Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials.

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 (R(g)) with the temperature (T) occurs, however, depends on the potential, i.e. ?T(MJ) ? 0.013-0.020, ?T(BT) ? 0.018-0.026, and ?T(BFKV) ? 0.006-0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of R(g) decreases on raising the temperature in a range ?T(A) ? 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ? q(-1/?), with the wave vector, q=2?/?, and the wavelength, ?, reveals a systematic change in the effective dimension (D(e)?1/?) of the histone with all potentials (MJ, BT, BFKV): D(e)?3 in the globular structure with D(e)?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.

SUBMITTER: Pandey RB 

PROVIDER: S-EPMC3498164 | biostudies-other | 2012

REPOSITORIES: biostudies-other