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• W2089032868 abstract "We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding tubes, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways." @default.
• W2089032868 created "2016-06-24" @default.
• W2089032868 creator A5023315429 @default.
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• W2089032868 date "2011-01-21" @default.
• W2089032868 modified "2023-09-25" @default.
• W2089032868 title "Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations" @default.
• W2089032868 cites W1960408443 @default.
• W2089032868 cites W1970440715 @default.
• W2089032868 cites W1974464394 @default.
• W2089032868 cites W1975718155 @default.
• W2089032868 cites W1977969550 @default.
• W2089032868 cites W1979070806 @default.
• W2089032868 cites W1981810374 @default.
• W2089032868 cites W1986155795 @default.
• W2089032868 cites W1990606222 @default.
• W2089032868 cites W1992422451 @default.
• W2089032868 cites W1994567486 @default.
• W2089032868 cites W1995156107 @default.
• W2089032868 cites W1996286018 @default.
• W2089032868 cites W2004194236 @default.
• W2089032868 cites W2008027871 @default.
• W2089032868 cites W2011542536 @default.
• W2089032868 cites W2013371652 @default.
• W2089032868 cites W2015943928 @default.
• W2089032868 cites W2016938198 @default.
• W2089032868 cites W2017698480 @default.
• W2089032868 cites W2017896410 @default.
• W2089032868 cites W2018265377 @default.
• W2089032868 cites W2020323428 @default.
• W2089032868 cites W2021662557 @default.
• W2089032868 cites W2025899185 @default.
• W2089032868 cites W2026134081 @default.
• W2089032868 cites W2028263411 @default.
• W2089032868 cites W2029564559 @default.
• W2089032868 cites W2030542905 @default.
• W2089032868 cites W2031092627 @default.
• W2089032868 cites W2035211954 @default.
• W2089032868 cites W2036425601 @default.
• W2089032868 cites W2040809566 @default.
• W2089032868 cites W2042490093 @default.
• W2089032868 cites W2042947255 @default.
• W2089032868 cites W2046285452 @default.
• W2089032868 cites W2046379303 @default.
• W2089032868 cites W2055484248 @default.
• W2089032868 cites W2056975402 @default.
• W2089032868 cites W2059608501 @default.
• W2089032868 cites W2061844749 @default.
• W2089032868 cites W2063913478 @default.
• W2089032868 cites W2065687924 @default.
• W2089032868 cites W2065919348 @default.
• W2089032868 cites W2066010782 @default.
• W2089032868 cites W2069288013 @default.
• W2089032868 cites W2078515575 @default.
• W2089032868 cites W2087356905 @default.
• W2089032868 cites W2087663875 @default.
• W2089032868 cites W2089298522 @default.
• W2089032868 cites W2095111795 @default.
• W2089032868 cites W2095911937 @default.
• W2089032868 cites W2096415083 @default.
• W2089032868 cites W2096649990 @default.
• W2089032868 cites W2101247857 @default.
• W2089032868 cites W2104395386 @default.
• W2089032868 cites W2104414143 @default.
• W2089032868 cites W2112154906 @default.
• W2089032868 cites W2120595908 @default.
• W2089032868 cites W2122220546 @default.
• W2089032868 cites W2138605281 @default.
• W2089032868 cites W2139882516 @default.
• W2089032868 cites W2142578757 @default.
• W2089032868 cites W2148691151 @default.
• W2089032868 cites W2151413338 @default.
• W2089032868 cites W2155418451 @default.
• W2089032868 cites W2158476854 @default.
• W2089032868 cites W2159923313 @default.
• W2089032868 cites W2160721947 @default.
• W2089032868 cites W2162561056 @default.
• W2089032868 cites W2164011287 @default.
• W2089032868 cites W2165890129 @default.
• W2089032868 cites W2169632544 @default.
• W2089032868 cites W2171144241 @default.
• W2089032868 cites W2171891719 @default.
• W2089032868 cites W2950069295 @default.
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• W2089032868 doi "https://doi.org/10.1021/jp1089596" @default.
• W2089032868 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3059588" @default.
• W2089032868 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/21254767" @default.
• W2089032868 hasPublicationYear "2011" @default.
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