NDLI: Mechanisms and kinetics of β-hairpin formation

Content Provider	PubMed Central
Author	Klimov, D. K. Thirumalai, D.
Copyright Year	2000
Abstract	Thermodynamics and kinetics of off-lattice models with side chains for the β-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except refolding time τF) there are no qualitative differences between the full model and the Gō version. The validity of the models is established by comparison of the calculated native structure with the Protein Data Bank coordinates and by reproducing the experimental results for the degree of cooperativity and τF. For the full model τF ≈ 2 μs at the folding temperature (experimental value is 6 μs); the Gō model folds 50 times faster. Upon refolding, structural changes take place over three time scales. On the collapse time scale compact structures with intact hydrophobic cluster form. Subsequently, hydrogen bonds form, predominantly originating from the turn by a kinetic zipping mechanism. The assembly of the hairpin is complete when most of the interstrand contacts (the rate-limiting step) is formed. The dominant transition state structure (located by using cluster analysis) is compact and structured. We predict that when hydrophobic cluster is moved to the loop τF marginally increases, whereas moving the hydrophobic cluster closer to the termini results in significant decrease in τF relative to wild type. The mechanism of hairpin formation is predicted to depend on turn stiffness.
Starting Page	2544
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	6
Volume Number	97
Language	English
Publisher	The National Academy of Sciences
Publisher Date	2000-03-14
Access Restriction	Open
Rights Holder	The National Academy of Sciences
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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