title: Variation in structure of a protein (H2AX) with knowledge-based interactions.
abstract: 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 (Rg ) of H2AX depends non-monotonically on temperature. The increase in Rg is followed by a decay on raising the temperature with a maximum at a characteristic value, Tc , which depends on the knowledge-based contact matrix, TcBFKV ≤ TcMJ ≤ TcBT . 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 ΔTMJ ≈ 0.015-0.022 with the MJ interaction expands and shifts up to ΔTBT ≈ 0.018-0.30 at higher temperatures with the BT interaction and shifts down with the BFKV interaction to ΔTBFKV ≈ 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.
authors.affiliation: Institute for Theoretical Physics, University of Heidelberg, Heidelberg, Germany.
authors.forename: Miriam
authors.initials: M
authors.lastname: Fritsche
authors.forename: Ras B
authors.initials: RB
authors.lastname: Pandey
authors.forename: Barry L
authors.initials: BL
authors.lastname: Farmer
authors.forename: Dieter W
authors.initials: DW
authors.lastname: Heermann
mesh_terms: D006657:Histones / Q000737:chemistry*; D006801:Humans; D007700:Kinetics; D051188:Knowledge Bases; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics
chemical_list: C468783:H2AX protein, human; D006657:Histones