Pathways to folding, nucleation events and native geometry

Details Pathways to folding, nucleation events and native geometry Pathways to folding, nucleation events and native geometry

2007-08-02

arxiv.org/abs/0708.0426v1

Biology

Quantitative Biology

Biomolecules

Accepted in J. Chem. Phys

Scientific paper

10.1063/1.2777150

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.

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