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Microscopic Calculation of Conformational Thermodynamics in Bio-Macromolecular Complexes

Microscopic Calculation of Conformational Thermodynamics in Bio-Macromolecular Complexes

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Microscopic Calculation of Conformational Thermodynamics in Bio-Macromolecular Complexes
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<strong>Seminar of the School of Physical Sciences -----------------------------------------------------------</strong> Title: <strong>Microscopic Calculation of Conformational Thermodynamics in Bio-Macromolecular Complexes</strong> Speaker: <strong>Jaydeb Chakrabarti</strong> (S.N. Bose National Centre for Basic Sciences, Kolkata) Date: <strong>March 12, 2015 </strong> <strong>Abstract: </strong>Bio-macromolecules undergo conformational change while they form complexes. These complexes form the basis of a large number of bio-molecular processes. NMR experiments show that the entropy changes associated with conformational changes play vital role in stabilizing such complexes. The theoretical routes to calculate the thermodynamics of conformational changes are not explored in details. The conventional methods based on thermodynamic integration are computationally too expensive to be implemented for large bio-molecules. We show that the conformational thermodynamics including the free energy and entropy can be extracted from the equilibrium distribution of the dihedral angles in bio-molecules with modest computational efforts. The conformational entropies calculated from such distributions agree well to those of protein-ligand complexes extracted from the NMR experiments [1]. We further show that the conformational thermodynamics data can (a) quantify the x-ray structural data of protein-protein interface [2] and (b) ascertain the functional roles of different residues in a protein [3]. [1] Das A, Chakrabarti J, Ghosh M. Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation. Biophysical Journal. 2013;104:1274-84. [2] Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein-protein complex. Mol Biosyst. 2014;10:437-45. [3] Sikdar S, Chakrabarti J, Ghosh M. A microscopic insight from conformational thermodynamics to functional ligand binding in proteins. Mol Biosyst. 2014, 10:3280-3289.

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