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An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Remote homology detection of integral membrane proteins using conserved sequence features
Andreas Bernsel1, Håkan Viklund, Arne Elofsson
1Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
Proteins
|December 14, 2007
Summary
A new method, Searcher for Homology Relationships of Integral Membrane Proteins (SHRIMP), improves detection of distant evolutionary relationships among transmembrane proteins by analyzing hydrophobicity patterns and sequence data.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Transmembrane proteins possess unique sequence constraints due to their membrane environment, differing from globular proteins.
- Existing homology detection algorithms, often designed for globular proteins, may be suboptimal for transmembrane proteins.
Purpose of the Study:
- To develop an improved method for detecting remote homology in transmembrane proteins.
- To leverage conserved features like hydrophobicity patterns and topology for enhanced detection.
Main Methods:
- Introduced a profile-profile based alignment method within a hidden Markov model framework.
- Integrated sequence information with transmembrane protein-specific constraints (hydrophobicity, topology).
- Developed the Searcher for Homology Relationships of Integral Membrane Proteins (SHRIMP) tool.
Main Results:
- Achieved substantial improvements in sensitivity and specificity for remote homology detection in transmembrane proteins.
- Enhanced alignment quality for distant transmembrane protein homologs.
- Identified new putative evolutionary relationships for uncharacterized protein families in Pfam, with some confirmed by other methods.
Conclusions:
- The SHRIMP method effectively detects remote homology in transmembrane proteins by incorporating membrane-specific features.
- This approach offers significant advantages over traditional methods for analyzing transmembrane protein evolution.
- SHRIMP provides a valuable tool for exploring evolutionary relationships within integral membrane protein families.
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