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

Arnab Mukherjee·Biman Bagchi
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Abstract

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), $C_{P}^{ij}(t)$, is introduced which shows multistage decay, including a {\it slow late stage dynamics} for a few specific pairs. {\it These pairs determine the long time folding rate}. Dynamics can be correlated with the landscape, relative contact order and topological contact.

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Arnab Mukherjee, Biman Bagchi. 2002-12-16. Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36. https://arxiv.org/abs/cond-mat/0212379

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