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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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

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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

Evolution of protein domain architectures.

Kristoffer Forslund1, Erik L L Sonnhammer

  • 1Stockholm Bioinformatics Centre, Stockholm University, Stockholm, Sweden.

Methods in Molecular Biology (Clifton, N.J.)
|March 9, 2012
PubMed
Summary

Protein domain architecture evolution is shaped by phylogenetic distribution and combinatorial propensities. Research explores genome evolution models, selective pressures, and ancestral reconstructions to understand domain arrangement origins.

Area of Science:

  • Evolutionary biology
  • Structural bioinformatics
  • Genomics

Background:

  • Protein domain architectures are fundamental to protein function and evolution.
  • Understanding their evolutionary trajectories is key to deciphering proteome complexity.
  • Phylogenetic distribution and domain family size distributions (power laws) provide foundational insights.

Purpose of the Study:

  • To review current research on the evolution of protein domain architectures.
  • To synthesize findings on genome evolution models and selective pressures influencing domain family expansion.
  • To explore principles of domain architecture evolution inferred from extant and ancestral arrangements.

Main Methods:

  • Analysis of phylogenetic distributions of proteins and protein domains.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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  • Examination of power law distributions in domain family size and multidomain architectures.
  • Review of genome evolution models and evidence for selective pressures.
  • Inference of ancestral domain architectures.
  • Assessment of monophyly versus polyphyly in domain architecture evolution.

    • Main Results:

    • Domain family sizes often follow power law distributions across genomes and evolutionary groups.
    • Multidomain architectures also exhibit power law distributions, suggesting underlying evolutionary principles.
    • Evidence suggests selective pressures favor expansion of certain domain families.
    • Domain versatility influences combinatorial propensities in architecture formation.
    • Analysis of extant and ancestral architectures reveals key evolutionary mechanisms.

    Conclusions:

    • Protein domain architecture evolution is influenced by combinatorial propensities and genome evolution dynamics.
    • Selective pressures play a significant role in shaping domain family expansion.
    • Understanding ancestral states and evolutionary mechanisms (monophyly/polyphyly) is crucial for a complete picture.