Variation in Structure of a Protein (H2AX) with Knowledge-Based Interactions

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 (ΔT) of non-monotonic thermal response and its decay pattern with the temperature are sensitive to interaction. A rather narrow temperature range of ΔT(MJ) ≈ 0.015–0.022 with the MJ interaction expands and shifts up to ΔT(BT) ≈ 0.018–0.30 at higher temperatures with the BT interaction and shifts down with the BFKV interaction to ΔT(BFKV) ≈ 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.