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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Search for fucose binding domains in recently sequenced hypothetical proteins using molecular modeling techniques and
Sujata Majumder1, Madhumita Patra, Chhabinath Mandal
1Drug Design, Development and Molecular Modelling Division Indian Institute of Chemical Biology Jadavpur, Kolkata, 700 032, India.
Glycoconjugate Journal
|May 13, 2006
Summary
This study explores unique protein-carbohydrate interactions by modeling fucose-binding lectins from Pseudomonas aeruginosa and related species. Molecular modeling reveals conserved calcium-binding loops crucial for fucose specificity.
Area of Science:
- Structural biology
- Biochemistry
- Bioinformatics
Background:
- The crystal structure of a fucose-binding lectin from Pseudomonas aeruginosa revealed a unique calcium-mediated binding mode for alpha-L-fucose.
- This interaction mode is distinct among known protein-carbohydrate interactions.
Purpose of the Study:
- To investigate unique protein-carbohydrate interactions by identifying and analyzing homologous proteins.
- To predict and analyze the 3-D structures of potential fucose-binding proteins using molecular modeling.
Main Methods:
- BLAST search to identify homologous protein sequences.
- Molecular modeling to predict 3-D structures of proteins and their carbohydrate complexes.
- Analysis of physicochemical forces and electrostatic environments in complex formation.
Main Results:
- Four homologous proteins from bacteria and archaea were identified.
- Conserved calcium-binding loops were observed in primary and tertiary structures.
- Highly negative electrostatic environments near calcium-binding loops were essential for Ca(+2) ion neutralization.
- Photorhabdus lectin showed lower binding affinity due to reduced acidity in the calcium-binding loop.
Conclusions:
- The identified proteins share conserved structural features with the Pseudomonas aeruginosa fucose-binding lectin.
- These proteins exhibit fucose specificity, with variations in binding affinity influenced by calcium-binding loop characteristics.
- Molecular modeling is effective for studying unique protein-carbohydrate interactions and conserved structural motifs.
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