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J. Chakrabarti

S. N. Bose National Centre for Basic Sciences, India

Title: Microscopic calculation of conformational thermodynamics in bio-macromolecular complexes

Biography

Biography: J. Chakrabarti

Abstract

Statement of the Problem: The microscopic basis of connection between protein conformation and function is a fundamental challenge. Recent experiments show the importance of conformational changes in providing stability to protein complexes. The changes in conformational state have both enthalpy and entropic components. It has been possible to quantify the entropy changes due conformational changes from Nuclear magnetic Resonance data. Here we show microscopic calculation of both the enthalpy and entropy contribution while protein conformations change from the equilibrium distribution of the dihedral angles of proteins. We have shown that the free-energetically destabilized and entropically disordered residues in a given conformation compared to a reference conformation act as binding residue in the giv en conformation. Here we show that this principle can: (1) ascertain ligand binding of a protein in different conformations; (2) supplement the structure of missing fragments in a protein; and (3) serve as a guideline for allosteric changes. All these applications point to tune protein in-silico which would help to design functional materials with protein as building blocks.

References:

  1. Conformational thermodynamics guided structural reconstruction of biomolcular fragments, Samapan Sikdar, J. Chakrabarti and Mahua Ghosh, Molecular Biosystems, 12, 444-453 (2016).          
  2. A microscopic insight from conformational thermodynamics to functional ligand binding in proteins, Samapan Sikdar, J. Chakrabarti and Mahua Ghosh, Molecular Biosystems, 10, 3280-3289 (2014).      
  3. Quantum chemical studies on the role of residues in calcium binding to Calmodulin, Samapan Sikdar, Mahua Ghosh, Molly De Raychaudhury and J. Chakrabarti, Chem Phys Lett, 605-606, 103-107(2014).
  4. Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation Amit Das, J. Chakrabarti and Mahua Ghosh, Biophysical Journal, 104, 1274 (2013).
  5. High-Affinity Quasi-Specific Sites in the Genome: How the DNA-Binding Proteins Cope with them  J. Chakrabarti, Navin Chandra, Paromita Raha, and Siddhartha Roy, Biophysical Journal, 101, 1123 (2011).