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Conformational Response To Solvent Interaction And Temperature Of A Protein (Histone H3.1) By A Multi-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer
Conformational Response To Solvent Interaction And Temperature Of A Protein (Histone H3.1) By A Multi-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer
Faculty Publications
Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low …
A Hierarchical Coarse-Grained (All-Atom-To-All-Residue) Computer Simulation Approach: Self-Assembly Of Peptides, Ras B. Pandey, Zhifeng Kuang, Barry L. Farmer
A Hierarchical Coarse-Grained (All-Atom-To-All-Residue) Computer Simulation Approach: Self-Assembly Of Peptides, Ras B. Pandey, Zhifeng Kuang, Barry L. Farmer
Faculty Publications
A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (1H 2S 3S 4Y 5W 6Y 7A 8F 9N 10N 11K 12T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular …