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Updated: Jun 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Investigating homology between proteins using energetic profiles.
James O Wrabl1, Vincent J Hilser
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America.
Local protein stability is generally conserved throughout evolution among homologous proteins. However, the thermodynamic mechanisms (enthalpy and entropy) driving stability show less conservation, suggesting fold evolution can occur via altered mechanisms.
Area of Science:
- Protein thermodynamics
- Structural biology
- Evolutionary biology
Background:
- Conservative mutations often preserve protein stability, but effects of large sequence/structure changes are less understood.
- The evolutionary conservation of local protein stability across different regions remains largely unknown.
Purpose of the Study:
- To investigate the evolutionary conservation of local protein stability.
- To analyze the thermodynamic basis (enthalpy and entropy) of stability conservation.
- To explore structure-thermodynamic relationships in protein evolution.
Main Methods:
- Computational thermodynamic analysis of over 3,000 proteins using the COREX/BEST algorithm.
- All-vs.-all pairwise structural alignment to compare proteins.
- Quantitative comparison of position-specific stability, enthalpy, and entropy between homologous and non-homologous proteins.
Main Results:
- Local stability of homologous proteins is significantly more correlated than non-homologous proteins, indicating evolutionary conservation.
- Enthalpy and entropy underlying local stability are less correlated between homologs, suggesting stability is conserved over variable mechanisms.
- Identified exceptional cases: homologous proteins with similar thermodynamics despite structural changes, and similar structures with different stabilities.
Conclusions:
- Local protein stability is generally conserved throughout evolution.
- Protein fold evolution may involve changes in thermodynamic mechanisms while preserving overall stability.
- Findings suggest a basis for a thermodynamically informed protein homology classification.
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