Recognition of spatial motifs in protein structures

Area of Science:

• Structural biology
• Computational biology
• Bioinformatics

Background:

• The increasing size of structural databases necessitates advanced methods for protein structure analysis and comparison.
• While protein fold classification is well-established, tools for analyzing small residue constellations are limited.

Purpose of the Study:

• To introduce two novel computational programs, SPASM and RIGOR, for the analysis of spatial motifs in protein structures.
• To demonstrate the utility of spatial motif recognition in functional and structural characterization of proteins.

Main Methods:

• SPASM program: identifies arbitrary main-chain and/or side-chain motifs in protein databases with "fuzzy pattern matching" capabilities.
• RIGOR program: scans individual protein structures for predefined motifs from a database.
• Application of spatial motif recognition and profile analysis for uncharacterized protein classification.

Main Results:

• SPASM enables flexible identification of spatial motifs, including those with relaxed residue type requirements.
• RIGOR efficiently detects known motifs within a single protein structure.
• Spatial motif analysis successfully assigned the class of a hypothetical protein and revealed the prevalence of short left-handed helical segments.

Conclusions:

• SPASM and RIGOR provide valuable tools for detailed analysis of protein structures.
• These methods have broad applications in analyzing new and existing structures, comparative analysis, protein design, and function prediction.