Publications
2008
Kondo J, Westhof E
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates Journal Article
In: Nucleic Acids Res, vol. 36, no. 8, pp. 2654-2666, 2008, ISBN: 18346970, (1362-4962 (Electronic) Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial/*chemistry RNA, Crystallography, Messenger/chemistry RNA, Molecular Nucleic Acid Conformation Point Mutation RNA/*chemistry/genetics RNA, Ribosomal/*chemistry RNA, Transfer/chemistry, Unité ARN, WESTHOF, WESTHOF Crystallography, X-Ray Hearing Loss/genetics Humans Models
@article{,
title = {The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates},
author = {J Kondo and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18346970},
isbn = {18346970},
year = {2008},
date = {2008-01-01},
journal = {Nucleic Acids Res},
volume = {36},
number = {8},
pages = {2654-2666},
abstract = {The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or bacteria have been solved. The resting 'off' state of the mitochondrial wild-type A site is surprisingly different from that of the bacterial A site. The mitochondrial A1555G mutant has two types of the 'off' states; one is similar to the mitochondrial wild-type 'off' state and the other is similar to the bacterial 'off' state. Our present results indicate that the dynamics of the A site in bacteria and mitochondria are different, a property probably related to the small number of tRNAs used for decoding in mitochondria. Based on these structures, we propose a hypothesis for the molecular mechanism of non-syndromic hearing loss due to the mitochondrial A1555G mutation.},
note = {1362-4962 (Electronic)
Journal Article},
keywords = {Bacterial/*chemistry RNA, Crystallography, Messenger/chemistry RNA, Molecular Nucleic Acid Conformation Point Mutation RNA/*chemistry/genetics RNA, Ribosomal/*chemistry RNA, Transfer/chemistry, Unité ARN, WESTHOF, WESTHOF Crystallography, X-Ray Hearing Loss/genetics Humans Models},
pubstate = {published},
tppubtype = {article}
}
2003
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}
}
1997
Massire C, Jaeger L, Westhof E
Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs Journal Article
In: RNA, vol. 3, no. 6, pp. 553-556, 1997, ISBN: 9174090, (1355-8382 Letter).
Links | BibTeX | Tags: Bacterial/*chemistry RNA, Base Sequence Comparative Study Databases, Catalytic/*chemistry Ribonuclease P Sequence Homology, Factual Endoribonucleases/*chemistry Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, Non-U.S. Gov't Variation (Genetics), Nucleic Acid Support, Unité ARN
@article{,
title = {Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs},
author = {C Massire and L Jaeger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9174090},
isbn = {9174090},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {6},
pages = {553-556},
note = {1355-8382
Letter},
keywords = {Bacterial/*chemistry RNA, Base Sequence Comparative Study Databases, Catalytic/*chemistry Ribonuclease P Sequence Homology, Factual Endoribonucleases/*chemistry Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, Non-U.S. Gov't Variation (Genetics), Nucleic Acid Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1995
Gaspin C, Westhof E
An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints Journal Article
In: J Mol Biol, vol. 254, no. 2, pp. 163-174, 1995, ISBN: 7490740, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Algorithms Base Sequence Endoribonucleases/*chemistry Escherichia coli/chemistry Introns Models, Bacterial/*chemistry RNA, Catalytic/*chemistry Ribonuclease P *Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN
@article{,
title = {An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints},
author = {C Gaspin and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7490740},
isbn = {7490740},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {254},
number = {2},
pages = {163-174},
abstract = {A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore of great interest. However, some of the suboptimal RNA secondary structures computed with classic methods are unsaturated structures, i.e. some structures are included into others. Thus, the incorporation of constraints during the process of folding is not possible, while the incorporation of constraints before the process of folding often introduces a bias into the energy function. This paper describes a new procedure which allows for the incorporation of constraints before and during the process of RNA folding. SAPSSARN is an interactive program which offers a framework, both to specify a secondary structure through a set of folding constraints and to compute all the supoptimal saturated RNA secondary structures which satisfy all the folding constraints. At the start, it relies on the computation of the probabilities of pairing of each base with all others according to McCaskill's algorithm. The constraint satisfaction formulation of the problem deals dynamically with a chosen set of folding constraints and, finally, a search algorithm computes all the suboptimal saturated secondary structures which satisfy those folding constraints. Within such a framework, it is possible to test new ideas about RNA folding and secondary structures, including pseudoknots, can be computed. The program is illustrated with RNA sequences on which we obtained results in agreement with known structures by using a protocol which mimics the hierarchical folding of RNA molecules.},
note = {0022-2836
Journal Article},
keywords = {Algorithms Base Sequence Endoribonucleases/*chemistry Escherichia coli/chemistry Introns Models, Bacterial/*chemistry RNA, Catalytic/*chemistry Ribonuclease P *Software Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}