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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Fold usage on genomes and protein fold evolution.

Sanne Abeln¹, Charlotte M Deane

¹Department of Statistics, University of Oxford, United Kingdom.

|July 8, 2005

Summary

This summary is machine-generated.

Protein fold usage across genomes reveals evolutionary insights. Bacteria possess more distinct folds, while eukaryotes have more copies, suggesting varied evolutionary paths for protein structures.

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Area of Science:

Genomics
Structural Biology
Evolutionary Biology

Background:

Understanding protein structure evolution is crucial for deciphering life's complexity.
Genome-wide analysis of protein fold usage provides insights into evolutionary relationships and fold age.

Purpose of the Study:

To investigate protein fold usage patterns across completed genomes.
To explore the relationships between different measures of fold usage and their evolutionary implications.

Main Methods:

Analysis of structural domain occurrences in 157 completed genome sequences from bacteria, archaea, and eukaryotes.
Comparison of fold usage metrics: copies per genome, families per fold, and genome occurrence.

Main Results:

Bacteria exhibit more distinct folds than archaea; eukaryotes show higher fold copy numbers.
The alpha/beta fold class may have an earlier origin, showing distinct distribution patterns.
Fold usage measures (copies, families, occurrence) are not always correlated and depend on fold class and kingdom.

Conclusions:

Genome-wide fold usage patterns offer insights into protein structure evolution and fold age.
Distinct evolutionary strategies exist across different life kingdoms regarding protein fold utilization.
The relationship between fold usage metrics is complex, highlighting the multifaceted nature of protein evolution.