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From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
Published on: July 4, 2016
Evolution of structural shape in bacterial globin-related proteins
1Department of Biology, Long Island University, 1 University Plaza, Brooklyn, NY 11201, USA. lmarsh@liu.edu
Journal of Molecular Evolution
|April 14, 2006
Summary
Protein structure evolves through changes in helix contacts. This study modeled globin evolution, finding contact changes occur slower than sequence changes and showing no evidence of convergent evolution in contact patterns.
Area of Science:
- Protein evolution
- Structural bioinformatics
- Phylogenetics
Background:
- The globin protein family displays conserved helix interaction patterns with notable variations.
- Understanding protein structural evolution is key to deciphering functional diversification.
Purpose of the Study:
- To model the evolution of protein structure using a simplified approach based on helix contact changes.
- To investigate the evolutionary dynamics of contact patterns within the globin family.
Main Methods:
- Developed a simplified model of protein structural evolution based on random helix contact changes.
- Utilized a parsimony approach to reconstruct ancestral structural states for 15 bacterial globin proteins.
- Analyzed contact changes and compared phylogenetic reconstructions based on sequence and contact patterns.
Main Results:
- Contact changes occurred more slowly than sequence changes within the globin domain.
- High levels of homoplasy were observed, with no evidence for invariant residue-residue contacts.
- Phylogenetic reconstruction using contact patterns was consistent with, but less resolved than, sequence-based phylogenies.
- No contact pattern convergence was detected between different globin families, suggesting constraints on selection for specific patterns.
Conclusions:
- Protein structure, specifically helix contact patterns, evolves at a slower rate than protein sequence.
- The study provides insights into the evolutionary mechanisms shaping protein structures and suggests limitations on convergent evolution of structural patterns.
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