A note on circular-dichroic-constrained prediction of protein secondary structure.
Circular dichroic (CD) spectra of bovine immunosuppressant binding proteins FKBP12 and FKBP25, and cyclophilins (peptidylprolyl isomerases) A (bCyP-18) and B(bCyP-20), the immunophilins which selectively bind the clinically useful immunosuppressants FK506, rapamycin and cyclosporin A, respectively, were analysed using the singular-value-decomposition algorithm augmented by a simplified variable selection method. The differences between the CD-estimated values of alpha-helix, beta-structure and beta-turn and those predicted by the Chou-Fasman algorithm were minimized using the CD data as constraints of an algorithm which utilizes the method of hierarchical updating of quasi-equipotential peptide segments of the Chou-Fasman prediction. The method allows one to correct the Chou-Fasman prediction of secondary structures in globular proteins.
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Department d'Ingénierie et d'Etudes des Proteines, D. S. V./C. E. A., Centre d'Etudes de Saclay, Gif-sur-Yvette, France.
D000591:Amino Acid Isomerases / Q000737:chemistry; D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry*; D002417:Cattle; D002942:Circular Dichroism; D021983:Cyclophilins; D004268:DNA-Binding Proteins / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry; D006360:Heat-Shock Proteins / Q000737:chemistry*; D006801:Humans; D008969:Molecular Sequence Data; D019696:Peptidylprolyl Isomerase; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D016559:Tacrolimus / Q000737:chemistry; D022021:Tacrolimus Binding Proteins
D001426:Bacterial Proteins; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D006360:Heat-Shock Proteins; C081786:cyclophilin B; C074856:FKBP3 protein, human; D000591:Amino Acid Isomerases; D021983:Cyclophilins; D022021:Tacrolimus Binding Proteins; D019696:Peptidylprolyl Isomerase; D016559:Tacrolimus