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Title: Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates
Authors: Kurniawan, N.A.
Enemark, S.
Rajagopalan, R. 
Issue Date: 20-Jun-2012
Citation: Kurniawan, N.A., Enemark, S., Rajagopalan, R. (2012-06-20). Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates. Journal of the American Chemical Society 134 (24) : 10200-10208. ScholarBank@NUS Repository.
Abstract: Crowded environments inside cells exert significant effects on protein structure, stability, and function, but their effects on (pre)folding dynamics and kinetics, especially at molecular levels, remain ill-understood. Here, we examine the latter for, as an initial candidate, a small de novo β-hairpin using extensive all-atom molecular dynamics simulations for crowder volume fractions φ up to 40%. We find that crowding does not introduce new folding intermediates or misfolded structures, although, as expected, it promotes compact structures and reduces the accessible conformational space. Furthermore, while hydrophobic-collapse-mediated folding is slightly enhanced, the turn-directed zipper mechanism (dominant in crowder-free situations) increases many-fold, becoming even more dominant. Interestingly, φ influences the stability of the folding intermediates (FI 1 and FI 2) in an apparently counterintuitive manner, which can be understood only by considering specific intrachain interactions and intermediate (and hierarchical) structural transitions. For φ values
Source Title: Journal of the American Chemical Society
ISSN: 00027863
DOI: 10.1021/ja302943m
Appears in Collections:Staff Publications

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