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Two proteins, one belonging to the mainly alpha class and the other belongingto the alpha/beta class, are selected to test a kinetic mechanism for proteinfolding. Targeted molecular dynamics is applied to generate folding pathwaysfor those two proteins, starting from two well defined initial conformations: afully extended and a alpha-helical conformation. The results show that for bothproteins the alpha-helical initial conformation provides overall lower energypathways to the native state. For the alpha/beta protein, 30 % (40%) of thepathways from an initial alpha-helix (fully extended) structure lead tounentangled native folds, a success rate that can be increased to 85 % by theintroduction of a well-defined intermediate structure. These results open up anew direction in which to look for a solution to the protein folding problem,as detailed at the end.

Low energy pathways for reproducible in vivo protein folding