Classification and Prediction of Low-Energy Membrane Protein Helix Configurations by Replica-Exchange Monte Carlo Method

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  • Kokubo Hironori
    Department of Theoretical Studies, Institute for Molecular Science
  • Okamoto Yuko
    Department of Theoretical Studies, Institute for Molecular Science Department of Functional Molecular Science, The Graduate University for Advanced Studies

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The effectiveness of our classification and prediction method for transmembrane helix configurations of membrane proteins by replica-exchange simulations is tested with glycophorin A transmembrane dimer. Replica-exchange simulations can sample wide configurational space without getting trapped in local-minimum free energy states and we can find stable structures at low temperatures. We classify low-energy configurations into clusters of similar structures by the principal component analysis. These clusters are identified as the global-minimum and local-minimum free energy states. Our classifications revealed that there are only two major groups of similar structures in the case of the simulation with the dielectric constant ε=1.0 and five such groups in the case of ε=4.0. The global-minimum free energy state in the case of ε=1.0 is very close to the structure of the NMR experiments and the prediction was successful, while in the case of ε=4.0 not the global-minimum but a local-minimum free energy state corresponds to the native structure. It is shown that the global-minimum free energy state at low temperatures is also the global-minimum potential energy state in both cases.

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