Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials.
PLoS One
; 7(11): e49352, 2012.
Article
en En
| MEDLINE
| ID: mdl-23166645
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. ΔT(MJ) ≈ 0.013-0.020, ΔT(BT) ≈ 0.018-0.026, and ΔT(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 ΔT(A) ≈ 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) â q(-1/ν), with the wave vector, q=2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (D(e)â¼1/ν) of the histone with all potentials (MJ, BT, BFKV) D(e)â¼3 in the globular structure with D(e)â¼2 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.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Conformación Proteica
/
Temperatura
/
Histonas
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Modelos Moleculares
/
Simulación de Dinámica Molecular
Tipo de estudio:
Clinical_trials
/
Health_economic_evaluation
/
Prognostic_studies
Idioma:
En
Revista:
PLoS One
Asunto de la revista:
CIENCIA
/
MEDICINA
Año:
2012
Tipo del documento:
Article
País de afiliación:
Estados Unidos