Publications
2009
Stombaugh J, Zirbel C L, Westhof E, Leontis N B
Frequency and isostericity of RNA base pairs Article de journal
Dans: Nucleic Acids Res, vol. 37, no. 7, p. 2294-2312, 2009, ISBN: 19240142, (1362-4962 (Electronic) Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.).
Résumé | Liens | BibTeX | Étiquettes: ase Pairing Base Sequence Models, Bacterial/chemistry RNA, Molecular Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal/chemistry Sequence Alignment Sequence Analysis, RNA, Unité ARN, WESTHOF
@article{,
title = {Frequency and isostericity of RNA base pairs},
author = {J Stombaugh and C L Zirbel and E Westhof and N B Leontis},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19240142},
isbn = {19240142},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {7},
pages = {2294-2312},
abstract = {Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson-Crick base pairs play a central role. Non-Watson-Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.},
keywords = {ase Pairing Base Sequence Models, Bacterial/chemistry RNA, Molecular Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal/chemistry Sequence Alignment Sequence Analysis, RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
2006
Kondo J, Urzhumtsev A, Westhof E
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site Article de journal
Dans: Nucleic Acids Res, vol. 34, no. 2, p. 676-685, 2006, ISBN: 16452297, (1362-4962 (Electronic) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry RNA, 18S/*chemistry Research Support, Animals Comparative Study Crystallography, Bacterial/chemistry RNA, Molecular Nebramycin/analogs & derivatives/chemistry Nucleic Acid Conformation RNA, Non-U.S. Gov't Ribosomes/chemistry Tetrahymena thermophila/genetics, Protozoan/chemistry RNA, Ribosomal, Unité ARN, WESTHOF, X-Ray Genetic Code Humans *Models
@article{,
title = {Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site},
author = {J Kondo and A Urzhumtsev and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16452297},
isbn = {16452297},
year = {2006},
date = {2006-01-01},
journal = {Nucleic Acids Res},
volume = {34},
number = {2},
pages = {676-685},
abstract = {The decoding A site of the small ribosomal subunit is an RNA molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. We have solved the crystal structure of an RNA fragment containing two Homo sapiens cytoplasmic A sites. Each of the two A sites presents a different conformational state. In one state, adenines A1492 and A1493 are fully bulged-out with C1409 forming a wobble-like pair to A1491. In the second state, adenines A1492 and A1493 form non-Watson-Crick pairs with C1409 and G1408, respectively while A1491 bulges out. The first state of the eukaryotic A site is, thus, basically the same as in the bacterial A site with bulging A1492 and A1493. It is the state used for recognition of the codon/anticodon complex. On the contrary, the second state of the H.sapiens cytoplasmic A site is drastically different from any of those observed for the bacterial A site without bulging A1492 and A1493.},
note = {1362-4962 (Electronic)
Journal Article},
keywords = {16S/chemistry RNA, 18S/*chemistry Research Support, Animals Comparative Study Crystallography, Bacterial/chemistry RNA, Molecular Nebramycin/analogs & derivatives/chemistry Nucleic Acid Conformation RNA, Non-U.S. Gov't Ribosomes/chemistry Tetrahymena thermophila/genetics, Protozoan/chemistry RNA, Ribosomal, Unité ARN, WESTHOF, X-Ray Genetic Code Humans *Models},
pubstate = {published},
tppubtype = {article}
}
2004
Auffinger P, Bielecki L, Westhof E
Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations Article de journal
Dans: J Mol Biol, vol. 335, no. 2, p. 555-571, 2004, ISBN: 14672663, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 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}
}