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The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference
1Centre for Molecular Biology Severo Ochoa(CSIC-UAM), Madrid, Spain. ubastolla@cbm.csic.es.
Methods in Molecular Biology (Clifton, N.J.)
|October 10, 2018
Summary
New stability-constrained substitution (SCS) models account for protein structure in evolutionary analysis. These models improve phylogenetic inference and ancestral sequence reconstruction by considering native state stability, outperforming traditional methods.
Area of Science:
- Computational Biology
- Molecular Evolution
- Biophysics
Background:
- Traditional protein evolution models assume independent site evolution, neglecting structural influences.
- Protein site structure impacts evolutionary rates and amino acid substitutions.
- Previous models incorporated structural properties via site-specific amino acid frequencies.
Purpose of the Study:
- To introduce and describe stability-constrained substitution (SCS) models for protein evolution.
- To incorporate native state stability against unfolding and misfolding into evolutionary models.
- To provide a mean-field approximation for phylogenetic inference and ancestral sequence reconstruction.
Main Methods:
- Development of stability-constrained substitution (SCS) models.
- Implementation of a mean-field approximation for independent site analysis.
- Validation using simulated and real protein data.
- Application within maximum likelihood phylogenetic inference frameworks.
Main Results:
- SCS models explicitly consider protein site stability.
- The mean-field SCS model integrates with maximum likelihood methods.
- Validation demonstrates the utility of SCS models for protein data analysis.
Conclusions:
- Stability-constrained substitution models offer improved phylogenetic inference.
- These models provide a more accurate representation of protein sequence evolution.
- Guidelines are provided for analyzing protein data with stability constraints.
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