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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

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Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
Evolution of New Traits in Microbes01:24

Evolution of New Traits in Microbes

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Convergent Evolution01:54

Convergent Evolution

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Related Experiment Video

Updated: May 22, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

Amino acid coevolution induces an evolutionary Stokes shift.

David D Pollock1, Grant Thiltgen, Richard A Goldstein

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Proceedings of the National Academy of Sciences of the United States of America
|May 2, 2012
PubMed
Summary
This summary is machine-generated.

Protein evolution is context-dependent. Amino acid preferences change predictably after replacements, similar to a Stokes shift, impacting evolutionary modeling.

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Area of Science:

  • Protein evolution
  • Molecular evolution
  • Biophysics

Background:

  • Amino acid replacement rates in proteins are context-dependent, influenced by local structure and function.
  • Predicting these changes is challenging due to assumed constant amino acid acceptabilities.
  • Evolutionary interactions between residue positions invalidate the assumption of constant amino acid preferences.

Purpose of the Study:

  • To investigate how amino acid propensities at a specific position change following an amino acid replacement.
  • To explore the concept of an 'evolutionary Stokes shift' in protein evolution.
  • To assess the implications of these findings for protein evolution modeling.

Main Methods:

  • Simulations of purple acid phosphatase evolution.
  • Analysis of amino acid propensities and their changes over evolutionary time.
  • Comparison of simulation results with predictions of stability changes in real proteins.

Main Results:

  • Amino acid propensities at a position predictably change after an amino acid replacement.
  • Following a replacement, the new amino acid and similar ones become more acceptable over time.
  • This dynamic shift, termed an evolutionary Stokes shift, suggests proteins equilibrate to amino acid changes.
  • Mutation reversals become less favorable over time, supporting the evolutionary Stokes shift concept.

Conclusions:

  • The study demonstrates that amino acid preferences are not static but evolve dynamically.
  • The observed 'evolutionary Stokes shift' has significant implications for understanding protein evolution.
  • This finding necessitates revised models for predicting protein evolution and stability.