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Three-dimensional profiles: a new tool to identify protein surface similarities
M de Rinaldis1, G Ausiello, G Cesareni
1I.N.F.M., Rome, Italy.
Journal of Molecular Biology
|December 5, 1998
Summary
We developed a 3D profile method to compare protein surfaces for homology searches. This method effectively identifies protein families with similar structures and functions, aiding in the discovery of new binding regions.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure analysis
Background:
- Protein surface comparison is crucial for understanding structural and functional relationships.
- Existing methods for homology searching primarily focus on sequence data, limiting the analysis of structural similarities.
- Identifying conserved features in protein families requires robust methods for comparing three-dimensional (3D) structures.
Purpose of the Study:
- To introduce a novel 3D profile method for describing and comparing protein surfaces.
- To extend the profile method for sensitive protein homology sequence searches into the 3D structural domain.
- To enable the identification of protein families with shared structural and functional properties based on surface characteristics.
Main Methods:
- Transposition of the profile method from sequence analysis to 3D protein surface representation.
- Derivation of 3D surface profiles from single protein structures or multiple structure alignments.
- Screening of protein structure databases using 3D profiles to find similar protein surfaces.
Main Results:
- The 3D profile method successfully identified all SH2 and SH3 binding regions in a test dataset.
- The p-loop 3D profile accurately recognized all p-loop-containing proteins within the dataset.
- Analysis revealed a conserved spatial position but not sequence identity for a positive charge within the p-loop profile.
- A non-p-loop protein, succinyl coenzyme A synthetase, was identified with a potential uncharacterized nucleotide-binding region.
Conclusions:
- The 3D surface profile method is a powerful tool for detecting similarities between protein surfaces and identifying protein families.
- This approach enhances homology searching by incorporating structural information, complementing traditional sequence-based methods.
- The method facilitates the discovery of conserved structural motifs and potential functional sites, even when sequence homology is low.