ArticleBMC bioinformatics2012
Convergent evolution in structural elements of proteins investigated using cross profile analysis.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.Nature communications · 2025Article
- Structural screens identify candidate human homologs of insect chemoreceptors and crypticeLife · 2023Article
- Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain.International journal of molecular sciences · 2022Article
- The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms.International journal of molecular sciences · 2020Article
- Finding an Optimal Corneal Xenograft Using Comparative Analysis of Corneal Matrix Proteins Across Species.Scientific reports · 2019Article
- Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.Genome biology and evolution · 2014Article
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3 authors.
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Abstract
backgroundEvolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. 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. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments.
resultsThis 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. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors.
conclusionsCross 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.
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