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However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information.The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment.As opposed to the monophyletic scenario of presently existing protein domains, Lupas ].
This report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster.
Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles.
These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles.
Cross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally.
The results presented here give us new insights into the evolution of short protein segments.