random coil to globular thermal response of a protein (h3.1) with three knowledge-based coarse-grained potentials随机线圈球状蛋白质的热响应(h3.1)和三个知识粗粒度的潜力.pdfVIP

Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials 1 2 Ras B. Pandey *, Barry L. Farmer 1 Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Missouri, United States of America, 2 Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio, United States of America Abstract 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. DTMJ 0.013–0.020, DTBT 0.018–0.026, and DTBFKV 0.006–0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of Rg decreases on raising the temperature in a range DTA 0.015–0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) / q21/n, with the wave vector, q = 2p/ l, and the wavelength, l, reveals a systematic change in the effective dimension (De,1/n) of the histone with all potentials (MJ, BT, BFKV): D ,3 in the globular structure with D ,2 for the random coil. Reproducibility of the general yet unique (monotonic) e e structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar