Native geometry and the dynamics of protein folding

Details Native geometry and the dynamics of protein folding Native geometry and the dynamics of protein folding

2004-11-26

arxiv.org/abs/q-bio/0411044v1

Biophysical Chemistry 115, 169-175 (2005)

Biology

Quantitative Biology

Biomolecules

Proceedings of the BIFI 2004 - I International Conference, Zaragoza (Spain) Biology after the genome: a physical view. To appe

Scientific paper

10.1016/j.bpc.2004.12.022

In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the G\={o} model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.

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