* PROTEIN DYNAMICS
We focus on understanding the relationship between protein structure, function, and dynamics. Research is focused into two major sub-groups: 1) molecular modeling of enzyme-substrate / enzyme-inhibitor interactions and 2) structure-based drug discovery. Studies are performed using computer simulation methods ranging from molecular dynamics simulations, Monte Carlo simulations, Brownian dynamics simulations, and protein-ligand docking. General properties that we address include change in protein structure and dynamics upon binding inhibitors and with mutations, ligand binding strength and specificity, and bound water structure.
* GREEN CHEMISTRY
Ionic liquids and super critical CO2 have been identified as promising green solvents for biotransformation, enzyme catalysis and long-term preservation of biomolecules. Our objective is to elucidate molecular level interactions between biomolecules and ionic liquids, modulated kinetics of protein folding and increased solubilization & enhanced extraction of proteins and other hydrophilic substances in water-in-CO2 reverse micelles, etc.
* NANO CLUSTERS
We, perform first-principle quantum mechanical calculations of gold, silver and gold-silver binary clusters to understand their electronic structures, magic number, vibrational spectra, adsorption behavior, response to electric field, catalysis, etc.
* In-vitro STUDIES
While rationalizing experimental behavior of biomolecules using molecular dynamics simulation remain our forte, we have moved on to use MD as a central engine of experimental research by validating our findings from computational studies using various spectroscopic & calorimetric techniques. With leads from our computational data we perform inhibitor synthesis, enzymatic assays and drug design in our laboratory.
40. S. L. Rath,S. Senapati*, “Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: Insights for rational drug design”, PLoS ONE 8(9): e73836.doi:10.1371/journal.pone/0073836.
39 N. Kathiresan, S. Senapati*, “Probing the Conformational Flexibility of Monomeric FtsZ in GTP-Bound, GDP-Bound, and Nucleotide-Free States”, Biochemistry 52,3543 − 3551 (2013).
38. A. Chandran, D. Ghoshdastidar, S. Senapati*, Groove binding mechanism of Ionic liquids: A key factor in long-term stability of DNA in hydrated Ionic liquids? J. Am. Chem. Soc., 134, 20330-39, (2012).
37. B. Sahu, J. Mohan, G. Sahu, P. Allu, L. Subramanian, P.J. Sonawane, P. Singh, B. Sasi, S. Senapati, S. Maji, A. Bera, B.S. Gomathi, A.S. Mullasari, N. Mahapatra*, “Functional Genetic Variants of the Catecholamine-Release-Inhibitory Peptide Catestatin in an Indian Population: Allele-Specific Effects on Metabolic Traits” J Biol Chem, (2012).
36. N. Kathiresan, J. Mohan and S. Senapati*. “Relating nucleotide dependent conformational changes in free tubulin dimer to tubulin assembly.” Biopolymers,99/5, 282-291(2012).
35. N. Kathiresan and S. Senapati* “Understanding the basis of drug resistance of the mutants of αβ-tubulin dimer via molecular dynamics simulations.” PLoS ONE 7(8): e42351, (2012).
34. B. Sahu, J. Mohan, G. Sahu, P. Singh, B. Sasi, P. Allu, S. Maji, A. Bera*, S. Senapati*, N. Mahapatra*, “Molecular mechanism of interactions of the physiological anti-hypertensive peptide catestatin with the neuronal nicotinic acetylcholine receptor”, J. Cell Sci. 125, 2323, (2012)
33. S. Karthik and S. Senapati*, “Dynamic Flaps in HIV-1 Protease Adopt Unique Ordering at Different Stages in the Catalytic Cycle”, Proteins 79, 1830, (2011).
32. A. Chandran, K. Prakash and S. Senapati*, “Self-assembled Inverted Micelles Stabilize Ionic Liquid Domains in Supercritical CO2″, J. Am. Chem. Soc. 132, 12511, (2010).
31. A. Chandran, K. Prakash and S. Senapati, “Structure and Dynamics of Acetate Anion-based Ionic Liquids from Molecular Dynamics Study”, Chem. Phys. 374, 46, (2010).
30. A. Harishchander, D. A. Anand and S. Senapati, “Analysis of Resistance to Human Immunodeficiency Virus Protease Inhibitors Using Molecular Mechanics and Machine Learning Strategies”, American Medical Journal 1(2): 100-106, (2010).
29. B. R. Prasad and S. Senapati*, “Explaining the differential solubility of flue gas components in ionic liquids from first-principle calculations”, J. Phys. Chem. B. 113,4739, (2009).
28. V. Torbeev, H. Raghuraman, K. Mandal, S. Senapati, S. Kent, “Dynamics of flap structures in three HIV-1 protease/inhibitor complexes”, J. Am. Chem. Soc. 131, 884, (2009).
27. G. Singh and S. Senapati*, “Molecular Dynamics Simulations of Ligand-induced Flap Closing in HIV-1 Protease Approach X-ray Resolution: Establishment of the Role of Bound Water in the Flap Closing Mechanism “, Biochemistry. 47, 10657 (2008).
26. V. S. V. Chaitanya and S. Senapati*, “Self-assembled Reverse Micelles in Supercritical CO2 Entrap Protein in Native State “, J. Am. Chem. Soc. 130, 1866 (2008).
