1auh: Difference between revisions
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==THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDE== | ==THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDE== | ||
<StructureSection load='1auh' size='340' side='right' caption='[[1auh]]' scene=''> | <StructureSection load='1auh' size='340' side='right'caption='[[1auh]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AUH FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1auh FirstGlance], [https://www.ebi.ac.uk/pdbsum/1auh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1auh ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Theoretical Model]] | [[Category: Theoretical Model]] | ||
[[Category: Large Structures]] | |||
[[Category: Cedergren, R J]] | [[Category: Cedergren, R J]] | ||
[[Category: Ellington, A D]] | [[Category: Ellington, A D]] | ||
Latest revision as of 18:01, 2 June 2021
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THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDETHEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDE
Structural highlights
Publication Abstract from PubMedBACKGROUND: In spite of the great interest in the interaction between RNAs and proteins, no general protocol for modelling these complexes is presently available. This methodological vacuum is particularly acute because the structure of few such complexes is known. RESULTS: A general strategy for docking and modelling RNA-protein complexes has been developed. The docking procedure involves minimizing electrostatic and van der Waals' interaction energies of conformationally rigid structures during docking. After docking, libraries of amino acid sidechain conformations are searched to obtain the best interactions between the peptide and the RNA. Using this method, we have reproduced the structure of a bovine immunodeficiency virus (BIV) Tat peptide bound to BIV TAR RNA and have developed a model for the structure of the arginine-rich HIV-1 Rev peptide (Rev34-50) interacting with the Rev-binding element (RBE). CONCLUSIONS: The resulting model of the Rev34-50-RBE complex predicts that although no single arginine sidechain is responsible for complex formation, residues Arg2, Arg5 and Arg11 are more important for binding than the other arginine residues in the peptide. One model is supported by binding measurements performed on wild-type and mutant RBE molecules with the peptide. A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV Rev-RBE.,Srinivasan J, Leclerc F, Xu W, Ellington AD, Cedergren R Fold Des. 1996;1(6):463-72. PMID:9080192[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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