Computer simulations of de novo designed helical proteins

Biophysical Journal
A SikorskiJ Skolnick

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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Citations

Sep 13, 2001·Journal of Molecular Graphics & Modelling·J PeiX He
Feb 9, 2006·Journal of the American Chemical Society·Hung D Nguyen, Carol K Hall
Jun 29, 2000·Annual Review of Biochemistry·W F DeGradoA Lombardi
Jun 29, 2007·Proteins·Yantao ChenJiandong Ding
Feb 8, 2002·The Journal of Biological Chemistry·Alex ChapeaurougeSérgio T Ferreira
Feb 12, 2004·Journal of the American Chemical Society·Jakob P Ulmschneider, William L Jorgensen

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