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Full-Text Articles in Physics
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 …
Random Coil To Globular Thermal Response Of A Protein (H3.1) With Three Knowledge-Based Coarse-Grained Potentials, Ras B. Pandey, Barry L. Farmer
Random Coil To Globular Thermal Response Of A Protein (H3.1) With Three Knowledge-Based Coarse-Grained Potentials, Ras B. Pandey, Barry L. Farmer
Faculty Publications
The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (Rg) with the temperature (T) occurs, however, depends on the potential, i.e. ΔTMJ ≈ 0.013–0.020, ΔTBT ≈ 0.018–0.026 …
Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman
Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman
Faculty Publications
Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input …