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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...
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...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Updated: May 24, 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

Protein conformational diversity modulates sequence divergence.

Ezequiel Juritz1, Nicolas Palopoli, Maria Silvina Fornasari

  • 1Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina.

Molecular Biology and Evolution
|March 8, 2012
PubMed
Summary
This summary is machine-generated.

Protein conformational diversity significantly impacts evolutionary sequence divergence. Specific protein conformations, often ligand-binding ones, better predict evolutionary changes, highlighting the need for new bioinformatics models.

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Published on: July 14, 2015

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Protein evolution
  • Structural biology
  • Bioinformatics

Background:

  • Protein structure conservation limits sequence divergence.
  • Protein native states exist as an ensemble of dynamic conformers.
  • Conformational diversity's role in evolution is understudied.

Purpose of the Study:

  • Investigate the influence of conformational diversity on protein sequence divergence.
  • Analyze how different protein conformations affect evolutionary substitution patterns.
  • Determine if specific conformers are more critical for predicting evolutionary trajectories.

Main Methods:

  • Utilized a dataset of 900 proteins with varying conformational diversity from the PCDB database.
  • Employed a structurally constrained protein evolutionary model.
  • Analyzed conformer-specific substitution patterns and predictive power for sequence divergence.

Main Results:

  • Conformational diversity significantly modulates protein substitution patterns.
  • 30% of structurally constrained sites are specific to certain conformers.
  • A single conformer predicted sequence divergence better in 76% of proteins, often the ligand-binding conformer.

Conclusions:

  • Conformational diversity plays a crucial role in modulating protein evolution.
  • Conformer-specific substitution patterns suggest a bias in evolutionary models.
  • Development of new evolutionary models and bioinformatics tools accounting for conformational diversity is recommended.