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Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models

Chan, Hue Sun; Zhang, Zhuqing; Wallin, Stefan LU and Liu, Zhirong (2011) In Annual Review of Physical Chemistry 62. p.301-326
Abstract
Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing... (More)
Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing interactions. Many of these principles have been elucidated by native-centric models, wherein nonnative interactions may be treated perturbatively. We discuss these developments as well as recent applications of coarse-grained chain modeling to knotted proteins and to intrinsically disordered proteins. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
native topology, Levinthal paradox, folding funnel, energy landscape, desolvation, enthalpic barrier
in
Annual Review of Physical Chemistry
volume
62
pages
301 - 326
publisher
Annual Reviews
external identifiers
  • wos:000290636800015
  • scopus:79953747234
ISSN
1545-1593
DOI
10.1146/annurev-physchem-032210-103405
language
English
LU publication?
yes
id
80f03362-142d-4171-be38-9cc7cb4a7cfe (old id 2029136)
date added to LUP
2011-07-26 14:17:19
date last changed
2017-11-19 03:11:13
@article{80f03362-142d-4171-be38-9cc7cb4a7cfe,
  abstract     = {Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing interactions. Many of these principles have been elucidated by native-centric models, wherein nonnative interactions may be treated perturbatively. We discuss these developments as well as recent applications of coarse-grained chain modeling to knotted proteins and to intrinsically disordered proteins.},
  author       = {Chan, Hue Sun and Zhang, Zhuqing and Wallin, Stefan and Liu, Zhirong},
  issn         = {1545-1593},
  keyword      = {native topology,Levinthal paradox,folding funnel,energy landscape,desolvation,enthalpic barrier},
  language     = {eng},
  pages        = {301--326},
  publisher    = {Annual Reviews},
  series       = {Annual Review of Physical Chemistry},
  title        = {Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models},
  url          = {http://dx.doi.org/10.1146/annurev-physchem-032210-103405},
  volume       = {62},
  year         = {2011},
}