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    A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

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    1605.07731v1.pdf
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    Genre
    Pre-print
    Date
    2016-12-13
    Author
    Wan, H
    Zhou, G
    Voelz, VA
    Subject
    Amino Acid Sequence
    Kinetics
    Markov Chains
    Molecular Dynamics Simulation
    Mutation
    Peptides
    Protein Folding
    Protein Structure, Secondary
    Tryptophan
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/4226
    
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    DOI
    10.1021/acs.jctc.6b00938
    Abstract
    © 2016 American Chemical Society. We present a maximum-caliber method for inferring transition rates of a Markov state model (MSM) with perturbed equilibrium populations given estimates of state populations and rates for an unperturbed MSM. It is similar in spirit to previous approaches, but given the inclusion of prior information, it is more robust and simple to implement. We examine its performance in simple biased diffusion models of kinetics and then apply the method to predicting changes in folding rates for several highly nontrivial protein folding systems for which non-native interactions play a significant role, including (1) tryptophan variants of the GB1 hairpin, (2) salt-bridge mutations of the Fs peptide helix, and (3) MSMs built from ultralong folding trajectories of FiP35 and GTT variants of the WW domain. In all cases, the method correctly predicts changes in folding rates, suggesting the wide applicability of maximum-caliber approaches to efficiently predict how mutations perturb protein conformational dynamics.
    Citation to related work
    American Chemical Society (ACS)
    Has part
    Journal of Chemical Theory and Computation
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    For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/4208
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