Open AccessVariation in Structure of a Protein (H2AX) with Knowledge-Based Interactions
Author(s) -
Miriam Fritsche,
Ras B. Pandey,
Barry L. Farmer,
Dieter W. Heermann
Publication year - 2013
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0064507
Subject(s) - radius of gyration , scaling , monotonic function , random coil , physics , atmospheric temperature range , thermodynamics , chemical physics , nuclear magnetic resonance , polymer , protein secondary structure , mathematics , mathematical analysis , geometry
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.