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Conservation of Protein Domains Over Different Proteins

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...

SDS-PAGE

SDS-PAGE

Gel electrophoresis is a method that separates biological macromolecules like nucleic acids or proteins by forcing them to pass through a gel matrix under an electric field.
A variation of gel electrophoresis, termed polyacrylamide gel electrophoresis (PAGE), is commonly used for separating proteins according to their molecular size by passing them through a polyacrylamide gel. Because of the varying charges associated with amino acid side chains, PAGE can be used to separate intact proteins...

Conservation of Protein Domains

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...

Bacterial Protein Maturation

Bacterial Protein Maturation

Bacterial protein maturation is a tightly regulated process that ensures newly synthesized polypeptides achieve correct functional conformations. This maturation involves a series of modifications, folding events, and quality control steps, often assisted by specialized chaperone proteins.N-Terminal ModificationsThe maturation of bacterial polypeptides begins cotranslationally as the polypeptide exits the ribosome. The first amino acid, N-formylmethionine (fMet), is typically modified at the...

Diversity of Archaea III

Diversity of Archaea III

Crenarchaeota, a prominent phylum of Archaea, is remarkable for its ability to thrive in extreme environments characterized by high temperatures and acidity. These microorganisms inhabit sulfuric hot springs, volcanic systems, and submarine hydrothermal vents, where temperatures often exceed 100°C. The unique adaptations of Crenarchaeota not only allow survival under such extreme conditions but also provide insights into the mechanisms of life in primordial Earth-like environments.Morphological...

Protein Families

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...

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Related Experiment Video

Updated: Jun 28, 2026

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

Published on: November 26, 2017

Do older taxa have older proteins?

Ricardo Ferreira¹, Frederico J S Pontes, Benício de Barros Neto

¹Departamento de Química Fundamental/CCEN, Universidade Federal de Pernambuco, 50670-901, Recife, Pernambuco, Brasil. rferreira100@yahoo.com

Zeitschrift Fur Naturforschung. C, Journal of Biosciences

|November 13, 2008

Summary

The study reveals a consistent decrease in the phi index across major taxa, suggesting a non-symmetrical evolutionary path from early life forms. This pattern supports the idea of ancient lineages having older protein sets.

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Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

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Published on: May 18, 2017

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Last Updated: Jun 28, 2026

Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans

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Published on: November 26, 2017

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Published on: May 18, 2017

Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

The phi index, a measure of relative (G, C) content in codons, has been previously described.
Understanding genomic evolution across diverse taxa is crucial for phylogenetic studies.

Purpose of the Study:

To investigate the trend of the phi index across major taxa.
To explore the relationship between taxon age and protein age.
To propose a model for phylogenetic divergence.

Main Methods:

Analysis of codon usage data from 728 species (≥10,000 codons) and a subset of 237 species (≥50,000 codons).
Statistical analysis of phi values for twelve proteins across over one thousand species.
Comparison of phi index trends across five major taxa: archaea, bacteria, eukaryotes (excluding metazoa), metazoa (excluding vertebrates), and vertebrates.

Main Results:

The mean phi values decrease monotonically across the five studied taxa.
A non-symmetrical phylogenetic tree is proposed for the divergence of these main taxa from an ancestral progenome.
Further divergence within eukaryotes (plants, fungi, protozoans) shows symmetrical branching.
Protein age correlates with taxon age for the first four taxa, but not for metazoa/vertebrates.

Conclusions:

The observed phi index trend supports a model of successive divergence from an ancestral progenome.
Phylogenetic branching patterns differ between early major divergences and later eukaryotic diversification.
The correlation between taxon age and protein age is largely supported, with some exceptions.