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Title: Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

Abstract

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramaticmore » local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

Authors:
 [1];  [1];  [2];  [3]
  1. Univ. of California, San Francisco, CA (United States)
  2. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  3. George Mason Univ., Fairfax, VA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1240106
Grant/Contract Number:  
AC03-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 11; Journal Issue: 10; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; electron density; glycine; peptides; crystal structure; peptide mapping; proteases; atoms; anisotropy

Citation Formats

Keedy, Daniel A., Fraser, James S., van den Bedem, Henry, and Shehu, Amarda. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit. United States: N. p., 2015. Web. doi:10.1371/journal.pcbi.1004507.
Keedy, Daniel A., Fraser, James S., van den Bedem, Henry, & Shehu, Amarda. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit. United States. doi:10.1371/journal.pcbi.1004507.
Keedy, Daniel A., Fraser, James S., van den Bedem, Henry, and Shehu, Amarda. Tue . "Exposing hidden alternative backbone conformations in X-ray crystallography using qFit". United States. doi:10.1371/journal.pcbi.1004507. https://www.osti.gov/servlets/purl/1240106.
@article{osti_1240106,
title = {Exposing hidden alternative backbone conformations in X-ray crystallography using qFit},
author = {Keedy, Daniel A. and Fraser, James S. and van den Bedem, Henry and Shehu, Amarda},
abstractNote = {Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.},
doi = {10.1371/journal.pcbi.1004507},
journal = {PLoS Computational Biology (Online)},
number = 10,
volume = 11,
place = {United States},
year = {2015},
month = {10}
}

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