An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20.
We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence.
Forschungszentrum Karlsruhe, Institut für Nanotechnologie, 76021 Karlsruhe, Germany.
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D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D003198:Computer Simulation; D019143:Evolution, Molecular; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*
D001426:Bacterial Proteins; C040045:L20 ribosomal protein, bacteria; D012269:Ribosomal Proteins