Publications
2005
Lescoute A, Leontis N B, Massire C, Westhof E
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments Article de journal
Dans: Nucleic Acids Res, vol. 33, no. 8, p. 2395-2409, 2005, ISBN: 15860776, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pairing Models, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Research Support, Nucleic Acid, P.H.S. *Sequence Alignment Sequence Analysis, Ribosomal/*chemistry Research Support, RNA/*methods Sequence Homology, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments},
author = {A Lescoute and N B Leontis and C Massire and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15860776},
isbn = {15860776},
year = {2005},
date = {2005-01-01},
journal = {Nucleic Acids Res},
volume = {33},
number = {8},
pages = {2395-2409},
abstract = {The occurrences of two recurrent motifs in ribosomal RNA sequences, the Kink-turn and the C-loop, are examined in crystal structures and systematically compared with sequence alignments of rRNAs from the three kingdoms of life in order to identify the range of the structural and sequence variations. Isostericity Matrices are used to analyze structurally the sequence variations of the characteristic non-Watson-Crick base pairs for each motif. We show that Isostericity Matrices for non-Watson-Crick base pairs provide important tools for deriving the sequence signatures of recurrent motifs, for scoring and refining sequence alignments, and for determining whether motifs are conserved throughout evolution. The systematic use of Isostericity Matrices identifies the positions of the insertion or deletion of one or more nucleotides relative to the structurally characterized examples of motifs and, most importantly, specifies whether these changes result in new motifs. Thus, comparative analysis coupled with Isostericity Matrices allows one to produce and refine structural sequence alignments. The analysis, based on both sequence and structure, permits therefore the evaluation of the conservation of motifs across phylogeny and the derivation of rules of equivalence between structural motifs. The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences.},
note = {1362-4962
Journal Article},
keywords = {Base Pairing Models, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Research Support, Nucleic Acid, P.H.S. *Sequence Alignment Sequence Analysis, Ribosomal/*chemistry Research Support, RNA/*methods Sequence Homology, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
1997
Auffinger P, Westhof E
RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin Article de journal
Dans: J Mol Biol, vol. 269, no. 3, p. 326-341, 1997, ISBN: 9199403, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry Base Composition *Computer Simulation Guanine/chemistry Hydrogen Bonding Models, Asp/*chemistry/metabolism Ribose/chemistry/metabolism Support, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Uridine/chemistry Water/*chemistry/metabolism, Transfer, Unité ARN
@article{,
title = {RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9199403},
isbn = {9199403},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {269},
number = {3},
pages = {326-341},
abstract = {The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.},
note = {0022-2836
Journal Article},
keywords = {Anticodon/*chemistry Base Composition *Computer Simulation Guanine/chemistry Hydrogen Bonding Models, Asp/*chemistry/metabolism Ribose/chemistry/metabolism Support, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Uridine/chemistry Water/*chemistry/metabolism, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1994
Michel F, Westhof E
Slippery substrates Article de journal
Dans: Nat Struct Biol, vol. 1, no. 1, p. 5-7, 1994, ISBN: 7656007, (1072-8368 News).
Liens | BibTeX | Étiquettes: Animals Binding Sites Models, Catalytic/*chemistry/genetics/metabolism Substrate Specificity Tetrahymena/enzymology/genetics, Molecular Nucleic Acid Conformation RNA, Unité ARN
@article{,
title = {Slippery substrates},
author = {F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7656007},
isbn = {7656007},
year = {1994},
date = {1994-01-01},
journal = {Nat Struct Biol},
volume = {1},
number = {1},
pages = {5-7},
note = {1072-8368
News},
keywords = {Animals Binding Sites Models, Catalytic/*chemistry/genetics/metabolism Substrate Specificity Tetrahymena/enzymology/genetics, Molecular Nucleic Acid Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}