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\iteman{io-port 02156983}
\itemau{Kokubo, Hironori; Okamoto, Yuko}
\itemti{Classification and prediction of low-energy membrane protein helix configurations by replica-exchange Monte Carlo method.}
\itemso{J. Phys. Soc. Japan 73, No. 9, 2571-2585 (2004).}
\itemab
Summary: 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 $\varepsilon=1.0$ and five such groups in the case of $\varepsilon=4.0$. The global-minimum free energy state in the case of $\varepsilon=1.0$ is very close to the structure of the NMR experiments and the prediction was successful, while in the case of $\varepsilon =4.0$ 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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\itemut{protein structure predictions; transmembrane helices; generalized-ensemble algorithms; replica-exchange method}
\itemli{doi:10.1143/JPSJ.73.2571}
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