Faculty Publications
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Item Hydrophilicity of the hydrophobic group: Effect of cosolvents and ions(Elsevier B.V., 2019) Dilip, H.N.; Chakraborty, D.Classical molecular dynamics simulations were performed to study the effect of cosolvents and ions on the solvation structure of zwitterionic glycine in liquid water. Simulations were carried out for 2 M and 1 M concentration of TMAO, Urea, KCl and LiCl solutions to observe the changes in liquid structure of water near the glycine molecule. Radial distribution functions and spatial distribution functions showed the presence of protective hydration layer near the C ? in presence of TMAO which gets reduced in case of urea, KCl and minimum in case of LiCl. LiCl is found to disrupt severely the solvation structure near the glycine molecule. For LiCl system, a small hydration layer is found near C ? unit at higher distances which is mainly due to the first hydration shell of lithium ion bonded to the carboxylate group. Presence of these hydration layers gives extra stabilization energy to the glycine water system. Stabilizing and destabilizing effect of water near the glycine molecule is calculated in terms of Potential Mean Force. The anomalous behaviour of lithium salts with respect to Group I cation salts in protein stabilization can be explained on the basis of this behaviour. We found maximum hydrogen bond lifetime for water molecules in presence of TMAO followed by LiCl, KCl and least in case of urea. The higher lifetimes in presence of ions are found mainly due to their electrostatic force. The stabilization of the hydrophobic part of the glycine molecule can be correlated with the stabilization of proteins in presence of these cosolvents. © 2019 Elsevier B.V.Item Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites(Elsevier B.V., 2022) Venugopal, P.P.; Singh, O.; Chakraborty, D.Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease. © 2022 Elsevier B.V.Item Controlling the Morphology and Orientation of the Helical Self-Assembly of Pyrazine Derivatives by Tuning Hydration Shells(John Wiley and Sons Inc, 2025) Sarkar, S.; Mathath, A.V.; Chakraborty, D.A combination of density functional theory (DFT) and classical molecular dynamics simulations is performed to unveil the guiding force in the self-assembly process of the pyrazine-based biopolymers to helical nanostructures. The highlight of the study shows the decisive role of the solvent-ligand H-bonding and the inter-molecular pi-pi stacking not only ensures the unidirectional packing of the helical structure but also the rotation of left-handed to the right-handed helical structure of the molecule. This transition is supported by the bulk release of the “ordered” water molecules. The extent of this bonding can be tuned by the temperature, concentration, and type of the metal ions. Smaller ions like Na+ and Al3+ destroy the structure, whereas bigger ions like Zn2+, Ni2+, and Au3+ preserve and rotate the structure according to their concentration. The interaction energy between the pyrazine derivatives is found to be high (?9000 kJ mol?1) for right-handed rotation of the helix, which increases further with the addition of D-histidine, forming a superhelical structure (?10300 kJ mol?1). The insights gained from this work can be used to generate nanostructures of desired morphology. © 2025 Wiley-VCH GmbH.