Exploring deep phylogenies using protein structure Event as iCalendar

22 March 2018

11am - 12pm

Venue: MAC 1 (Biology 106-112)

Location: City Campus

Host: Centre for Computational Evolution

Cost: Free


Title: Exploring deep phylogenies using protein structure

Ashar Malik
PhD candidate, Massey University
Supervisors: Jane Allison (Massey University) and Ant Poole (SBS, UOA)

The primary step in the process of characterising a novel protein sequence is by comparison with those already characterised. Similarity based functional characterisation and determination of an evolutionary origin can become a non-trivial problem for significantly diverged proteins.

Protein structure, on the other hand, is considered to be conserved over longer evolutionary timescales. An evolutionary signal lost from the sequence may therefore still be retained within the conserved structure.

Current times are seeing an exponential growth in protein structural data, presenting a unique opportunity to explore deep evolutionary questions. However, a poor understanding of protein structural evolution prevents usage of classical sequence-based phylogenetic methods. Empirical distance-based methods have been employed, however the lack of a method to gauge the robustness of evolutionary relationships inferred limits their traction.

A novel molecular dynamics-based bootstrap approach is presented which allows for the quantitative assessment of evolutionary relationships inferred from protein structural phylogenies. The novel ability to associate a measure of robustness with inferences allows protein structure-based phylogenies to uncover answers to deep evolutionary questions. In this talk I will present the framework of the method, some results and limitations of this method.