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Related Experiment Video

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Daily Transfers, Archiving Populations, and Measuring Fitness in the Long-Term Evolution Experiment with Escherichia coli

Daily Transfers, Archiving Populations, and Measuring Fitness in the Long-Term Evolution Experiment with Escherichia coli

Published on: August 18, 2023

Chasing long-range evolutionary couplings in the AlphaFold era.

Theodoros K Karamanos¹

¹Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.

|February 8, 2023

Summary

This summary is machine-generated.

Researchers identified distant protein residue couplings not explained by direct contact. This analysis of evolutionary data, aided by AlphaFold models, reveals insights into protein function and structure determination.

Keywords:

AlphaFold coevolution computational biology intrinsically disordered proteins protein structure

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Microfluidic Mixers for Studying Protein Folding

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Published on: April 10, 2012

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Coevolution of protein residues typically implies direct physical contact.
Multiple sequence alignments (MSAs) contain rich evolutionary information beyond spatial proximity, including functional couplings.
Mining this information is challenging due to sequence space complexity and lack of structural data.

Purpose of the Study:

To identify coevolutionary couplings in proteins that are not explained by spatial proximity.
To leverage the AlphaFold database for analyzing evolutionary couplings.
To uncover long-range functional interactions and conformational changes.

Main Methods:

Performed direct coupling analysis on multiple sequence alignments (MSAs).
Utilized the AlphaFold (AF) database to obtain structural models for protein families.
Identified coevolving residue pairs whose couplings were not satisfied in any AF models.

Main Results:

Approximately 12% of identified coevolving residue pairs were spatially distant.
Spatially distant coevolving residues were more likely to be disordered compared to contacting pairs.
The method was applied to 2012 protein families.

Conclusions:

Coevolutionary analysis can reveal functionally relevant residue couplings beyond direct contact.
This approach enhances the utility of coevolutionary data for protein structure determination.
The findings suggest potential for identifying allosteric cross-talk between distant residues.