertiary structure formation in both major domains, while weakening of stem P7 only interferes with folding of the P3-P9 domain. The different impact of mutations on the tertiary structure suggests that they interfere with folding at different stages. These results provide a first insight into the structure of folding intermediates and suggest a putative order of events in a hierarchical folding pathway in vivo.
Leontis N B, Stombaugh J, Westhof E
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules Journal Article
In: Biochimie, vol. 84, no. 9, pp. 961-973, 2002, ISBN: 12458088, (0300-9084 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules},
author = {N B Leontis and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458088},
isbn = {12458088},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {961-973},
abstract = {The traditional way to infer RNA secondary structure involves an iterative process of alignment and evaluation of covariation statistics between all positions possibly involved in basepairing. Watson-Crick basepairs typically show covariations that score well when examples of two or more possible basepairs occur. This is not necessarily the case for non-Watson-Crick basepairing geometries. For example, for sheared (trans Hoogsteen/Sugar edge) pairs, one base is highly conserved (always A or mostly A with some C or U), while the other can vary (G or A and sometimes C and U as well). RNA motifs consist of ordered, stacked arrays of non-Watson-Crick basepairs that in the secondary structure representation form hairpin or internal loops, multi-stem junctions, and even pseudoknots. Although RNA motifs occur recurrently and contribute in a modular fashion to RNA architecture, it is usually not apparent which bases interact and whether it is by edge-to-edge H-bonding or solely by stacking interactions. Using a modular sequence-analysis approach, recurrent motifs related to the sarcin-ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs (16S- and 23S-like) before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts. This provides the opportunity to evaluate the predictive power of motif-level sequence analysis, with the goal of automating the process for predicting RNA motifs in genomic sequences. The process of inferring structure from sequence by constructing accurate alignments is a circular one. The crucial link that allows a productive iteration of motif modeling and realignment is the comparison of the sequence variations for each putative pair with the corresponding isostericity matrix to determine which basepairs are consistent both with the sequence and the geometrical data.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The traditional way to infer RNA secondary structure involves an iterative process of alignment and evaluation of covariation statistics between all positions possibly involved in basepairing. Watson-Crick basepairs typically show covariations that score well when examples of two or more possible basepairs occur. This is not necessarily the case for non-Watson-Crick basepairing geometries. For example, for sheared (trans Hoogsteen/Sugar edge) pairs, one base is highly conserved (always A or mostly A with some C or U), while the other can vary (G or A and sometimes C and U as well). RNA motifs consist of ordered, stacked arrays of non-Watson-Crick basepairs that in the secondary structure representation form hairpin or internal loops, multi-stem junctions, and even pseudoknots. Although RNA motifs occur recurrently and contribute in a modular fashion to RNA architecture, it is usually not apparent which bases interact and whether it is by edge-to-edge H-bonding or solely by stacking interactions. Using a modular sequence-analysis approach, recurrent motifs related to the sarcin-ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs (16S- and 23S-like) before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts. This provides the opportunity to evaluate the predictive power of motif-level sequence analysis, with the goal of automating the process for predicting RNA motifs in genomic sequences. The process of inferring structure from sequence by constructing accurate alignments is a circular one. The crucial link that allows a productive iteration of motif modeling and realignment is the comparison of the sequence variations for each putative pair with the corresponding isostericity matrix to determine which basepairs are consistent both with the sequence and the geometrical data.
Fedor M J, Westhof E
Ribozymes: the first 20 years Journal Article
In: Mol Cell, vol. 10, no. 4, pp. 703-704, 2002, ISBN: 12419214, (1097-2765 Congresses).
Abstract | Links | BibTeX | Tags: Catalysis Introns/genetics RNA Precursors/genetics/metabolism RNA Splicing RNA, Catalytic/chemistry/genetics/*metabolism, Unité ARN, WESTHOF
@article{,
title = {Ribozymes: the first 20 years},
author = {M J Fedor and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12419214},
isbn = {12419214},
year = {2002},
date = {2002-01-01},
journal = {Mol Cell},
volume = {10},
number = {4},
pages = {703-704},
abstract = {Twenty years have passed since the first reports that certain RNAs mediate self-splicing and precursor tRNA processing reactions in the absence of proteins. An entire field emerged to learn how RNAs that lack the chemical versatility of amino acids nonetheless assemble into enzymes that accelerate chemical reactions with efficiencies that rival those of their protein counterparts.},
note = {1097-2765
Congresses},
keywords = {Catalysis Introns/genetics RNA Precursors/genetics/metabolism RNA Splicing RNA, Catalytic/chemistry/genetics/*metabolism, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Twenty years have passed since the first reports that certain RNAs mediate self-splicing and precursor tRNA processing reactions in the absence of proteins. An entire field emerged to learn how RNAs that lack the chemical versatility of amino acids nonetheless assemble into enzymes that accelerate chemical reactions with efficiencies that rival those of their protein counterparts.
