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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
AH-DB: collecting protein structure pairs before and after binding
Darby Tien-Hao Chang1, Tsung-Ju Yao, Chen-Yu Fan
1Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan. darby@mail.ncku.edu.tw
Nucleic Acids Research
|November 16, 2011
Summary
The Apo-Holo DataBase (AH-DB) offers a unified resource for protein conformational changes, providing over 746,000 apo-holo structure pairs. This database simplifies the study of protein binding and functional transitions.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein conformational transitions are crucial for biological functions, involving changes from apo (unbound) to holo (bound) states.
- Existing collections of apo-holo structure pairs are often small-scale and difficult to compile.
- Copper-zinc superoxide dismutase (SOD1) exemplifies proteins undergoing significant conformational shifts upon binding.
Purpose of the Study:
- To introduce the Apo-Holo DataBase (AH-DB), a comprehensive and unified resource for apo-holo protein structure pairs.
- To facilitate the investigation of protein conformational transitions and identify critical residues involved in binding.
- To provide a user-friendly platform for accessing and analyzing large-scale apo-holo structural data.
Main Methods:
- Developed a method to identify and map protein molecules across different Protein Data Bank (PDB) entries.
- Implemented a refined alignment scheme to accurately identify conformational transitions, even with incomplete protein structures.
- Aggregated a dataset of 746,314 apo-holo pairs, significantly larger than existing collections.
Main Results:
- AH-DB provides 746,314 apo-holo pairs, approximately 30 times more than the next largest collection.
- The database successfully overcomes challenges posed by fragmented protein structures in the PDB.
- Offers sophisticated interfaces for searching and exploring conformational transitions.
Conclusions:
- AH-DB represents a significant advancement in resources for studying protein conformational dynamics.
- The database simplifies the process of data collection and analysis for researchers investigating protein binding.
- Provides a valuable tool for understanding the functional implications of apo-holo structural changes.
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