Sampling the equilibrium kinetic network of Trp-cage in explicit solvent

We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un)folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14 ×...

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Bibliographic Details
Published inThe Journal of chemical physics Vol. 140; no. 19; p. 195102
Main Authors Du, Weina, Bolhuis, Peter G
Format Journal Article
LanguageEnglish
Published United States 21.05.2014
Subjects
Binding Sites
Computer Simulation
Kinetics
Models, Chemical
Models, Molecular
Peptides - chemistry
Protein Binding
Protein Conformation
Protein Denaturation
Protein Folding
Solvents - chemistry
Thermodynamics
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Summary:We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un)folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14 × 14 rate matrix. Analysis of the kinetic rate matrix indicates the presence of a near native intermediate state characterized by a fully formed alpha helix, a slightly disordered proline tail, a broken salt-bridge, and a rotated arginine residue. This intermediate was also found in recent IR experiments. Moreover, the predicted rate constants and timescales are in agreement with previous experiments and simulations.
ISSN:1089-7690
DOI:10.1063/1.4874299