Waugh A, Gendron P, Altman R, Brown J W, Case D, Gautheret D, Harvey S C, Leontis N, Westbrook J, Westhof E, Zuker M, Major F
RNAML: a standard syntax for exchanging RNA information Journal Article
In: RNA, vol. 8, no. 6, pp. 707-717, 2002, ISBN: 12088144, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: *Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {RNAML: a standard syntax for exchanging RNA information},
author = {A Waugh and P Gendron and R Altman and J W Brown and D Case and D Gautheret and S C Harvey and N Leontis and J Westbrook and E Westhof and M Zuker and F Major},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12088144},
isbn = {12088144},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {6},
pages = {707-717},
abstract = {Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.},
note = {1355-8382
Journal Article},
keywords = {*Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.
Auffinger P, Masquida B, Westhof E
Strucutral and dynamical characterization of nucleic acids water and ion binding sites. Book Chapter
In: Schlick, T; Gan, H H (Ed.): Computational methods for macromolecules: challenges and applications. Proceedings of the 3rd international workshop on algorithms for macromolecular modeling, New York, October 12-14, 2000. Lecture Notes in Computational Science and Engineering., vol. 24, pp. 61-70, Springer, 2002.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@inbook{,
title = {Strucutral and dynamical characterization of nucleic acids water and ion binding sites.},
author = {P Auffinger and B Masquida and E Westhof},
editor = {T Schlick and H H Gan},
url = {http://books.google.fr/books?id=DLDdglVVhVIC&pg=PA61&lpg=PA61&dq=Structural+and+dynamical+characterization+of+nucleic+acids+water+and+ion+binding+sites.&source=bl&ots=hmiZnqX_lA&sig=PbZPEKPo3NitnY9sMj0S0TAHS58&hl=fr&sa=X&ei=e4T9T-GlMsenhAfJqrCDAg&ved=0CFQQ6AEwAA#v=onepage&q=Structural%20and%20dynamical%20characterization%20of%20nucleic%20acids%20water%20and%20ion%20binding%20sites.&f=false},
year = {2002},
date = {2002-01-01},
booktitle = {Computational methods for macromolecules: challenges and applications. Proceedings of the 3rd international workshop on algorithms for macromolecular modeling, New York, October 12-14, 2000. Lecture Notes in Computational Science and Engineering.},
volume = {24},
pages = {61-70},
publisher = {Springer},
abstract = {Recent methodological developments led to longer and more accurate
molecular dynamics (MD) simulations. In parallel, methods have been designed
with the purpose of characterizing water and ion binding features. Here, we give
an outline of some of the methods we used in order to extract structural and
dynamical information concerning the first water and ion coordination shell, from
MD simulations conducted on RNA and DNA structures. Coordinates for the water and ion binding sites located in the first coordination shell of r(G=C), d(G=C), r(AU),
and d(A-T) base-pairs are provided, along with calculated ﾓpseudoﾔ thermal
factors.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {inbook}
}
Recent methodological developments led to longer and more accurate
molecular dynamics (MD) simulations. In parallel, methods have been designed
with the purpose of characterizing water and ion binding features. Here, we give
an outline of some of the methods we used in order to extract structural and
dynamical information concerning the first water and ion coordination shell, from
MD simulations conducted on RNA and DNA structures. Coordinates for the water and ion binding sites located in the first coordination shell of r(G=C), d(G=C), r(AU),
and d(A-T) base-pairs are provided, along with calculated ﾓpseudoﾔ thermal
factors.
molecular dynamics (MD) simulations. In parallel, methods have been designed
with the purpose of characterizing water and ion binding features. Here, we give
an outline of some of the methods we used in order to extract structural and
dynamical information concerning the first water and ion coordination shell, from
MD simulations conducted on RNA and DNA structures. Coordinates for the water and ion binding sites located in the first coordination shell of r(G=C), d(G=C), r(AU),
and d(A-T) base-pairs are provided, along with calculated ﾓpseudoﾔ thermal
factors.
Leontis N, Westhof E
The annotation of RNA motifs Journal Article
In: Comp Funct Genom, vol. 3, no. 6, pp. 518-524, 2002.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF, WESTHOF RNA motif Annotation Non-WatsonCrick basepair Shallow-groove Sugar-edge WatsonCrick edge Hoogsteen edge Isostericity matrix
@article{,
title = {The annotation of RNA motifs},
author = {N Leontis and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448414},
doi = {10.1002%2Fcfg.213},
year = {2002},
date = {2002-01-01},
journal = {Comp Funct Genom},
volume = {3},
number = {6},
pages = {518-524},
abstract = {The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNARNA and quaternary RNAprotein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-WatsonCrick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-WatsonCrick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved.},
keywords = {Unité ARN, WESTHOF, WESTHOF RNA motif Annotation Non-WatsonCrick basepair Shallow-groove Sugar-edge WatsonCrick edge Hoogsteen edge Isostericity matrix},
pubstate = {published},
tppubtype = {article}
}
The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNARNA and quaternary RNAprotein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-WatsonCrick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-WatsonCrick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved.
