Analysis of disulphide bond connectivity patterns in protein tertiary structure

Area of Science:

• Structural Bioinformatics
• Computational Biology
• Protein Science

Background:

• Disulphide bonds are crucial for protein structure and function.
• Understanding disulphide bond patterns aids in protein classification and modeling.
• The Protein Data Bank (PDB) is a primary resource for protein structural data.

Purpose of the Study:

• To analyze and categorize proteins containing disulphide bonds in the PDB.
• To develop a database and web tool for querying disulphide bond information.
• To facilitate the identification of protein structural templates for homology modeling.

Main Methods:

• Analysis of 27,209 protein structures from the PDB.
• Categorization of intra-chain disulphide bond proteins based on bond number and connectivity patterns (DBCPs).
• Development of a web-based computational tool for database querying.

Main Results:

• 12,832 proteins contain intra-chain disulphide bonds; 811 contain inter-chain bonds.
• 256 categories of intra-chain disulphide bond proteins were identified, linked to 509 unique SCOP superfamilies.
• A searchable database correlating DBCPs with SCOP superfamilies and protein properties was created.

Conclusions:

• The study provides a comprehensive classification of disulphide bond patterns in PDB proteins.
• The developed web tool enables efficient retrieval of information on disulphide bond proteins.
• This resource can aid in selecting appropriate structural templates for comparative protein modeling.