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Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.

ABSTRACT: We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.

SUBMITTER: Das A

PROVIDER: S-EPMC3602779 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.

Das Amit A Chakrabarti J J Ghosh Mahua M

Biophysical journal 20130319 6

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-en ...[more]

PMID: 23528087

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