Leontis N B, Stombaugh J, Westhof E
The non-Watson-Crick base pairs and their associated isostericity matrices Journal Article
In: Nucleic Acids Res, vol. 30, no. 16, pp. 3497-3531, 2002, ISBN: 12177293, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Algorithms *Base Pairing Base Sequence Hydrogen Bonding Models, Molecular RNA/*chemistry/classification/genetics Sequence Homology Support, Non-P.H.S. Support, P.H.S. Terminology, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {The non-Watson-Crick base pairs and their associated isostericity matrices},
author = {N B Leontis and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12177293},
isbn = {12177293},
year = {2002},
date = {2002-01-01},
journal = {Nucleic Acids Res},
volume = {30},
number = {16},
pages = {3497-3531},
abstract = {RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.},
note = {1362-4962
Journal Article},
keywords = {Algorithms *Base Pairing Base Sequence Hydrogen Bonding Models, Molecular RNA/*chemistry/classification/genetics Sequence Homology Support, Non-P.H.S. Support, P.H.S. Terminology, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 A resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
1992
Westhof E
Westhof's rule Journal Article
In: Nature, vol. 358, no. 6386, pp. 459-460, 1992, ISBN: 1641036, (0028-0836 Letter).
Links | BibTeX | Tags: *Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF
@article{,
title = {Westhof's rule},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1641036},
isbn = {1641036},
year = {1992},
date = {1992-01-01},
journal = {Nature},
volume = {358},
number = {6386},
pages = {459-460},
note = {0028-0836
Letter},
keywords = {*Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Pauly M, Treger M, Westhof E, Chambon P
The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements Journal Article
In: Nucleic Acids Res, vol. 20, no. 5, pp. 975-982, 1992, ISBN: 1312710, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence DNA Mutational Analysis DNA, Genetic/*genetics, Non-U.S. Gov't TATA Box/*genetics Transcription, Unité ARN, Viral/*genetics Hela Cells Human Molecular Sequence Data Nucleic Acid Conformation Simian virus 40/*genetics Support, Viral/chemistry/genetics Electrophoresis Genes, WESTHOF
@article{,
title = {The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements},
author = {M Pauly and M Treger and E Westhof and P Chambon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1312710},
isbn = {1312710},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {5},
pages = {975-982},
abstract = {To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, each independently directing the accurate initiation of transcription from a specified set of start sites, EES1 and EES2, respectively. The sequence of TATA element I fits best with the compiled 'consensus' sequence found in eukaryotic gene promoters and is the most efficient in directing transcription initiation. Mutations which improve this fit can still increase the rate of transcription, confirming the theory of a correlation between the nucleotide sequence of a TATA element and its functional efficiency. Moreover, some mutations which simultaneously modify the angle of DNA curvature in the T + A-rich promoter region and the rate of transcription reveal a correlation between DNA bending and transcription initiation.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis DNA, Genetic/*genetics, Non-U.S. Gov't TATA Box/*genetics Transcription, Unité ARN, Viral/*genetics Hela Cells Human Molecular Sequence Data Nucleic Acid Conformation Simian virus 40/*genetics Support, Viral/chemistry/genetics Electrophoresis Genes, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, each independently directing the accurate initiation of transcription from a specified set of start sites, EES1 and EES2, respectively. The sequence of TATA element I fits best with the compiled 'consensus' sequence found in eukaryotic gene promoters and is the most efficient in directing transcription initiation. Mutations which improve this fit can still increase the rate of transcription, confirming the theory of a correlation between the nucleotide sequence of a TATA element and its functional efficiency. Moreover, some mutations which simultaneously modify the angle of DNA curvature in the T + A-rich promoter region and the rate of transcription reveal a correlation between DNA bending and transcription initiation.
Rippe K, Fritsch V, Westhof E, Jovin T M
Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex Journal Article
In: EMBO J, vol. 11, no. 10, pp. 3777-3786, 1992, ISBN: 1396571, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF
@article{,
title = {Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex},
author = {K Rippe and V Fritsch and E Westhof and T M Jovin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1396571},
isbn = {1396571},
year = {1992},
date = {1992-01-01},
journal = {EMBO J},
volume = {11},
number = {10},
pages = {3777-3786},
abstract = {The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.
