We have developed a postoprocessing method that allows atomistic representation of proteins in folding and binding processes under crowding [1, 2]. I will briefly outline this method and present three applications. The first deals with the conformational changes of a number of proteins during ligand binding [3]. The second deals with the folding of several proteins [4]. The third deals with the association rates of proteins. Comparison with experimental results [5, 6] will also be presented.1. S. Qin and H.-X. Zhou (2009). Biophys. J. 97, 12-19.2. S. Qin, D. D. L. Minh, J. A. McCammon, and H.-X. Zhou (2010). J. Phys. Chem. Lett. 1, 107-110.3. H. Dong, S. Qin, and H.-X. Zhou (2010). PLoS Comput. Biol. 6, e1000833.4. H. Tjong and H.-X. Zhou (2010). Biophys. J. 98, 2273-2280.5. J. Batra, K. Xu, and H.-X. Zhou (2009). Proteins 77, 133-138.6. J. Batra, K. Xu, S. Qin, and H.-X. Zhou (2009). Biophys. J. 97, 906-911.

Atomistic simulations of protein folding and binding under crowding

244th National Meeting (2012)

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