A lattice model for protein structure prediction at low resolution.
The prediction of the folded structure of a protein from its sequence has proven to be a very difficult computational problem. We have developed an exceptionally simple representation of a polypeptide chain, with which we can enumerate all possible backbone conformations of small proteins. A protein is represented by a self-avoiding path of connected vertices on a tetrahedral lattice, with several amino acid residues assigned to each lattice vertex. For five small structurally dissimilar proteins, we find that we can separate native-like structures from the vast majority of non-native folds by using only simple structural and energetic criteria. This method demonstrates significant generality and predictive power without requiring foreknowledge of any native structural details.
Hinds
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Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford University School of Medicine, CA 94305.
Levitt
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D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D004268:DNA-Binding Proteins; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009498:Neurotoxins / Q000737:chemistry; D011487:Protein Conformation; D012097:Repressor Proteins / Q000648:ultrastructure; D012269:Ribosomal Proteins / Q000648:ultrastructure; D012416:Rubredoxins / Q000648:ultrastructure; D013816:Thermodynamics; D014361:Trypsin Inhibitors / Q000648:ultrastructure; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D009498:Neurotoxins; D012097:Repressor Proteins; D012269:Ribosomal Proteins; D012416:Rubredoxins; D014361:Trypsin Inhibitors; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; C016700:ribosomal protein L7-L12