Side-chain Conformations Cooperatively Restricted in Protein Secondary Structure : I. A Novel Method for Exhaustive Structure Searching

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Protein side-chain conformations were examined by searching for all combinations of the side-chain rotamers, with energies near the global minimum, that were found in advance by the dead-end elimination algorithm. Using this method, the side-chain configurational entropies and their correlations were analyzed for the hydrophobic sides of the secondary structures of proteins. The conformations of several bulky side-chains in α-helices were found to be cooperatively fixed by the restricted side-chain conformations of the neighboring β-branched amino acids. In β-sheet, the side-chain conformations are not restricted by the backbone structures of the individual β-strands, but those in the inner stands are restricted, due to the correlation between the side-chains on the neighboring strands.
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