StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

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Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate ... continued below

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Zemla, A; Lang, D; Kostova, T; Andino, R & Zhou, C November 29, 2010.

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Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.

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PDF-file: 51 pages; size: 1 Mbytes

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  • Journal Name: BMC Bioinformatics; Journal Volume: 12

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  • Report No.: LLNL-JRNL-463671
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 1027977
  • Archival Resource Key: ark:/67531/metadc840242

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  • November 29, 2010

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  • May 19, 2016, 3:16 p.m.

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  • Dec. 2, 2016, 12:45 p.m.

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Zemla, A; Lang, D; Kostova, T; Andino, R & Zhou, C. StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase, article, November 29, 2010; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc840242/: accessed October 15, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.