Computer simulations of de novo designed helical proteins.
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.
Sikorski
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A
Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. sikorski@chem.uw.edu.pl
Kolinski
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Skolnick
J
J
D000595:Amino Acid Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D019281:Dimerization; D015195:Drug Design; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins