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 Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides(Elsevier B.V., 2020) Dilip, H.N.; Chakraborty, D.Effects of two naturally occurring osmolytes, urea and trimethylamine-N-oxide (TMAO) on the solvation structure of hydrophobic moiety of alanine, glycine, N-methylacetamide and acetamide are investigated by classical molecular dynamics simulations. Our results are analysed in terms of site-site radial distribution functions (RDF), spatial distribution functions (SDF), number of hydrogen bonds, orientation profile, KB integrals, preferential binding coefficient and hydrogen bond dynamics. RDF and SDF showed presence of an extra hydration shell near the hydrophobic unit when TMAO is present in the solution. This hydration shell mainly consists of broken hydrogen bonds. In urea-water solution, intramolecular association is favoured compared to intermolecular association: which is in contrast to the TMAO-water solution. Alanine, glycine, NMA and acetamide showed preferred interactions with the water molecules in presence of TMAO compared to urea. Urea and TMAO both are found to be excluded from the alanine, glycine, NMA and acetamide surface but presence of urea was slightly favoured at higher distances in case of NMA and acetamide. The strong hydrogen bond between TMAO-water increases the hydrogen bond lifetime of other hydrogen bonds in the system. The preferential binding affinity of water with the protein molecules and strong hydrogen bonds are found to be the key reasons for stability in presence of TMAO. © 2019 Elsevier B.V.Item Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- And High-Density Regions(American Chemical Society service@acs.org, 2020) Priyadarsini, A.; Biswas, A.; Chakraborty, D.; Mallik, B.S.Water is believed to be a heterogeneous liquid comprising multiple density regions that arise because of the presence of interstitial molecules and can be differentiated by their structure as well as the existence of hydrogen-bonded pairs with varying strengths. First-principles molecular dynamics studies were performed at six different temperatures to investigate the effect of temperature on the thermophysical, structure, dynamics, and vibrational spectral properties of the water molecules using dispersion-corrected density functional theory. The variation of properties like density, cohesive energy, and compressibility with a change in temperature produces a trend that matches with the experiments and resembles the experimentally observed anomalous behavior. We explore the possibility of explaining the trends in calculated properties by analyzing the structure and dynamics of the water molecules in terms of instantaneous low- and instantaneous high-density regions that are found during the simulation time. The dynamics of these two types of water molecules were studied by calculating the lifetime from the proposed autocorrelation functions. The lifetime of formation of instantaneous low-density water is found to decrease with an increase in temperature, whereas the lifetime of instantaneous high-density water is found to be maximum at 298 K among all the considered temperatures. The presence of more interstitial water molecules is observed at this temperature. The signature of these water molecules is found in the radial distribution function, spatial distribution function, void distribution, configurational space, orientational dynamics, and spectral diffusion calculations. It is also found that around 298 K, these water molecules are present distinctively that mix up with the first and second solvation shells with the rise of the temperature. The outlook of the reported results can be extended to other thermodynamic conditions to explain some of the anomalous properties, which can be related to the presence of the interstitial molecules in water. © © 2020 American Chemical Society.Item Preferential binding affinity of ions and their effect on structure and dynamics of water near antimicrobial peptide(Elsevier B.V., 2021) Singh, O.; Chakraborty, D.Water containing dissolved salts is often found to play important roles in many chemical and biological processes. They affect the stability of the amino acids and proteins by altering the liquid water structure. The formation of a mixture of non-uniform density regions in liquid water; commonly known as Low-density water and High-density water is a well-known fact experimentally; which lends uniqueness to the ubiquitous water. The behavior of these different types of water at the interface and the bulk region of the biomolecules around the hydrophobic and hydrophilic residues under the influence of different alkali metal ions, such as LiCl, NaCl, and KCl is an important unexplored question in understanding of many biomolecular processes. To address this, we carried out MD simulation of antimicrobial peptide (PDB ID: 5Z32) for two different model potentials (CHARMM-SPC/E and AMBER-TIP4P) and performed the structural analysis of water in terms of the radial distribution function, number of hydrogen bonds, orientation, tetrahedral order parameter, voids analysis to analyze the related dynamical properties like preferential binding affinity, diffusion, hydrogen bond dynamics, entropy. The water molecules around the hydrophilic environment are found to be more disruptive containing more broken hydrogen bonds in comparison to the hydrophobic environment. It is also found that the water molecules present near the protein surface are of low density and that near the bulk is of high density. This leads to the higher self-diffusion coefficient of the water molecules and less hydrogen bond lifetime at the bulk. The maximum difference is found for the solutions containing high charge density, Lithium ions. Lithium ions have a strong preferential binding affinity towards protein surface resulting in strong solvation shells containing more tetrahedral-like water structure which has low diffusion, low entropy, and higher hydrogen bond lifetime. The diffusion of the water molecules, however, increases towards the higher solvation shells. Potassium on the other hand has less preference to live on protein surfaces resulting in similar diffusion values in the bulk and interface water molecules. © 2021 Elsevier B.V.