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Analysis of protein-protein interaction networks based on binding affinity
K Yugandhar, M Michael Gromiha1
1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India. gromiha@iitm.ac.in.
Current Protein & Peptide Science
|September 29, 2015
Summary
This study analyzed protein-protein interaction (PPI) networks using binding affinity. Eukaryotes favor high-affinity interactions, while prokaryotes show the opposite, offering insights for drug discovery.
Area of Science:
- Systems Biology
- Biochemistry
- Computational Biology
Background:
- Protein-protein interaction (PPI) networks are vital for understanding disease mechanisms.
- Previous PPI network analyses have largely overlooked binding affinity as a key parameter.
Purpose of the Study:
- To systematically analyze PPI networks across five organisms, incorporating binding affinity.
- To investigate the role of binding affinity in network topology and identify potential drug targets.
Main Methods:
- Systematic analysis of PPI networks in five organisms, focusing on binding affinity.
- Examination of interaction types (hub-hub, hub-nonhub, nonhub-nonhub) and motif significance.
- Analysis of clustering coefficients and amino acid properties.
Main Results:
- Eukaryotes exhibit a prevalence of high-affinity complexes, contrasting with prokaryotes.
- Hub-hub interactions show the highest proportion of high-affinity interactions.
- Organisms display specific enrichment of hubs with either high or low affinity complexes.
Conclusions:
- Binding affinity significantly influences PPI network organization across different organisms.
- Network motifs and hub properties vary based on interaction affinity.
- Findings provide valuable insights for drug discovery and target identification.
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