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Physics-based method to validate and repair flaws in protein structures.

A method that makes use of information provided by the combination of [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America October 15, 2013, Vol.110(42), pp.16826-16831
Main Author: Martin, Osvaldo A
Other Authors: Arnautova, Yelena A , Icazatti, Alejandro A , Scheraga, Harold A , Vila, Jorge A
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1315525110
Link: http://search.proquest.com/docview/1443424634/?pq-origsite=primo
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title: Physics-based method to validate and repair flaws in protein structures.
format: Article
creator:
  • Martin, Osvaldo A
  • Arnautova, Yelena A
  • Icazatti, Alejandro A
  • Scheraga, Harold A
  • Vila, Jorge A
subjects:
  • Models, Molecular–Chemistry
  • Nuclear Magnetic Resonance, Biomolecular–Chemistry
  • Protein Folding–Chemistry
  • Protein Structure, Tertiary–Chemistry
  • Proteins–Chemistry
  • Proteins
ispartof: Proceedings of the National Academy of Sciences of the United States of America, October 15, 2013, Vol.110(42), pp.16826-16831
description: A method that makes use of information provided by the combination of [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ~90%; and (ii) provide a set of ([chi]1/[chi](2) torsional angles that leads to optimal agreement between the observed and computed [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of ([chi]1/ [chi]2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts for ~94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range [less than or equal to] 0.5 [Angstrom], in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of ([chi]1/[chi]2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models. www.pnas.org/cgi/doi/ 10.1073/pnas.1315525110
language: eng
source:
identifier: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1315525110
fulltext: fulltext
issn:
  • 10916490
  • 1091-6490
url: Link


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descriptionA method that makes use of information provided by the combination of [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ~90%; and (ii) provide a set of ([chi]1/[chi](2) torsional angles that leads to optimal agreement between the observed and computed [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of ([chi]1/ [chi]2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed [sup.13][C.sup.[alpha]] and [sup.13][C.sup.[beta]] chemical shifts for ~94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range [less than or equal to] 0.5 [Angstrom], in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of ([chi]1/[chi]2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models. www.pnas.org/cgi/doi/ 10.1073/pnas.1315525110
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