Kinetic definition of protein folding transition state ensembles and reaction coordinates

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Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue beta beta alpha beta protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points along each free energy barrier. We introduced a method for determining transition states by employing the transmission probability, P-trans, and determined which conformations were transition state ensemble members (P-trans approximate to 0.5). The transmission probability may be used to characterize the barrier in several ways. For example, we ran simulations at 82 degrees C, determined the change in Ptrans with temperature for all 2,000 conformations, and quantified Hammond behavior directly using Ptrans correlation. Additionally, we propose that diffusion along Ptrans may provide the configurational diffusion rate at the top of the barrier. Specifically, given a transition state conformation x(0) with estimated P-trans = 0.5, we selected a large set of subsequent conformations from independent trajectories, each exactly a small time delta t after x(0) (250 ps). Calculating P-trans for the new trial conformations, we generated the P(P-trans vertical bar delta t = 250 ps) distribution that reflected diffusion. This approach provides a novel perspective on the diffusive nature of a protein folding transition and provides a framework for a quantitative study of activated relaxation kinetics.
Publisher
BIOPHYSICAL SOCIETY
Issue Date
2006-07
Language
English
Article Type
Article
Keywords

MOLECULAR-DYNAMICS SIMULATIONS; N-TERMINAL DOMAIN; BETA-HAIRPIN; ISOMERIZATION DYNAMICS; IRREVERSIBLE-PROCESSES; RECIPROCAL RELATIONS; PEPTIDE; PATHS; MODEL; L9

Citation

BIOPHYSICAL JOURNAL, v.91, no.1, pp.14 - 24

ISSN
0006-3495
DOI
10.1529/biophysj.105.075689
URI
http://hdl.handle.net/10203/225412
Appears in Collection
CH-Journal Papers(저널논문)
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