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Updated: Jan 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Correlated Evolution Drives Structural Convergence of Interacting Proteins.

Ksenia Macias Calix¹, Antara Anika Piya¹, Raquel Assis^2,3,4

¹Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, 33431, USA.

Journal of Molecular Evolution

|November 28, 2025

Summary

Protein structure and interactions are linked, especially in conserved protein interactions (interologs). Conserved interactions show structural similarity and less disorder, suggesting optimization for biological function.

Keywords:

Coevolution Interolog Protein disorder Protein structure Protein-protein interaction Structural convergence

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Published on: December 23, 2022

Area of Science:

Proteomics
Structural Biology
Evolutionary Biology

Background:

Understanding protein structure-interaction relationships is crucial in biology.
Protein structural features and interaction patterns are key to biological function.
Divergent taxa like rodents and yeast offer insights into conserved biological principles.

Purpose of the Study:

To investigate the link between protein structural features and interaction patterns.
To compare these relationships across evolutionarily divergent species (rodents and yeast).
To determine if conserved interactions (interologs) exhibit distinct structural properties.

Main Methods:

Comparative analysis of protein structures and interaction data in rodents and yeast.
Identification and analysis of evolutionarily conserved interactions (interologs).
Assessment of intrinsic disorder, structural similarity, and evolutionary divergence in interacting proteins.

Main Results:

Positive correlation between intrinsic disorder of interacting proteins in both taxa.
This correlation is primarily observed in evolutionarily conserved interactions (interologs).
Interologs display greater structural similarity, less evolutionary divergence, and reduced intrinsic disorder compared to non-interologs.

Conclusions:

Conserved protein interactions are associated with structural convergence.
Structural similarities in interologs may enhance functional and structural stability.
The study highlights the co-evolution of protein structure and interactions for biological fitness across species.