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Related Experiment Video

Updated: May 7, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Protein evolution along phylogenetic histories under structurally constrained substitution models.

Miguel Arenas¹, Helena G Dos Santos, David Posada

¹Centre for Molecular Biology 'Severo Ochoa', Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain and Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.

Bioinformatics (Oxford, England)

|September 17, 2013

Summary

Simulating protein evolution using stability and realistic evolutionary histories generates more accurate amino acid distributions and stable proteins. This approach improves in silico protein evolution modeling for research.

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

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

Published on: July 14, 2015

Area of Science:

Molecular Evolution
Computational Biology
Structural Bioinformatics

Background:

Current molecular evolution models often neglect protein structure information.
Structure-based protein evolution models are not widely used in phylogenetic analyses and may overlook processes like recombination.

Purpose of the Study:

To develop a simulation framework integrating protein stability and phylogenetic histories for realistic in silico protein evolution.
To generate more accurate in silico evolved proteins by accounting for folding stability and evolutionary processes.

Main Methods:

Developed a method combining protein folding stability models (considering unfolding and misfolding) with phylogenetic histories.
Integrated complex evolutionary scenarios, including recombination, demographics, and migration.
Implemented the framework in a program named ProteinEvolver.

Main Results:

The new models produced amino acid distributions more closely resembling those in real protein families compared to empirical models.
Proteins simulated using this framework were predicted to be more stable.
The ProteinEvolver program was developed to facilitate these simulations.

Conclusions:

Evolutionary models incorporating protein stability and realistic evolutionary histories provide a better approximation of the actual evolutionary process.
This integrated approach enhances the realism of in silico protein evolution for various applications.
The findings suggest a significant improvement in simulating protein evolution by considering structural stability.