25. S. Senapati*, “How strongly can calcium ion influence the hydrogen-bond dynamics at complex aqueous interfaces?”, J. Chem. Phys. 126, 204710 (2007).
24. S. Senapati*, Y. Cheng, and J. A. McCammon, “In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: Configurational selection imposed by steric interactions”, J. Med. Chem. 49, 6222, (2006).
23. S. Senapati*, J. M. Bui, and J. A. McCammon, “Induced Fit in Mouse Acetylcholinesterase upon Binding a Femtomolar Inhibitor: A Molecular Dynamics Study ”, J. Med. Chem. 48, 8155 (2005).
22. S. Senapati*, C. F. Wong and J. A. McCammon, “Finite concentration effects on diffusion-controlled reactions”, J. Chem. Phys. 121, 7896 (2004).
21. S. Senapati and M. L. Berkowitz, “Computer simulation studies of water states in perfluoropolyether reverse micelles: Effects of changing the counterion”, J. Phys. Chem. A 108, 9768 (2004).
20. S. Senapati and M. L. Berkowitz, “Molecular dynamics simulation studies of ployether and perfluoropolyether surfactant based reverse micelles in supercritical carbon dioxide”, J. Phys. Chem. B 107, 12906 (2003).
19. S. Senapati and M. L. Berkowitz, “Water structure and dynamics in phosphate fluorosurfactant based reverse micelle: A computer simulation study”, J. Chem. Phys. 118, 1937 (2003).
18. S. Senapati*, “A molecular dynamics simulation study of the dimethyl sulfoxide liquid-vapor interface”, J. Chem. Phys. 117, 1812 (2002).
17. C. D. Bruce, S. Senapati, M. L. Berkowitz, L. Perera, and M.D.E. Forbes, “Molecular dynamics simulations of sodium dodecyl sulfate micelle in water: The behavior of water”, J. Phys. Chem. B 106, 10902 (2002).
16. S. Senapati, J. S. Keiper, J. M. DeSimone, G. D. Wignall, Y. B. Melnichenko, H. Frienlinghaus, and M. L. Berkowitz, “Structure of phosphate fluorosurfactant based reverse micelles in supercritical carbon dioxide”, Langmuir 18, 7371 (2002).
15. S. Senapati and M. L. Berkowitz, “Computer simulation study of the interface width of the liquid/liquid interface”, Phys. Rev. Lett. 87, 176101 (2001).
14. S. Senapati and A. Chandra, “Effects of confinement on structure, dielectric and dynamics of water in small hydrophobic cavity”, J. Phys. Chem. B 105, 5106 (2001).
13. S. Senapati and A. Chandra, “Surface charge induced modifications of the structure and dynamics of mixed dipolar liquids at solid-liquid interfaces: A molecular dynamics simulation study”, J. Chem. Phys. 113, 8817 (2000).
12. S. Senapati and A. Chandra,”Structure of a mixed dipolar liquid near a metal surface: A combined approach of weighted density and perturbative approximations”, Phys. Rev. E 62, 1017 (2000).
11. S. Senapati and A. Chandra, “Dynamics of polarization relaxation in a dipolar mixture at solid-liquid interface”, J. Chem. Phys. 113, 377 (2000).
10. S. Senapati and A. Chandra, “Interfacial structure of a mixed dipolar liquid in contact with a charged solid surface”, J. Chem. Phys. 112, 10467 (2000).
9. S. Senapati and A. Chandra, “Interfacial structure of a solute-solvent mixture in contact with a semipermeable membrane”, Ind. J. Chem. A 39, 219 (2000).
8. S. Senapati and A. Chandra, “Molecular dynamics simulations of simple dipolar liquids in spherical cavity: Effects of confinement on structural, dielectric and dynamical properties”, J. Chem. Phys. 111, 1223 (1999).
7. D. Das, S. Senapati and A. Chandra, “Structure of dipolar liquids near charged solid surfaces: A nonlinear theory based on a density functional approach and Monte Carlo simulations”, J. Chem. Phys. 110, 8129 (1999).
6. S. Senapati and A. Chandra, “Nonlinear theory of metal-solvent interface using density functional approach”, Phys. Rev. E, 59, 3140 (1999).
5. S. Senapati and A. Chandra, “Structure and dynamics of mixed dipolar liquids near solid surfaces: A molecular dynamics simulation study”, Chem. Phys. 242, 353 (1999).
4. A. Chandra, S. Senapati and D. Sudha, “Dynamics of polarization relaxation at soild-liquid interface”, J. Chem. Phys. 109, 10439 (1998).
3. S. Senapati and A. Chandra, “Computer simulation of dipolar liquids near charged solid surfaces: Electric field induced modifications of structure and dynamics of interfacial solvent”, J. Mol. Struc. (Theochem), 455, 1 (1998).
2. A. Chandra and S. Senapati, “Rotational dielectric friction and molecular relaxation at metal-solvent interfaces”, J. Mol. Liq. 77, 77 (1998).
1. S. Senapati and A. Chandra, “Molecular relaxation in simple dipolar liquids confined between two solid surfaces”, Chem. Phys. 231, 65 (1998).
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