How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.

@article{Deng2013HowKW,
  title={How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.},
  author={Nan-Jie Deng and Wei Dai and Ronald M. Levy},
  journal={The journal of physical chemistry. B},
  year={2013},
  volume={117 42},
  pages={12787-99}
}
Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultralong MD simulation; MSM-MD can be… CONTINUE READING
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