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Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.

The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble.... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America October 28, 2014, Vol.111(43), pp.15396-15401
Main Author: Baxa, Michael C
Other Authors: Haddadian, Esmael J , Jumper, John M , Freed, Karl F , Sosnick, Tobin R
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1407768111
Link: http://search.proquest.com/docview/1618826066/?pq-origsite=primo
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title: Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
format: Article
creator:
  • Baxa, Michael C
  • Haddadian, Esmael J
  • Jumper, John M
  • Freed, Karl F
  • Sosnick, Tobin R
subjects:
  • Amino Acids–Chemistry
  • Entropy–Chemistry
  • Magnetic Resonance Spectroscopy–Chemistry
  • Protein Denaturation–Chemistry
  • Protein Folding–Chemistry
  • Protein Structure, Secondary–Chemistry
  • Ubiquitin–Chemistry
  • Amino Acids
  • Ubiquitin
  • NMR Order Parameters
  • Denatured State
  • Helix Propensity
  • Molecular Dynamics
  • Sheet Propensity
ispartof: Proceedings of the National Academy of Sciences of the United States of America, October 28, 2014, Vol.111(43), pp.15396-15401
description: The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is T[DELTA][S.sub.Total] = 1.4 kcal x [mol.sup.-1] per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding ([[OMEGA].sub.U]/[[OMEGA].sub.N]). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (T[DELTA][S.sub.helix-sheet] = 0.5 kcal x [mol.sup.-1]), a property not fully reflected in the amide N-H and carbonyl C=0 bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. NMR order parameters | molecular dynamics | helix propensity | sheet propensity | denatured state www.pnas.org/cgi/doi/10.1073/pnas.1407768111
language: eng
source:
identifier: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1407768111
fulltext: fulltext
issn:
  • 10916490
  • 1091-6490
url: Link


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titleLoss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
creatorBaxa, Michael C ; Haddadian, Esmael J ; Jumper, John M ; Freed, Karl F ; Sosnick, Tobin R
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identifierE-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1407768111
subjectAmino Acids–Chemistry ; Entropy–Chemistry ; Magnetic Resonance Spectroscopy–Chemistry ; Protein Denaturation–Chemistry ; Protein Folding–Chemistry ; Protein Structure, Secondary–Chemistry ; Ubiquitin–Chemistry ; Amino Acids ; Ubiquitin ; NMR Order Parameters ; Denatured State ; Helix Propensity ; Molecular Dynamics ; Sheet Propensity
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descriptionThe loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is T[DELTA][S.sub.Total] = 1.4 kcal x [mol.sup.-1] per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding ([[OMEGA].sub.U]/[[OMEGA].sub.N]). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (T[DELTA][S.sub.helix-sheet] = 0.5 kcal x [mol.sup.-1]), a property not fully reflected in the amide N-H and carbonyl C=0 bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. NMR order parameters | molecular dynamics | helix propensity | sheet propensity | denatured state www.pnas.org/cgi/doi/10.1073/pnas.1407768111
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