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IDPM: an online database for ion distribution in protein molecules
Xilun Xiang1,2, Haiguang Liu3
1Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, China.
BMC Bioinformatics
|March 18, 2018
Summary
This study statistically analyzes ion distribution around amino acids in protein structures. It reveals preferences in ion-amino acid interactions, creating a database for biomolecular research.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Most ion-protein interaction studies focus on specific binding sites.
- A statistical approach to ion-protein interactions is crucial for a comprehensive understanding.
- Examining ion distribution around amino acids provides insights into general interaction patterns.
Purpose of the Study:
- To conduct a systematic survey of ion-amino acid pairing interactions.
- To develop a publicly available database of ion-protein interactions.
- To statistically analyze ion distributions around all proteinogenic amino acids.
Main Methods:
- Utilized the Protein Data Bank (PDB) for structural data.
- Created a non-redundant dataset to minimize protein sequence redundancy bias.
- Mapped ion positions relative to amino acid coordinates to quantify interactions.
Main Results:
- Approximately 40% of protein records in the PDB contain ions.
- Statistical distributions of ions around amino acids were investigated and summarized.
- Observed variations in ion-amino acid interactions align with physicochemical principles.
Conclusions:
- Documented and analyzed the spatial distribution of ions around amino acids.
- The generated statistics can aid in identifying ion types at specific biomolecular sites.
- This data has potential applications in predicting ion positions within protein structures.
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