Variation in Structure of a Protein (H2AX) with Knowledge-Based Interactions
Physics and Astronomy
The structure of a protein (H2AX) as a function of temperature is examined by three knowledge-based phenomenological interactions, MJ (Miyazawa and Jernigan), BT (Betancourt and Thirumalai), and BFKV (Bastolla et al.) to identify similarities and differences in results. Data from the BT and BFKV residue-residue interactions verify finding with the MJ interaction, i.e., the radius of gyration (R-g) of H2AX depends non-monotonically on temperature. The increase in R-g is followed by a decay on raising the temperature with a maximum at a characteristic value, T-c, which depends on the knowledge-based contact matrix, T-cBFKV <= T-cMJ <= T-cBT. The range (Delta T) of non-monotonic thermal response and its decay pattern with the temperature are sensitive to interaction. A rather narrow temperature range of Delta T-MJ approximate to 0.015-0.022 with the MJ interaction expands and shifts up to Delta T-BT approximate to 0.018-0.30 at higher temperatures with the BT interaction and shifts down with the BFKV interaction to Delta T-BFKV approximate to 0.011-0.018. The scaling of the structure factor with the wave vector reveals that the structure of the protein undergoes a transformation from a random coil at high temperature to a globular conformation at low temperatures.
Pandey, R. B.,
Farmer, B. L.,
Heermann, D. W.
(2013). Variation in Structure of a Protein (H2AX) with Knowledge-Based Interactions. PLoS One, 8(5).
Available at: http://aquila.usm.edu/fac_pubs/7762