Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

2004 ◽  
Vol 121 (1) ◽  
pp. 415 ◽  
Author(s):  
Nina Singhal ◽  
Christopher D. Snow ◽  
Vijay S. Pande
Keyword(s):  
Path Sampling ◽  
Folding Rate ◽  
Beta Hairpin ◽  
State Models ◽  
Tryptophan Zipper

scholarly journals Modeling the Mechanism of CLN025 Beta-Hairpin Formation

2017 ◽  
Author(s):  
Keri A. McKiernan ◽  
Brooke E. Husic ◽  
Vijay S. Pande
Keyword(s):  
Force Fields ◽  
Test Case ◽  
Conformational Ensemble ◽  
Folding Process ◽  
Hydrophobic Collapse ◽  
Rate Determining Step ◽  
Beta Hairpins ◽  
Beta Hairpin ◽  
State Models ◽  
Protein Force Fields

Beta-hairpins are a substructure found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

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