We present our coarse-grained model for calculations of protein structure and protein-folding dynamics, termed UNRES (from UNited RESidue). In the UNRES model, a polypeptide chain is represented as a sequence of a-carbon atoms with attached united side chains and peptide groups positioned halfway between the consecutive a-carbons. UNRES is a physics-based model and the corresponding force field is defined as the potential of mean force of the protein system in aqueous environment, with those degrees of freedom not present in the model averaged out. Langevin molecular dynamics and replica exchange molecular dynamics have been implemented to simulate the dynamics and thermodynamics of protein folding. The program package, which includes tools for production simulations and analysis of results is available to the academic community at www.unres.pl.  In this talk, the applications of UNRES in (i) physics-based protein structure prediction, (ii) simulations of protein-folding pathways, (iii) simulation of the thermodynamics of protein folding, and (iv) applications to biological problems such as, e.g., amyloid formation, signaling, and investigating the mechanism of the action of Hsp70 chaperones, will be presented.  We will discuss the results of the last CASP experiment, in which UNRES outperformed other methods in predicting the structures of two new-fold proteins.

Coarse-grained approach to protein structure and dynamics

246th National Meeting (2013)

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