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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...

Conservation of Protein Domains

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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.
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Microbial Phylogeny

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,...

Conserved Binding Sites

Conserved Binding Sites

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Evolutionary Relationships through Genome Comparisons

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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...

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The primary structure of a protein is its amino acid sequence.

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

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

Published on: July 16, 2017

Domain tree-based analysis of protein architecture evolution.

Kristoffer Forslund¹, Anna Henricson, Volker Hollich

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

Molecular Biology and Evolution

|November 21, 2007

Summary

Protein domain architecture reinvention is common, with 12.4% of architectures having multiple origins. This suggests convergent evolution plays a significant role in protein evolution and function.

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Area of Science:

Evolutionary biology
Proteomics
Bioinformatics

Background:

Protein architecture evolution is crucial for understanding protein function.
Rearrangement and duplication events drive the creation of complex protein architectures.
Domain architecture reinvention, a form of convergent evolution, is an important area of study.

Purpose of the Study:

To investigate the prevalence of domain architecture reinvention across 96 genomes.
To develop and apply a novel domain tree-based method for inferring ancestral protein architectures.
To analyze the frequency and potential functional implications of multiply created domain architectures.

Main Methods:

Utilized a novel domain tree-based method employing maximum parsimony to infer ancestral protein architectures.
Analyzed domain architectures from the Pfam database.
Ensured robustness by applying the method to bootstrap trees and considering statistically supported results.

Main Results:

Detected multiple origins for 12.4% of scored protein architectures across 96 genomes.
Identified a lower figure of 5.6% for multiply created architectures in a subset of completely domain-assigned proteins.
Found no strong functional bias associated with architectures exhibiting multiple origins.

Conclusions:

Domain architecture reinvention is a more frequent phenomenon in protein evolution than previously recognized.
The findings highlight the significant role of convergent evolution in shaping protein repertoires.
Further research may explore the specific evolutionary pressures driving domain architecture reinvention.