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Simulations of the role of water in the protein-folding mechanism
Stanford University.
Stanford University.
Stanford University.
Stanford University.ORCID iD: 0000-0002-2734-2794
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2004 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 17, 6456-6461 p.Article in journal (Refereed) Published
Abstract [en]

There are many unresolved questions regarding the role of water in protein folding. Does water merely induce hydrophobic forces, or does the discrete nature of water play a structural role in folding? Are the nonadditive aspects of water important in determining the folding mechanism? To help to address these questions, we have performed simulations of the folding of a model protein (BBA5) in explicit solvent. Starting 10,000 independent trajectories from a fully unfolded conformation, we have observed numerous folding events, making this work a comprehensive study of the kinetics of protein folding starting from the unfolded state and reaching the folded state and with an explicit solvation model and experimentally validated rates. Indeed, both the raw TIP3P folding rate (4.5 +/- 2.5 micros) and the diffusion-constant corrected rate (7.5 +/- 4.2 micros) are in strong agreement with the experimentally observed rate of 7.5 +/- 3.5 micros. To address the role of water in folding, the mechanism is compared with that predicted from implicit solvation simulations. An examination of solvent density near hydrophobic groups during folding suggests that in the case of BBA5, there are water-induced effects not captured by implicit solvation models, including signs of a "concurrent mechanism" of core collapse and desolvation.

Place, publisher, year, edition, pages
2004. Vol. 101, no 17, 6456-6461 p.
Keyword [en]
explicit solvation model, distributed computing, molecular dynamics
National Category
Biophysics Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-82631DOI: 10.1073/pnas.0307898101ISI: 000221107900025PubMedID: 15090647OAI: oai:DiVA.org:kth-82631DiVA: diva2:498423
Note
QC 20120221Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2017-12-07Bibliographically approved

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Lindahl, Erik

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