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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Recognizing very distant sequence relationships among proteins by family profile analysis
P K Mehta1, P Argos, A D Barbour
1Biochemisches Institut der Universität Zürich, Switzerland.
Proteins
|June 26, 1999
Summary
Family profile analysis (FPA) enhances protein family relationship detection by comparing all homologous sequences, unlike traditional methods. This sensitive approach identifies evolutionary links and new homologies across diverse protein families.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Conventional sequence profile analysis uses single target sequences.
- Recognizing structural relationships benefits from increased sequence information.
Purpose of the Study:
- To introduce and evaluate Family Profile Analysis (FPA) for detecting evolutionary relationships between protein families.
- To compare FPA's sensitivity against conventional methods.
Main Methods:
- FPA compares all homologous amino acid sequences of a target family against a probe family profile.
- Z-scores of target sequences are averaged and compared to reference families, yielding an F-Zscore.
- A statistically significant evolutionary relationship is indicated by an F-Zscore above 3.5.
Main Results:
- FPA demonstrated significantly higher sensitivity in detecting distant relationships compared to other methods.
- Tested protein families included vitamin B6-dependent enzymes, (beta/alpha)8-barrel proteins, beta-trefoil proteins, and globins.
- Numerous novel homologies were identified using FPA.
Conclusions:
- FPA is a sensitive technique for identifying evolutionary relationships between protein families.
- The method can both test suspected relationships and discover potential target families in large sequence databases.
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