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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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Related Experiment Video

Updated: Jul 10, 2026

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

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

Published on: July 14, 2015

Detecting coevolution in and among protein domains.

Chen-Hsiang Yeang1, David Haussler

  • 1Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America. chyeang@ias.edu

Plos Computational Biology
|November 7, 2007
PubMed
Summary

Sequence coevolution analysis reveals functional protein relationships. New methods identify spatially coupled amino acids, highlighting structural and functional constraints in proteins.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Evolution

Background:

  • Coevolutionary sequence analysis provides insights into molecular structures and interactions.
  • Existing methods for coevolution analysis often compromise on generality, simplicity, phylogenetic information, or interaction-specific knowledge.
  • A comprehensive screening for coevolution across all protein domains is lacking.

Purpose of the Study:

  • To develop an advanced model for sequence coevolution analysis.
  • To conduct a large-scale screening of coevolution across the protein domain database (Pfam).
  • To investigate the relationship between sequence coevolution and protein structure/function.

Main Methods:

  • Proposed an augmented continuous-time Markov process model for sequence coevolution.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Related Experiment Videos

Last Updated: Jul 10, 2026

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

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

Published on: July 14, 2015

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

  • The model accommodates diverse interaction types, integrates phylogenetic information and sequence substitution, and has minimal free parameters.
  • Performed large-scale screenings on the Pfam database, executing 0.1 trillion tests.

    • Main Results:

    • Identified that the majority of inferred coevolving protein domains are functionally related.
    • Demonstrated that coevolving amino acid residues are spatially coupled.
    • Found coevolving positions frequently located at functionally critical sites, including enzyme active sites and protein-protein interaction interfaces.

    Conclusions:

    • Sequence coevolution reflects underlying structural and functional constraints in proteins.
    • The findings suggest a strong link between sequence coevolution and selective pressures.
    • Further research into the complex relationships between coevolution and selective constraints is warranted.