Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

0
-1
-2
-3

Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical Unfolding

Source:

From Computational Biophysics to Systems Biology (CBSB11) Proceedings, 8:83–90, 2012

Abstract

Coarse-grained protein modeling tool, CABS, is used in multiscale modeling of protein dynamics. It is demonstrated that the stochastic (Monte Carlo) dynamics, combined with all-atom refinement of the coarse-grained structures follows observed in experiments folding pathways of small proteins. The model is also used in model studies of chaperonin-assisted protein folding. It is shown that Iterative Annealing Mechanism of chaperonin action, where periodic distortion of the polypeptide chains by non-specific hydrophobic interactions can promote rapid folding and leads to a decrease in folding temperature. It is also demonstrated how chaperonin action prevents kinetically trapped conformations and modulates the observed folding mechanisms from nucleation-condensation to a more framework-like. Finally, the CABS model is used in simulations of mechanical unfolding, providing new ways for interpretation of Atomic Force Microscopy experiments.