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Related Concept Videos

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...
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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Related Experiment Video

Updated: Jun 23, 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

Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution.

Aartjan J W Te Velthuis1, Christoph P Bagowski

  • 1Institute of Biology, Department of Molecular Virology, Leiden University Medical Centre, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.

Current Genomics
|May 15, 2009
PubMed
Summary

Protein domains are key to understanding protein function and evolution. Analyzing domain evolution using comparative genomics and phylogenetics reveals protein origins and functional relationships.

Keywords:
DomainMPDZMUPPPDZalignmentmolecular evolutionmolecular modelingmultiple PDZ domain protein.phylogenyprotein folding

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Last Updated: Jun 23, 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

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Protein domains are fundamental units of globular proteins, crucial for understanding protein function.
  • Proteomes evolve through domain recombination and duplication, forming protein superfamilies.
  • Shared domains suggest similar function and evolutionary history, but convergent evolution can lead to similar functions and architectures.

Purpose of the Study:

  • To explore protein (domain) evolution principles and recent advancements in molecular evolution.
  • To provide insights into comparative genomics for understanding protein evolution.
  • To predict functions, evolutionary pathways, and origins of novel proteins.

Main Methods:

  • Comparative genomics and homology analysis.
  • Structural modeling and phylogenetics.
  • Integration of transcriptional data with evolutionary data.

Main Results:

  • Demonstrated how domain analysis aids in predicting protein function and evolutionary history.
  • Highlighted the role of convergent evolution in protein architecture and function.
  • Presented molecular models and a comparative genomic analysis of the MUPP-1 protein's evolution.

Conclusions:

  • Understanding protein domain evolution is vital for deciphering protein function and relationships.
  • Comparative genomics, phylogenetics, and structural modeling are powerful tools for evolutionary analysis.
  • Linking evolutionary data with gene activity provides insights into the evolution of stable and rapidly evolving proteins.