Protein motif by computer: the perfect Greek key jell yroll designer

• Published in: Bioinformatics 1993-12, Vol.9 (6), p.709-722
• Main Author: Henneke, Christina M.
• Format: Article
• Language: English
• ISSN: 1367-4803; 1460-2059
• DOI: 10.1093/bioinformatics/9.6.709

A program that generates amino acid sequences that are compatible with the Greek key protein motif is presented. Using statistical data derived from the structures of molecules from the protein databank, the novel algorithm generates amino acid sequences compatible with an 8-stranded perfect Greek key jellyroll motif In this motif, all hydrogen bonds present in the theoretical originating (β-hairpin stay in register as the whole 8-stranded domain fokis at once in an anti clockwise swirl. Eight residues are generated per strand and 32 residues per sheet making 64 residues in the antiparallel (β-barrel. The seven loops between β-stands contain an additional 27 residues. All recognized features of (β-sheets and β-strands such as alternating hydrophobic, hydrophilic residues with hydrophobics on the narrow-hydrogen-bond-pair, concave side of the theoretical originating (β-ribbon; sheet twist, strand twist, side chain rotation about the strands; the theories of side chain packing between the sheets; an average 30° rotation between (β-sheets; the theoretical anti complementary patch residues of each sheet; and the anticomplementaty, isotropically stressed hyperbolic parabloid shape of each sheet, are taken into account in the program. The sequences of the loops between strands are designed by turn type and strand twist is considered in the design of the motif's single (β-hairpin turn. Secondary structure parameters and between-strand amino acid pair correlations also figure importantly in the novel algorithm.