Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36

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The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to model the complex interaction potential. The resulting structure of the model protein mimics the native state of the real protein with a RMSD of 4.5 Å. A contact pair distance time correlation function (CPCF), Cₚij(t), is introduced which shows multistage decay, including a slow late stage dynamics for a few specific pairs. These pairs determine the long time folding rate. Dynamics can be correlated with the landscape, relative contact order and topological contact.