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| About Dhananjay Bhattacharyya |
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Dr. Dhananjay Bhattacharyya, Ph.D. (Indian Institute of Science, Bangalore) carried out post-doctoral research at the National Institutes of Health, Bethesda before joining the Saha Institute of Nuclear Physics as Lecturer in 1996. His present position is Professor-F, equivalent to an Associate Professor. Dr. Bhattacharyya has worked on nucleic acid structure analysis using different theoretical techniques, such as crystal structure database analysis, molecular dynamics simulations, quantum chemistry etc. and has developed a pioneering software for analysis of orientations of nucleic acid base pairs with respect to their neighbors. These base pair parameters are the most effective parameters now in describing nucleic acid structural features leaving beside the conventional torsion angle analysis. Using a model-building study along with quantum chemical calculations, Dr. Bhattacharyya proposed a mechanism of peptide bond formation in ribosomes without mediating the so-called but unidentified peptidyl transferase enzyme. This model has generally been accepted as the correct mechanism after verification by various experiments by different groups. He proposed that sequence-directed DNA double helix rigidity, as obtained from different experiments as well as crystal database analysis, might arise due to formation of cross-strand bifurcated hydrogen bonds between successive base pairs. Such hydrogen bonds require pyramidal amino groups of nucleotide bases, which have also been established by Dr. Bhattacharyya by comparison of quantum chemical calculations and flouroscence experiments on different model systems. His recent interest is in the analysis of structure, frequency of occurrence, and interaction strengths of different types of non-canonical base pairs in RNA and their role in RNA three-dimensional structure and function.
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Dynamics of Proteins and Receptor-Ligand Complexes
Dhananjay Bhattacharyya, Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
It is generally accepted that a biomolecule or its complex with a ligand would be most stable at its lowest energy conformation. However, many biopolymers have a very complex energy landscape with several low-energy states separated by energy barriers of different heights, which can often be overcome by thermal motions at physiological temperature. Monte Carlo (MC), Genetic Algorithm (GA) and Molecular Dynamics (MD) simulation algorithms are generally used to obtain a complete ensemble of structures. In MD simulation Newton’s law of motion is represented in a form of a differential equation, which is then numerically and iteratively integrated to obtain position and velocities with respect to time for all the atoms of a system. Such MD simulations for several nano seconds duration for 1 to 100 million steps lead to sufficient sampling of the conformational space to estimate some average properties such as ligand-receptor interaction energy, ligand-induced motions of the receptor, natural breathing processes of DNA base pairs, etc. HIV protease is a well studied enzyme, which cleaves the HIV nascent polypeptide into different functional proteins. Several attempts have been taken to stop its action by binding with a peptide mimic, which would not be cleaved by the enzyme but would block its active site. We will attempt to understand this mechanism by MD simulation of HIV protease with a normal peptide as well as a peptide mimic. Energy parameters for the amino acids forming peptides or proteins are available with all MD softwares; however, those of the peptide mimics are not available. We will develop energy parameters of a peptide mimic, carry out MD simulation of the peptide mimic with protein as well as analyze previously simulated MD trajectories of the complex to understand the differential mechanism.
The group will subsequently prepare a workshop case study problem for MD simulation and discuss initial results.
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