Pseudotorsional OCCO backbone angle as a single descriptor of protein secondary structure.
Protein secondary structure is conventionally identified using characteristic ranges of two backbone torsional angles phi and psi. We suggest that the secondary structure can be adequately characterized by a single descriptor, the Oi-1Ci-1CiOi (where i is the residue number) pseudotorsional backbone angle. A set of 102 structurally distinct protein chains from the Protein Data Bank was used to evaluate the adequacy of this descriptor. We find that a specific range of OCCO angles corresponds to each major secondary structure. The complete range of OCCO angles (-180 degrees to 179 degrees) was broken into 18 consecutive subranges of 20 degrees each, and each subrange was assigned a letter. Thus, the OCCO profiles for each protein in the database were "translated" into a sequence of letters. The Needleman-Wunsch primary sequence alignment algorithm was then used for secondary/tertiary structure comparison and alignment. Preliminary results indicate that this new approach has a significant potential for rapid identification of fold families in the Protein Data Bank.
Laboratory for Molecular Modeling, School of Pharmacy, University of North Carolina at Chapel Hill 27599, USA.
S
S
Laiter
D L
DL
Hoffman
R K
RK
Singh
I I
II
Vaisman
A
A
Tropsha
D000595:Amino Acid Sequence; D006801:Humans; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid