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A classification of disulfide patterns and its relationship to protein structure and function
Abhas Gupta1, Herman W T Van Vlijmen, Juswinder Singh
1Computational Drug Design Group, Biogen Idec, Inc., Cambridge, Masschusetts 02142, USA.
Protein Science : a Publication of the Protein Society
|July 27, 2004
Summary
This study classifies disulfide patterns in proteins, revealing that similar patterns correlate with similar protein structures and functions. This classification aids in understanding protein folding, stability, and identifying novel protein structures.
Area of Science:
- Proteomics
- Structural Biology
- Bioinformatics
Background:
- Disulfide bonds are crucial for protein structure and function.
- Existing databases lack comprehensive disulfide pattern information.
- Understanding disulfide patterns can reveal evolutionary relationships and functional similarities.
Purpose of the Study:
- To develop a detailed classification system for disulfide patterns in protein domains.
- To create a comprehensive and searchable database of disulfide patterns.
- To investigate the relationship between disulfide patterns, protein structure, and function.
Main Methods:
- A novel classification system for disulfide patterns was developed.
- A unique database of disulfide patterns was constructed using SwissProt and Pfam data.
- Protein domains were clustered by disulfide patterns and visualized using a 'classification wheel'.
- Classification effectiveness was validated against SCOP and Pfam databases.
Main Results:
- The study classified disulfide patterns across 40,620 protein domains.
- Proteins with similar disulfide patterns generally exhibit similar structures and functions, even with low sequence similarity.
- A predominance of less complex disulfide topologies was observed.
- Analysis revealed the impact of disulfide loss or addition on protein characteristics.
Conclusions:
- The developed classification and database provide a valuable resource for studying disulfide patterns.
- This resource aids in understanding protein structure, folding, and stability.
- Disulfide clusters lacking structural information are potential targets for structural genomics.