期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 102, 期 19, 页码 6801-6806出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0408970102
关键词
graph; master equation; protein G
资金
- NIGMS NIH HHS [R01 GM030580, GM30580] Funding Source: Medline
We present an approach to the study of protein folding that uses the combined power of replica exchange simulations and a network model for the kinetics. We carry out replica exchange simulations to generate a large (approximate to 10(6)) set of states with an all-atom effective potential function and construct a kinetic model for folding, using an ansatz that allows kinetic transitions between states based on structural similarity. We use this network to perform random walks in the state space and examine the overall network structure. Results are presented for the C-terminal peptide from the B1 domain of protein G. The kinetics is two-state after small temperature perturbations. However, the coil-to-hairpin folding is dominated by pathways that visit metastable helical conformations. We propose possible mechanisms for the alpha-helix/ beta-hairpin interconversion.
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