title: 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.
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Das
authors.forename: J
authors.initials: J
authors.lastname: Chakrabarti
authors.forename: Mahua
authors.initials: M
authors.lastname: Ghosh
mesh_terms: D002118:Calcium / Q000378:metabolism; D002147:Calmodulin / Q000737:chemistry / Q000378:metabolism*; D019277:Entropy; D008853:Microscopy; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary
chemical_list: D002147:Calmodulin; D010455:Peptides; D002118:Calcium