Source:From Computational Biophysics to Systems Biology (CBSB11) Proceedings, 8:213–216, 2012
Formation of the beta-hairpin is the first step along the 2GB1 protein folding pathway. This -structure is one of the nuclei during this process and controls the rate of the whole protein folding. We present an attempt to improve the Replica ExchangeMolecular Dynamics (REMD) by utilising the output structures from the coarse-grainedMonte Carlo dynamics as the input for the all-atom REMD. This approach enables effective sampling and can be helpful in elucidating the mechanisms of beta-hairpin folding. Thermodynamics and dynamics is analyzed focusing on the number of native contacts during simulations. The energy landscape is analyzed by means of the Histogram Method.