| Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. | |
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MedLine Citation:
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PMID: 19453123 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Proteins are highly complex molecules with features exquisitely selected by nature to carry out essential biological functions. Physical chemistry and polymer physics provide us with the tools needed to make sense of this complexity. Upon translation, many proteins fold to a thermodynamically stable form known as the native state. The native state is not static, but consists of a hierarchy of conformations, that are continuously explored through dynamics. In this review we provide a brief introduction to some of the core concepts required in the discussion of the protein native dynamics using energy landscapes ideas. We first discuss recent works which have challenged the structure-function paradigm by demonstrating function in disordered proteins. Next we examine the hierarchical organization in the energy landscapes using atomistic molecular dynamics simulations and principal component analysis. In particular, the role of direct and water-mediated contacts in sculpting the landscape is elaborated. Another approach to studying the native state ensemble is based on choosing high-resolution order parameters for computing one- or two-dimensional free energy surfaces. We demonstrate that 2D free energy surfaces provide rich thermodynamic and kinetic information about the native state ensemble. Brownian dynamics simulations on such a surface indicate that protein conformational dynamics is weakly activated. Finally, we briefly discuss implicit and coarse-grained protein models and emphasize the solvent role in determining native state structure and dynamics. |
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Authors:
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Pavel I Zhuravlev; Christopher Kroboth Materese; Garegin A Papoian |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: The journal of physical chemistry. B Volume: 113 ISSN: 1520-6106 ISO Abbreviation: J Phys Chem B Publication Date: 2009 Jul |
Date Detail:
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Created Date: 2009-06-25 Completed Date: 2009-08-18 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101157530 Medline TA: J Phys Chem B Country: United States |
Other Details:
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Languages: eng Pagination: 8800-12 Citation Subset: IM |
Affiliation:
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Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Kinetics Models, Molecular Protein Conformation Proteins / chemistry*, metabolism* Thermodynamics* Water / chemistry, metabolism |
| Chemical | |
Reg. No./Substance:
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0/Proteins; 7732-18-5/Water |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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