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Simulated annealing for alpha-helical protein folding: searches in vicinity of the "molten globule" state
I V Grigoriev1, A B Rakhmaninova, A A Mironov
1Research Institute for Genetics of Industrial Microorganisms, Moscow, Russia. IVGrigoriev@lbl.gov
Abstract:
A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on a vicinity of "molten globule" states of a protein. In contrast to the majority of the known approaches for estimation of a protein free energy we introduce a simplified potential of interactions with solvent and consider conformational energy of the loops in addition to mean-force potential. The model was applied to several globular alpha-helical proteins and demonstrated high prediction accuracy in comparison with other known models.