Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials
Physics and Astronomy
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 (R-g) with the temperature (T) occurs, however, depends on the potential, i.e. Delta T-MJ approximate to 0.013-0.020, Delta T-BT approximate to 0.018-0.026, and Delta T-BFKV approximate to 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 Delta T-A approximate to 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) infinity q(-1/nu), with the wave vector, q = 2 pi/lambda, and the wavelength, lambda, reveals a systematic change in the effective dimension (D-e similar to/nu) of the histone with all potentials (MJ, BT, BFKV): D-e similar to 3 in the globular structure with D-e similar to 2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions.
Pandey, R. B.,
(2012). Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials. PLOS ONE, 7(11).
Available at: http://aquila.usm.edu/fac_pubs/7580