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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Genetic Drift03:33

Genetic Drift

Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.Life is not fair. A deer grazing contentedly in a field can have her meal cut tragically short by a bolt of lightning. If the doomed doe is one of only three in the population, 1/3 of the population’s gene pool is lost. Random events like this can...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Mutation, Gene Flow, and Genetic Drift01:09

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).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...

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Updated: Jul 5, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Intense neutral drifts yield robust and evolvable consensus proteins.

Shimon Bershtein1, Korina Goldin, Dan S Tawfik

  • 1Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.

Journal of Molecular Biology
|May 23, 2008
PubMed
Summary

High mutation rates drive protein evolution by creating diverse gene ensembles that maintain function. These ensembles, enriched with stabilizing mutations, increase genetic diversity and the potential for new protein functions.

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

  • Molecular Biology
  • Evolutionary Biology
  • Biochemistry

Background:

  • Natural proteins evolve under varying mutation rates.
  • Understanding protein evolution under high mutation rates is crucial.

Purpose of the Study:

  • To investigate changes in protein ensembles under neutral drift with high mutation rates.
  • To explore the generation of genetic diversity and functional maintenance.

Main Methods:

  • Subjecting TEM-1 beta-lactamase populations to prolonged neutral drift.
  • Applying high mutation rates and purifying selection for penicillinase activity.
  • Analyzing sequence changes, genetic diversity, and functional emergence.

Main Results:

  • Purifying selection and beneficial mutations maintained protein function and structure.
  • Back-to-consensus mutations increased kinetic and thermodynamic stability, acting as global suppressors.
  • High genetic diversity and increased probability of new functions (cefotaxime degradation) were observed.

Conclusions:

  • Large, polymorphic neutral ensembles under high mutational loads exhibit unique evolutionary features.
  • Protein progenitors may have evolved under high mutational loads.
  • Back-to-consensus changes can generate diverse and evolvable gene libraries.