The Go model revisited: Native structure and the geometric coupling between local and long-range contacts

Details The Go model revisited: Native structure and the geometric coupling between local and long-range contacts The Go model revisited: Native structure and the geometric coupling between local and long-range contacts

2004-11-26

arxiv.org/abs/q-bio/0411046v2

Proteins: Structure, Function and Bioinformatics 60, 712-722 (2005)

Biology

Quantitative Biology

Biomolecules

12 pages, 26 figures, RevTex. Accepted in Proteins: Structure, Function and Bioinformatics

Scientific paper

10.1002/prot.20521

Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long-range interactions to the native state's energy is decreased from ~50% towards zero. However, the dispersion of the simulated folding times depends strongly on the native geometry and Go polymers folding to one of the target structures exhibit folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long-range contacts meaning that, when this coupling exists, the formation of long-range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling leads to kinetics that are more sensitive to the interaction energy parameters; in this case the formation of local contacts is not sufficient to promote the establishment of long-range ones when these are strongly penalized energetically, leading to longer folding times.

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