Structure of a protein (H2AX): a comparative study with knowledge-based interactions

The structural and conformational properties of the histone protein H2AX (with143 residues) is studied by a coarse-grained model as a function of temperature (T). Three knowledge-based phenomenological interactions (MJ [1], BT [2], and BFKV [3]) are used as input to a generalized Lennard-Jones potential for residue-residue interactions. Large-scale Monte Carlo simulations are performed to identify similarity and differences in the equilibrium structures with these potentials. Multi-scale structures of the protein are examined by a detailed analysis of their structure functions. We find that the radius of gyration ($R_{g})$ of H2AX depends non-monotonically on temperature with a maximum at a characteristic value $T_{c}$, a common feature to each interaction. The characteristic temperature and the range of non-monotonic thermal response and decay pattern are, however, sensitive to interactions. A comparison of the structural properties emerging from three potentials will be presented in this talk. \\[4pt] [1] S. Miyazawa and R.L. Jernigan, Macromolecules 18, 534 (1985).\\[0pt] [2] M.R. Betancourt and D. Thirumalai, Protein Sci. 2, 361 (1999).\\[0pt] [3] U. Bastolla et al. Proteins 44, 79 (2001).