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2000
Michel F, Costa M, Massire C, Westhof E
Modeling RNA tertiary structure from patterns of sequence variation Article de journal
Dans: Methods Enzymol, vol. 317, p. 491-510, 2000, ISBN: 10829297, (0076-6879 Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: Base Pairing Base Sequence Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer/*chemistry Sequence Alignment, Unité ARN
@article{,
title = {Modeling RNA tertiary structure from patterns of sequence variation},
author = {F Michel and M Costa and C Massire and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10829297},
isbn = {10829297},
year = {2000},
date = {2000-01-01},
journal = {Methods Enzymol},
volume = {317},
pages = {491-510},
note = {0076-6879
Journal Article
Review
Review, Tutorial},
keywords = {Base Pairing Base Sequence Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer/*chemistry Sequence Alignment, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1999
Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges Article de journal
Dans: Structure, vol. 7, no. 11, p. 1439-49, 1999, ISBN: 10574792, (0969-2126 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adenine/*chemistry Base Pair Mismatch Base Sequence Crystallography, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support, X-Ray Dimerization HIV-1/*genetics Magnesium/metabolism Magnetic Resonance Spectroscopy Manganese/metabolism Models
@article{,
title = {The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges},
author = {E Ennifar and M Yusupov and P Walter and R Marquet and B Ehresmann and C Ehresmann and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10574792},
isbn = {10574792},
year = {1999},
date = {1999-01-01},
journal = {Structure},
volume = {7},
number = {11},
pages = {1439-49},
abstract = {BACKGROUND: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.},
note = {0969-2126
Journal Article},
keywords = {Adenine/*chemistry Base Pair Mismatch Base Sequence Crystallography, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support, X-Ray Dimerization HIV-1/*genetics Magnesium/metabolism Magnetic Resonance Spectroscopy Manganese/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.
1994
Tuschl T, Gohlke C, Jovin T M, Westhof E, Eckstein F
A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements Article de journal
Dans: Science, vol. 266, no. 5186, p. 785-789, 1994, ISBN: 7973630, (0036-8075 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence Energy Transfer Fluoresceins Least-Squares Analysis *Models, Catalytic/*chemistry Rhodamines Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN
@article{,
title = {A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements},
author = {T Tuschl and C Gohlke and T M Jovin and E Westhof and F Eckstein},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7973630},
isbn = {7973630},
year = {1994},
date = {1994-01-01},
journal = {Science},
volume = {266},
number = {5186},
pages = {785-789},
abstract = {For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.},
note = {0036-8075
Journal Article},
keywords = {Base Composition Base Sequence Energy Transfer Fluoresceins Least-Squares Analysis *Models, Catalytic/*chemistry Rhodamines Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.
1993
Sturchler C, Westhof E, Carbon P, Krol A
Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec) Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 5, p. 1073-1079, 1993, ISBN: 8464694, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN
@article{,
title = {Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec)},
author = {C Sturchler and E Westhof and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464694},
isbn = {8464694},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {5},
pages = {1073-1079},
abstract = {Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*chemistry *Selenocysteine Support, Animals Base Sequence Cloning, Molecular Computer Simulation DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Xenopus laevis, Single-Stranded Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.
Hou Y M, Westhof E, Giege R
An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 14, p. 6776-6780, 1993, ISBN: 8341698, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/*metabolism Base Sequence Escherichia coli/*chemistry/genetics/metabolism Hydrogen Bonding Models, Cys/*chemistry/genetics/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA},
author = {Y M Hou and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8341698},
isbn = {8341698},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {14},
pages = {6776-6780},
abstract = {The nucleotides in a tRNA that specifically interact with the cognate aminoacyl-tRNA synthetase have been found largely located in the helical stems, the anticodon, or the discriminator base, where they vary from one tRNA to another. The conserved and semiconserved nucleotides that are responsible for the tRNA tertiary structure have been shown to have little role in synthetase recognition. Here we report that aminoacylation of Escherichia coli tRNA(Cys) depends on the anticodon, the discriminator base, and a tertiary interaction between the semiconserved nucleotides at positions 15 and 48. While all other tRNAs contain a purine at position 15 and a complementary pyrimidine at position 48 that establish the tertiary interaction known as the Levitt pair, E. coli tRNA(Cys) has guanosine -15 and -48. Replacement of guanosine -15 or -48 with cytidine virtually eliminates aminoacylation. Structural analyses with chemical probes suggest that guanosine -15 and -48 interact through hydrogen bonds between the exocyclic N-2 and ring N-3 to stabilize the joining of the two long helical stems of the tRNA. This tertiary interaction is different from the traditional base pairing scheme in the Levitt pair, where hydrogen bonds would form between N-1 and O-6. Our results provide evidence for a role of RNA tertiary structure in synthetase recognition.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/*metabolism Base Sequence Escherichia coli/*chemistry/genetics/metabolism Hydrogen Bonding Models, Cys/*chemistry/genetics/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The nucleotides in a tRNA that specifically interact with the cognate aminoacyl-tRNA synthetase have been found largely located in the helical stems, the anticodon, or the discriminator base, where they vary from one tRNA to another. The conserved and semiconserved nucleotides that are responsible for the tRNA tertiary structure have been shown to have little role in synthetase recognition. Here we report that aminoacylation of Escherichia coli tRNA(Cys) depends on the anticodon, the discriminator base, and a tertiary interaction between the semiconserved nucleotides at positions 15 and 48. While all other tRNAs contain a purine at position 15 and a complementary pyrimidine at position 48 that establish the tertiary interaction known as the Levitt pair, E. coli tRNA(Cys) has guanosine -15 and -48. Replacement of guanosine -15 or -48 with cytidine virtually eliminates aminoacylation. Structural analyses with chemical probes suggest that guanosine -15 and -48 interact through hydrogen bonds between the exocyclic N-2 and ring N-3 to stabilize the joining of the two long helical stems of the tRNA. This tertiary interaction is different from the traditional base pairing scheme in the Levitt pair, where hydrogen bonds would form between N-1 and O-6. Our results provide evidence for a role of RNA tertiary structure in synthetase recognition.
