A genetic algorithm that seeks native states of peptides and proteins.
We describe a computer algorithm to predict native structures of proteins and peptides from their primary sequences, their known native radii of gyration, and their known disulfide bonding patterns, starting from random conformations. Proteins are represented as simplified real-space main chains with single-bead side chains. Nonlocal interactions are taken from structural database-derived statistical potentials, as in an earlier treatment. Local interactions are taken from simulations of (phi, psi) energy surfaces for each amino acid generated using the Biosym Discover program. Conformational searching is done by a genetic algorithm-based method. Reasonable structures are obtained for melittin (a 26-mer), avian pancreatic polypeptide inhibitor (a 36-mer), crambin (a 46-mer), apamin (an 18-mer), tachyplesin (a 17-mer), C-peptide of ribonuclease A (a 13-mer), and four different designed helical peptides. A hydrogen bond interaction was tested and found to be generally unnecessary for helical peptides, but it helps fold some sheet regions in these structures. For the few longer chains we tested, the method appears not to converge. In those cases, it appears to recover native-like secondary structures, but gets incorrect tertiary folds.
Structural Biochemistry Program, Frederick Biomedical Supercomputing Center, National Cancer Institute, Frederick Cancer Research and Development Center, Maryland 21702, USA.
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D000465:Algorithms; D000595:Amino Acid Sequence; D023181:Antimicrobial Cationic Peptides; D001030:Apamin / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins; D055592:Biophysical Phenomena; D001703:Biophysics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D008555:Melitten / Q000737:chemistry / Q000235:genetics; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010191:Pancreatic Polypeptide / Q000037:antagonists & inhibitors; D010455:Peptides / Q000737:chemistry* / Q000235:genetics*; D010456:Peptides, Cyclic / Q000737:chemistry / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D012260:Ribonucleases / Q000737:chemistry / Q000235:genetics; D014452:Ubiquitins / Q000737:chemistry / Q000235:genetics; D016335:Zinc Fingers / Q000235:genetics
D023181:Antimicrobial Cationic Peptides; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D010455:Peptides; D010456:Peptides, Cyclic; D010940:Plant Proteins; D011506:Proteins; D014452:Ubiquitins; C057636:tachyplesin peptide, Tachypleus tridentatus; D008555:Melitten; D001030:Apamin; C009725:pancreatic polypeptide, avian; D010191:Pancreatic Polypeptide; C024934:crambin protein, Crambe abyssinica; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease