Steered Molecular Dynamics
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General Area of Interest:
Soft Matter Physics.
Statistical Mechanics.
Biophysics and computational physics.
Computational Chemistry.
Broad Area of Interest:
Structural & dynamical properties of bio molecules like protein.
Coarse grained modelling of biomolecules.
Nucleosome dynamics at AA and CG levelThe direction of this research explores nucleosome dynamics through the integration of all-atom (AA) and coarse-grained (CG) molecular dynamics simulations, with a particular focus on the SIRAH force field. AA simulations offer detailed insights but face limitations in addressing extended timescales due to high computational demands. In contrast, CG simulations allow efficient exploration of nucleosome behavior over broader timescales, effectively capturing large-scale conformational changes and interactions. By combining these methodologies, this research aims to provide a comprehensive understanding of nucleosome dynamics.
- AGM, RP, AO, SML, Journal of Chemical Physics, 2025.
- PK, PKT, AGM, RP, AM, SML, J. Phys. Chem. B 2024, 128, 13, 3090–3101
Crystal structure of human ⍺-satellite palindromic sequence (ASP) sequence (PDB 717 ID:1KX5) and its coarse-grained representation. DNA is marked in blue, while histone is marked 718 in red.
Coarse-grained model of the proteinSometimes one needs a coarse grained (CG) model to describe complex cellular phenomena. We build a CG model of proteins with structural information based on an effective force field obtained from all-atom molecular dynamics simulations. Each bead is assigned a couple of degrees of freedom, representing the backbone dihedral angles. We show that using such a model, one can reproduce the protein structure comparable to the crystal structure well. This can pave the way for CG models with structural information.
- AGM, KK, JC, Coarse-grained model of protein with structural information (Submitted).
All atoms to CG representation. Amino acids are characterized based on their solvophobic or solvophilic nature.
Water dynamics at the interfaceWater molecules present at the surface of protein (Interfacial water, IW) play an important role in mediating protein ligand interactions. We probe the dynamics of interfacial water in BAMLET complex. We find water molecules that are close to both protein and ligand have slower residence time and mean square displacement, suggesting the heterogeneous behavior of water at the protein-ligand interface.
- AGM, JC, Dynamics of water at protein-ligand interface in molten globule state (In Preparation).
Conformational fluctuations and binding in the molten globule state of α-lactalbuminA molten globule (MG) state is an intermediate state of a protein observed during the unfolding of the native structure. We consider a milk protein, α-lactalbumin (aLA), which shows an MG state at low pH upon removal of the calcium (Ca2+) ion. We use the dihedral principal component analysis, the density based clustering method, and the machine learning technique to identify the conformational fluctuations of protein at MG state. We further characterize binding of aLA with OA microscopically. We find the binding mode between MG-aLA and OLA using the conformational thermodynamics method. We also estimate the binding free energy using the umbrella sampling (US) method for both the MG state and the neutral state. Furthermore, we find that the binding free energy obtained from the US is comparable with earlier experimental results.
- AGM,JC, Physical Chemistry Chemical Physics, 2022, 24, 21348-21357.
- AGM, JC, Journal Of Chemical Information and Modeling, 2023, 63, 17, 5583-91.
Correlation between protein bond vector & dihedral fluctuation:
Dihedral fluctuations are not directly amenable due to the limitation of the experimental probe. NMR experiments probe dipolar fluctuations given in terms of cross-correlated relaxation (CCR) rates, given by the zero frequency spectral density function of the fluctuations. Here, we calculate the zero frequency spectral function from molecular dynamics trajectories for dipolar and dihedral angle fluctuations and show that they are correlated. Thus, the CCR can be a marker of dihedral fluctuations.
Dihedral fluctuations are not directly amenable due to the limitation of the experimental probe. NMR experiments probe dipolar fluctuations given in terms of cross-correlated relaxation (CCR) rates, given by the zero frequency spectral density function of the fluctuations. Here, we calculate the zero frequency spectral function from molecular dynamics trajectories for dipolar and dihedral angle fluctuations and show that they are correlated. Thus, the CCR can be a marker of dihedral fluctuations.
- AGM, JC, Chemical Physics Letters 797 (2022) 139574.
- AGM, JC, AIP Conference Proceedings 2265, 030036, 2020.
Cartoon representation of dihedral angle. Schematic representation of dipoles used in NMR.
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