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Conservation of polyproline II helices in homologous proteins: Implications for structure prediction by model building by Alexei A. Adzhubei; Michael J.E. Sternberg is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract Left‐handed polyproline II (PPII) helices commonly occur in globular proteins in segments of 4–8 residues. This paper analyzes the structural conservation of PPII‐helices in 3 protein families: serine proteinases, aspartic proteinases, and immunoglobulin constant domains. Calculations of the number of conserved segments based on structural alignment of homologous molecules yielded similar results for the PPII‐helices, the α‐helices, and the β‐strands. The PPII‐helices are consistently conserved at the level of 100–80% in the proteins with sequence identity above 20% and RMS deviation of structure alignments below 3.0 Å. The most structurally important PPII segments are conserved below this level of sequence identity. These results suggest that the PPII‐helices, in addition to the other 2 secondary structure classes, should be identified as part of structurally conserved regions in proteins. This is supported by similar values for the local RMS deviations of the aligned segments for the structural classes of PPII‐helices, α‐helices, and β‐strands. The PPII‐helices are shown to participate in supersecondary elements such as PPII‐helix/α‐helix. The conservation of PPII‐hel

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Author

Alexei A. Adzhubei; Michael J.E. Sternberg

Publisher

Cold Spring Harbor Laboratory Press; Wiley (John Wiley & Sons); Wiley-Blackwell; Wiley (ISSN 0961-8368)

Published

1994

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)