Sampling the equilibrium kinetic network of Trp-cage in explicit solvent
نویسندگان
چکیده
منابع مشابه
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 × 14 rate matrix. Analysis of the kinetic rate matrix indicates the presence of a near native inte...
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We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un...
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We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between...
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Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently deve...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2014
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4874299