title: Conformational thermodynamics guided structural reconstruction of biomolecular fragments.
abstract: Computational prediction of structure for macromolecular fragments is a formidable challenge. Here we show that the differences in conformational thermodynamics, computed using the equilibrium distribution of dihedral angles from molecular dynamics simulation, can identify the better model for the missing residues in the metal ion free (apo) skeletal muscle Troponin C (TnC). We use the model to understand Troponin I interaction with calcium (Ca(2+)) ion bound TnC. Our method to compare conformational thermodynamics between different models can be easily generalized to any macromolecule to understand the structure and function even if experimental structures are not resolved.
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, India. jaydeb@bose.res.in mahuaghosh@bose.res.in.
authors.forename: Samapan
authors.initials: S
authors.lastname: Sikdar
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, India. jaydeb@bose.res.in mahuaghosh@bose.res.in and Also at Unit of Nanoscience and Technology-II and The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Center for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, India.
authors.forename: J
authors.initials: J
authors.lastname: Chakrabarti
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, India. jaydeb@bose.res.in mahuaghosh@bose.res.in.
authors.forename: Mahua
authors.initials: M
authors.lastname: Ghosh
mesh_terms: D001059:Apoproteins / Q000737:chemistry*; D001665:Binding Sites; D002118:Calcium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D019209:Troponin C / Q000737:chemistry*; D019210:Troponin I / Q000737:chemistry*
chemical_list: D001059:Apoproteins; D019209:Troponin C; D019210:Troponin I; D002118:Calcium