Linking evolution of protein structures through fragments

Sanne Abeln,Charlotte Deane

doi:10.1186/1752-0509-1-s1-s12

Abstract

Motivation At present there is no universal understanding of how proteins can change topology during evolution, and how such pathways can be determined in a systematic way. The ability to create links between fold topologies would have important consequences for structural classification, structure prediction and homology modeling. Several methods based on geometrical measures have been proposed to create links between topologies, e.g. [1,2]. It has proven difficult, however, to show the evolutionary relevance of such links. Here we use our previously developped age measure for protein superfamilies [3] to investigate the relationship between structural fragments and protein structure evolution.

Highlights

We used a set of pairwise fragments to create a network of structural links between superfamilies
New proteins are thought to be created through duplication and point mutations of structural domains
We show evidence that this might occur on a scale below the domain level: fragments are shared more often with older superfamilies, which is expected in a model where new topologies can be built through an assembly of, or multiple insertions of, fragments from existing proteins

Summary

Introduction

We used a set of pairwise fragments to create a network of structural links between superfamilies. When comparing the number of fragment-links that young and old superfamilies make with other superfamilies, it becomes clear that the distribution of younger folds is skewed towards fewer links (Figure 1). We can compare the number of links that each superfamily has with a set of young and a set of old superfamilies.

Results

Conclusion