Dr Thomas Shafee
College of Science, Health and Engineering
School of Molecular Sciences
Department of Biochemistry and Genetics
La Trobe Institute for Molecular Science
MA Cantab (Cambridge), PhD (Cambridge)
Area of study
Biochemistry and Molecular Biology
My main interests are in the ancient evolution of proteins and how we can use this information to engineer and design new proteins. Some superfamilies of proteins have existed since the dawn of cellular life so studying them can shed light on evolutionary events from over a billion years ago. Since nature has run millions of years' worth of experiments for us, we can use this information to inform protein engineering strategies.
My current work focusses on the defensins, a diverse class of small, cationic, disulphide-rich proteins. Using techniques to investigate their ancient evolution, I demonstrated that there are two independent evolutionary origins the defensins. The two resulting superfamilies show a remarkable degree of convergent evolution in their sequences, structures and functions.
Although the superfamilies encompass many functions, my focus is on the antimicrobial members involved in innate immunity and host defence. I use a variety of phylogenetic and non-phylogenetic methods to investigate the early evolution of their sequences and functions to try to explain the extreme diversity observed in the superfamilies. In particular, I am developing techniques to make quantitative maps of 'protein sequence space', based on my time studying evolvability by directed evolution during my PhD.
Better understanding of defensin how mutations have altered functions and mechanisms of action in defensins over their evolutionary history should ultimately enable us to engineer improved antimicrobial variants for use in biotechnology.
In addition to my research, I have an interest in scientific communication. I work to bring scientific content in Wikipedia up to academic standards, since it is typically the most read information source for most topics. This is firstly through directly editing the encyclopedia (articles I've written of overhauled have >30 million views per annum). Additionally, I am part of a new wave of collaboration between academic publishers and Wikipedia. I am a Front Section Editor for PLOS Genetics and an Editorial Board member for WikiJournal of Medicine.