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Related Experiment Video

Updated: Feb 4, 2026

Evolution of Staircase Structures in Diffusive Convection

Evolution of Staircase Structures in Diffusive Convection

Published on: September 5, 2018

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Jonathan D Tyzack¹, Nicholas Furnham², Ian Sillitoe³

¹EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, UK. tyzack@ebi.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)

|October 10, 2018

Summary

This summary is machine-generated.

This study explores enzyme evolution using the FunTree resource, integrating sequence, structure, and functional data to understand how enzymes adapt. It details methods for analyzing protein superfamilies and their evolutionary trajectories.

Keywords:

CATH EC-Blast Enzyme evolution FunTree Phylogenetic tree

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Last Updated: Feb 4, 2026

Evolution of Staircase Structures in Diffusive Convection

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Published on: September 5, 2018

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

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Published on: March 16, 2011

Molecular Evolution of the Tre Recombinase

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

Area of Science:

Biochemistry and Molecular Biology
Evolutionary Biology
Bioinformatics

Background:

Understanding enzyme evolution is crucial for molecular biology.
Enzymes adapt their functions, specificities, and mechanisms over time.
Investigating evolution requires integrated biological data.

Purpose of the Study:

To enhance understanding of molecular-level biology, focusing on enzyme evolution.
To present the FunTree resource for investigating enzyme evolution within superfamilies.
To detail the computational tools and analyses for extracting evolutionary information.

Main Methods:

Utilizing FunTree, which integrates sequence, structure, phylogenetic, and chemical data for enzyme superfamilies.
Clustering proteins into structurally similar groups (SSGs) using sequence and structural alignments.
Generating phylogenetic trees with ancestral character estimations (ACE) and functional similarity measures.

Main Results:

FunTree provides a comprehensive resource for studying enzyme evolution across 2340 CATH superfamilies.
Phylogenetic trees are augmented with functional, taxonomic, and Enzyme Commission (EC) annotations.
New measures of functional similarity assess enzyme reactions based on bond changes and metabolite structures.

Conclusions:

The FunTree resource facilitates in-depth investigation of enzyme evolution.
Integrated data and computational tools enable detailed analysis of protein superfamilies.
The findings contribute to understanding molecular adaptations and enzyme functional diversification.