Conservation of polyproline II helices in homologous proteins: Implications for structure prediction by model building

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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‐helices depends on the conservation of a supersecondary element as a whole. PPII‐helices also form links, possibly flexible, in the interdomain regions. The role of the PPII‐helices in model building by homology is 2‐fold: they serve as additional conserved elements in the structure allowing improvement of the accuracy of a model and provide correct chain geometry for modeling of the segments equivalenced to them in a target sequence. The improvement in model building is demonstrated in 2 test studies.