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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
Published on: November 28, 2017
The subunit interfaces of weakly associated homodimeric proteins
Sucharita Dey1, Arumay Pal, Pinak Chakrabarti
1Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.
Journal of Molecular Biology
|February 17, 2010
Summary
This study analyzed protein interfaces in homodimers, finding that "weak" dimers have smaller, loosely packed interfaces. These interfaces show high evolutionary conservation, offering insights into dynamic protein interactions.
Area of Science:
- Structural biology
- Protein-protein interactions
- Evolutionary biology
Background:
- Homodimers are common protein structures with essential biological functions.
- Understanding subunit interfaces is crucial for deciphering protein assembly and function.
- Weak dimers, in equilibrium with monomers, present unique interface characteristics.
Purpose of the Study:
- To analyze the structural and evolutionary properties of homodimer subunit interfaces.
- To compare interfaces of stable homodimers with "weak" homodimers.
- To investigate the evolutionary conservation of interface residues.
Main Methods:
- Analysis of 315 homodimer X-ray structures from the Protein Data Bank.
- Literature validation for dimeric state and equilibrium in solution.
- Calculation of Shannon entropy for homologous sequences to assess evolutionary conservation.
Main Results:
- Weak dimer interfaces are significantly smaller (2.4x) and more loosely packed than stable homodimer interfaces.
- Interface hydrophobicity and amino acid composition are similar across homodimers and transient complexes.
- Interface residues are highly conserved (93% of homodimers), including those in weak dimers.
- Weak dimer homologs may also exist as heterodimers.
Conclusions:
- Loosely packed interfaces likely contribute to the low stability of weak dimers.
- Highly conserved interface residues suggest strong evolutionary selection pressure.
- Weak dimer interfaces serve as models for labile contacts in dynamic protein assemblies, allosteric regulation, and molecular machines.
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