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 dynamical properties of water in surfactant-like peptide-based nanotubes: Effect of pore size, tube length and charge(Elsevier B.V., 2021) Dilip, H.N.; Chakraborty, D.Atomistic molecular dynamics simulations were carried out to study the structural and dynamical properties of water molecules around pre-assembled surfactant-like peptide (SLP) nanotubes in aqueous media. These SLPs can be thought as a class of biocompatible and biodegradable surfactants for biomedical applications. Nanotube-like structures were considered where glycine and lysine (G6K) are taken as the constituents for the composition of the SLPs. The nanotubes considered were of different dimensions; such as 18 × 15 (number of peptides on the circumference x number of peptides layers), 18 × 12 and 16 × 12 for both charged and neutral analogues. The charged composition consists of protonated nitrogen in the lysine subunit and chlorine/bromine as counter ions. It is found that the neutral SLPs have less hydrated inner core consisting of more tetrahedral water compared to their charged analogues. The hydrogen bond lifetime of water-water and water-peptide molecules increases in the inner pore and found to be maximum for charged 16 × 12 system. Outside the pore, charged analogue of 18 × 15 have more water-water hydrogen bond lifetime compared to all other systems. However, protein-water hydrogen bond lifetime was found to be more for neutral analogues outside the pore due to more probable interactions of SLPs with water molecules. © 2020 Elsevier B.V.Item Growth Reaction of Gold Nanorods in the Presence of Mutated Peptides and Amine-Modified Single-Stranded Nucleic Acids(John Wiley and Sons Ltd, 2023) Sahu, J.K.; Singh, O.; Chakraborty, D.; Sadhu, K.K.Conformation of biomolecules like DNA, peptides and amino acids play vital role during nanoparticle growth. Herein, we have experimentally explored the effect of different noncovalent interaction between a 5′-amine modified DNA sequence (NH2−C6H12-5′-ACATCAGT-3′, PMR) and arginine during the seed-mediated growth reaction of gold nanorods (GNRs). Amino acid-mediated growth reaction of GNRs results in a snowflake-like gold nanoarchitecture. However, in case of Arg, prior incubation of GNRs with PMR selectively produces sea urchin-like gold suprastructures, via strong hydrogen bonding and cation-π interaction between PMR and Arg. This distinctive structure formation strategy has been extended to study the structural modulation caused by two structurally close α-helical RRR (Ac-(AAAAR)3A−NH2) peptide and the lysine mutated KKR (Ac−AAAAKAAAAKAAAARA−NH2) peptide with partial helix at the amino terminus. Simulation studies confirm that a greater number of hydrogen bonding and cation-π interaction between the Arg residues and PMR resulted in the gold sea urchin structure for RRR peptide against KKR peptide. © 2023 Wiley-VCH GmbH.Item Effect of peptide hydrophilicity on membrane curvature and permeation(American Institute of Physics, 2024) Mathath, A.V.; Chakraborty, D.Using a well-developed reaction coordinate in umbrella sampling, we studied the single peptide permeation through a model cancerous cell membrane, varying the hydrophilicity and the charge of the peptides. Two peptides, melittin and pHD108, were studied. The permeation mechanism differs from a barrel-stave-like mechanism to toroidal pore and vesicle formation based on the number and the placement of the hydrophilic amino acids in the peptide. Membrane curvature changes dynamically as the permeation process occurs. In the case of vesicles, the peptide traverses along a smooth, homogenous pathway, whereas a rugged, steep pathway was found when lipid molecules did not line up along the wall of the membrane (barrel-stave-like mechanism). A mechanism similar to a toroidal pore consists of multiple minima. Higher free energy was found for the permeating terminal containing charged amino acid residues. Vesicle formation was found for pHD108 peptide N-terminal with a maximum membrane thinning effect of 54.4% with free energy cost of 8.20 ± 0.10 kcal mol?1 and pore radius of 2.33 ± 0.07 nm. Insights gained from this study can help to build synthetic peptides for drug delivery. © 2024 Author(s).