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Abstract: In this study we evaluate, at full atomic detail, the folding processes oftwo small helical proteins, the B domain of protein A and the Villin headpiece.Folding kinetics are studied by performing a large number of ab initio MonteCarlo folding simulations using a single transferable all-atom potential. Usingthese trajectories, we examine the relaxation behavior, secondary structureformation, and transition-state ensembles TSEs of the two proteins andcompare our results with experimental data and previous computational studies.To obtain a detailed structural information on the folding dynamics viewed asan ensemble process, we perform a clustering analysis procedure based on graphtheory. Moreover, rigorous pfold analysis is used to obtain representativesamples of the TSEs and a good quantitative agreement between experimental andsimulated Fi-values is obtained for protein A. Fi-values for Villin are alsoobtained and left as predictions to be tested by future experiments. Ouranalysis shows that two-helix hairpin is a common partially stable structuralmotif that gets formed prior to entering the TSE in the studied proteins. Theseresults together with our earlier study of Engrailed Homeodomain and recentexperimental studies provide a comprehensive, atomic-level picture of foldingmechanics of three-helix bundle proteins.



Author: Jae Shick Yang, Stefan Wallin, Eugene Shakhnovich

Source: https://arxiv.org/







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