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

Annual Review of Physical Chemistry - Tập 62 Số 1 - Trang 301-326 - 2011
Hue Sun Chan1, Zhuqing Zhang1, Stefan Wallin2, Zhirong Liu3
1Departments of Biochemistry, of Molecular Genetics, and of Physics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;, [email protected]
2Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, SE-223 62 Lund, Sweden;
3College of Chemistry and Molecular Engineering, Center for Theoretical Biology, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China;

Tóm tắt

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.

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Annual Review of Physical Chemistry

Tập 62 Số 1

301-326

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