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Updated: May 12, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

Michael J Wise¹

¹School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia. Michael.Wise@uwa.edu.au

|April 25, 2013

Summary

This summary is machine-generated.

A new method, Mean Protein Evolutionary Distance (MeaPED), identifies viral protein roles by measuring evolutionary resistance. This analysis highlights host interaction proteins as evolutionary hot-spots and polymerase proteins as cold-spots, suggesting new therapeutic targets.

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Last Updated: May 12, 2026

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Published on: February 5, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Area of Science:

* Evolutionary biology
* Virology
* Bioinformatics

Background:

* Proteins evolve under constraints, with varying rates across different proteins within an organism.
* Comparative analysis of protein evolution can reveal protein functions and roles.
* Previous methods relied on patristic distance, but a new approach offers enhanced analysis.

Purpose of the Study:

* To introduce and validate the Mean Protein Evolutionary Distance (MeaPED) method for analyzing comparative protein evolution.
* To identify proteins that are evolutionary hot-spots and cold-spots across diverse viral proteomes.
* To explore the potential of evolutionary cold-spot proteins as therapeutic targets.

Main Methods:

* Development and application of the Mean Protein Evolutionary Distance (MeaPED) method.
* Analysis of proteomes from various viruses including influenza A, hepatitis C, HIV, dengue, rotavirus A, polyomavirus BK, and measles.
* Comparison of evolutionary rates across different viral protein families.

Main Results:

* MeaPED successfully measures differential resistance to evolutionary pressure across viral proteomes.
* Host interaction proteins (e.g., hemagglutinin, agnoprotein, p7, VPU) identified as evolutionary hot-spots.
* RNA-directed RNA polymerase and internal serine protease proteins identified as evolutionary cold-spots.
* Contrasting evolutionary patterns observed between influenza hemagglutinin (hot-spot) and measles H protein (cold-spot).

Conclusions:

* The MeaPED method provides insights into viral protein roles and evolutionary dynamics.
* Evolutionary hot-spot proteins are often involved in host interactions and are more antigenically exposed.
* Evolutionary cold-spot proteins, being more conserved, represent promising targets for novel antiviral therapeutics, especially when vaccines targeting hot-spots are ineffective.