Simulated Annealing for Alpha-Helical Protein Folding: Searches in Vicinity of the “Molten Globule” State

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.