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Updated: May 25, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Convergent evolution in structural elements of proteins investigated using cross profile analysis.
Kentaro Tomii1, Yoshito Sawada, Shinya Honda
1Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto Ward, Tokyo 135-0064, Japan.
BMC Bioinformatics
|January 17, 2012
Summary
Cross Profile Analysis reveals previously hidden sequence-structure patterns, suggesting ancient short-peptide ancestors and uncovering convergent evolution in protein segments. This method enhances understanding of protein evolution.
Area of Science:
- Biochemistry
- Structural Biology
- Evolutionary Biology
Background:
- Evolutionary relationships of shared protein segments across folds are debated.
- Existing methods for identifying sequence-structure similarities have limitations.
- A novel approach combining sequence and structure profiles is needed.
Purpose of the Study:
- To develop and apply Cross Profile Analysis for comparing sequence and structure profiles.
- To identify novel sequence-structure patterns in protein segments.
- To investigate the evolutionary origins of protein segments.
Main Methods:
- Development of Cross Profile Analysis (CPA).
- Comparison of sequence-based and structure-based profiles using CPA.
- Analysis of amino acid occurrences within protein segment clusters.
- Conformational analysis of deduced peptides.
Main Results:
- CPA identified strong correlations between structural clusters (9- and 15-residue segments) and specific sequence profiles.
- Previously undetectable sequence-structure patterns transcending protein families and folds were discovered.
- Evidence suggests the existence of ancient short-peptide ancestors.
Conclusions:
- Cross Profile Analysis revealed polyphyletic and convergent evolution of beta-hairpin-like structures.
- Findings were experimentally and computationally verified.
- The study provides new insights into the evolution of short protein segments.
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