Computer simulations of de novo designed helical proteins

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Abstract

In the context of reduced protein models, Monte Carlo simulations of three de novo designed helical proteins (four-member helical bundle) were performed. At low temperatures, for all proteins under consideration, protein-like folds having different topologies were obtained from random starting conformations. These simulations are consistent with experimental evidence indicating that these de novo designed proteins have the features of a molten globule state. The results of Monte Carlo simulations suggest that these molecules adopt four-helix bundle topologies. They also give insight into the possible mechanism of folding and association, which occurs in these simulations by on-site assembly of the helices. The low-temperature conformations of all three sequences have the features of a molten globule state.

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Sikorski, A., Kolinski, A., & Skolnick, J. (1998). Computer simulations of de novo designed helical proteins. Biophysical Journal, 75(1), 92–105. https://doi.org/10.1016/S0006-3495(98)77497-1

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