BIOPHYSICAL THEORY AND MODELING |
Folding pathway of the B1 domain of protein G explored by
a multiscale modeling
Sebastian Kmiecik 1 and Andrzej Kolinski 1*
1 University of Warsaw
* To whom correspondence should be addressed. E-mail: kolinski{at}chem.uw.edu.pl.
Submitted on June 25, 2007
Revised on August 25, 2007
Accepted on 4 September 2007
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Abstract |
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The understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, ab initio simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow structure fine-tuning. Remarkably, a subset of native interactions drives the folding from the very beginning. The emerging comprehensive picture of GB1 folding perfectly matches and extends the previous experimental and theoretical studies.
Key Words:
Monte Carlo simulation, folding nucleus, knowledge-based potentials, molten globule, protein denatured state, reduced modeling
