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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
Published on: October 2, 2017
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ProCarbDB: a database of carbohydrate-binding proteins
Liviu Copoiu1, Pedro H M Torres1, David B Ascher1,2
1Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
Nucleic Acids Research
|October 11, 2019
Summary
Researchers created ProCarbDB, a new database for protein-carbohydrate interactions. It clarifies carbohydrate structures in 3D X-ray crystal structures, aiding the study of these vital biological interactions.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Carbohydrate-binding proteins are essential in biological systems.
- Complex carbohydrate structures and inconsistent reporting hinder interface analysis.
- Understanding protein-carbohydrate interactions is crucial for biological research.
Purpose of the Study:
- To develop a comprehensive, open-access database for protein-carbohydrate interactions.
- To address the challenges in characterizing protein-carbohydrate interfaces.
- To provide a user-friendly resource for studying these complexes.
Main Methods:
- Developed ProCarbDB, an open-access database.
- Included over 5200 3D X-ray crystal structures of protein-carbohydrate complexes.
- Distinguished complete carbohydrate ligands from monomeric units and annotated interactions.
Main Results:
- ProCarbDB clearly distinguishes and annotates complete carbohydrate ligands.
- The database visualizes all interactions within protein-carbohydrate complexes.
- Provides curated data on binding affinity and mutation effects where available.
Conclusions:
- ProCarbDB offers a valuable resource for understanding protein-carbohydrate interfaces.
- Facilitates detailed analysis of protein-carbohydrate interactions.
- The ProCarbDB web server is freely accessible for researchers worldwide.
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