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Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
Published on: May 26, 2011
Residue centrality in alpha helical polytopic transmembrane protein structures
I Arnold Emerson1, K M Gothandam
1School of Bio Sciences and Technology, VIT University, Vellore-632014, Tamil Nadu, India.
Journal of Theoretical Biology
|June 23, 2012
Summary
Central residues in polytopic transmembrane proteins are crucial for function, often acting as binding sites and exhibiting high mutation sensitivity. These slowly evolving sites are key to protein stability and activity.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Transmembrane proteins are vital for cellular functions like signal transduction and transport.
- Polytopic transmembrane proteins, spanning the membrane multiple times, play critical roles in biological processes.
Purpose of the Study:
- To investigate the significance of central residues in polytopic transmembrane proteins.
- To understand the relationship between residue centrality, conservation, and functional importance.
Main Methods:
- Representing proteins as undirected graphs with residues as nodes and interactions as edges.
- Calculating residue centrality by node removal in the protein contact network.
- Analyzing conservation, ligand/ion interactions, mutation sensitivity, and z-scores.
Main Results:
- 80% of central residues showed below-average conservation, indicating slow evolution.
- 56% of amino acids interacted with ligands/ions, with central residues comprising 84% of binding/active sites.
- 89% of central residues exhibited deleterious mutations, and 87% were identified as hub residues.
Conclusions:
- Central residues are critical for the function and stability of polytopic transmembrane proteins.
- These residues are often involved in ligand binding and are sensitive to mutations.
- The study highlights the importance of centrality analysis in understanding protein function and evolution.
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