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PInteract: Detecting Aromatic-Involving Motifs in Proteins and Protein-Nucleic Acid Complexes.
Dong Li1,2, Fabrizio Pucci1,2, Marianne Rooman1,2
1Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium.
Biomolecules
|August 28, 2025
Summary
A new algorithm, PInteract, identifies crucial π-involving interactions in molecular complexes. This tool detects various π interactions and motifs, aiding in understanding protein structure and function.
Area of Science:
- Computational Biology
- Structural Biology
- Biochemistry
Background:
- Accurate protein structure prediction is now widely available, necessitating efficient algorithms for detecting molecular interactions.
- Non-covalent interactions are vital in biological systems, including protein-protein, protein-nucleic acid, and protein-ligand complexes.
- Aromatic π molecular orbital interactions are significant due to electron delocalization, impacting protein aggregation and function.
Purpose of the Study:
- To develop a fast algorithm, PInteract, for detecting π-involving non-covalent interactions.
- To identify various types of π interactions, including π-π, cation-π, amino-π, His-π, and sulfur-π.
- To detect interaction chains, clusters, and specific motifs like stair motifs at nucleic acid interfaces.
Main Methods:
- PInteract algorithm based on geometric criteria for detecting π-involving interactions.
- Analysis of protein structures, protein-DNA, protein-RNA, and protein-ligand complexes.
- Identification of interaction chains, clusters, and stair motifs.
Main Results:
- PInteract successfully detects multiple types of π-involving interactions.
- The algorithm identifies chains and clusters of π interactions.
- Recurrent stair motifs at protein-DNA/RNA interfaces are characterized.
Conclusions:
- PInteract provides a fast and effective method for identifying π-involving interactions in diverse molecular complexes.
- The algorithm aids in understanding the role of π interactions in biological processes and structural motifs.
- This tool is essential for analyzing the vast number of available protein structures.
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