The evolution of multiple active site configurations in a designed enzyme – New Nature Communications Paper!

 

NANSOOKPAPER copy.jpg

Congratulations to Nansook and everyone involved in this project! This has been a great collaboration with Lynn Kamerlin (Uppsala University), Chris Easton (ANU) and Michelle Coote’s (ANU) groups.

In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.

https://www.nature.com/articles/s41467-018-06305-y

Postdoctoral Fellow Position in the Jackson Lab – Apply Now!

Come and work with us on an exciting, collaborative project at the Australian National University!

Screen Shot 2018-09-24 at 9.33.02 am.png

The ANU Grand Challenge Research Program on Novel Miniaturized Medical Sensor Technology is now advertising Postdoctoral Fellow / Research Fellow positions located each in the Research Schools of Chemistry, Engineering, and Physics to work on the development of novel miniaturized biomedical sensors that can be integrated into wearable and point-of-care devices. These positions will work synergistically with the ANU Grand Challenge team benefitting from the breadth of the research programs and expertise. This project aims to revolutionise personalised medicine by providing new means for non-invasive collection and analysis of health data including the development of miniaturized sensors for detection of biomarkers in multiple sclerosis and diabetes.

The Research School of Chemistry Research Fellow will work in Associate Professor Colin Jackson’s group, and be responsible for design, engineering, and production of proteins as a key component of these biosensors. This could include engineering binding selectivity, optimizing ligand affinity, and chemical modification of the protein to function as part of a complex matrix, such as protein hydrogels.

For more details on how to apply, please follow this link: http://jobs.anu.edu.au/cw/en/job/526630/postdoctoral-fellow

 

 

Galen hits ‘Submit’ on his PhD Thesis!

GalenSubmitGIF

Congratulations to Galen Correy who submitted his PhD thesis last week! Here he is clicking on the ‘submit’ button. Well done Galen!

 

Check out a few of Galen’s papers:

 

 

 

 

Ben Clifton awarded ‘Best Thesis’

Ex-Jackson group member Dr. Ben Clifton has been awarded the ‘ANU Research School of Chemistry Director’s award for the Best Thesis 2017’. Ben’s PhD thesis ‘Functional evolution of solute-binding proteins’ describes the use of ancestral protein reconstruction to explore the molecular evolution of binding specificity and catalysis in amino-acid binding proteins.

You can find some of Ben’s published work here:

 

Congratulations Ben!

New Nature Chemical Biology paper!

Screen Shot 2018-08-04 at 10.18.04 AM.png

Image result for Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS

 

Link to paper

The amino acid glycine is an important inhibitory neurotransmitter and co-agonist of the N-methyl-D-aspartate receptors involved in synaptic plasticity. In this work, published in Nature Chemical Biology, we describe the computational design, development, and application of the first optical sensor for glycine. This FRET sensor can be used with single and two-photon excitation fluorescence microscopy. Here, we show that it can be used in combination with electrophysiology to investigate the spatial distribution of glycine in the extracellular space, and to probe how glycine concentrations change in response to plasticity-inducing stimuli.

This work was done in collaboration with Christian Henneberger’s group (University of Bonn, Institute of Cellular Neurosciences). Congratulations to Will, Michel and everyone involved in this work.

 

Modulating enzyme activity via incorporation of non-canonical amino acids – new chapter

Kirk_Jackson_Huber_modulating_enzyme_activity_via_incorporation_of_non-canonical_amino_acids

Colin and Jules have recently published a chapter, with Thomas Huber (ANU), about using non-canonical amino acids for the modulation of enzyme activity. This chapter, published in Modern Biocatalysis: Advances Towards Synthetic Biological Systems (RSC Publishing), outlines the use of unnatural amino acids (UAAs) in protein engineering. Examples of how UAAs have successfully been used to engineer proteins for enhanced thermostability, catalytic efficiency, specificity and selectivity are provided, and remaining challenges within the field are discussed. This work also describes the engineering of tRNA synthetases for the site-specific incorporation of UAAs into proteins.

The chapter can be found here.

 

New Publication! – “Hydrogel-Immobilized Supercharged Proteins”

eleanorpaper

 

Immobilizing enzymes on a solid support can help improve their stability, rendering them more suitable for industrial and medical applications. However, standard covalent attachment approaches can be costly, often require many steps, and commonly lead to unfavourable orientations of the enzymes on the solid media. In this work, recently published in Advanced Biosystems, we produced enzyme-hydrogel complexes using anionic hydrogels and an engineered cationic supercharged phosphotriesterase. We show this system is capable of detoxifying organophosphates and catalyzing enantioselective reactions, and is remarkably robust and long-lasting (even when exposed to organic solvents). Additionally, degraded enzyme can be easily stripped from the gel and replaced with fresh protein, resulting in a very flexible system that could be readily scaled up for use in industry, synthesis, and bioremediation. Congratulations to Eleanor and everyone involved with this project.

New Nature Chemical Biology paper

header

Nature Chemical Biology Abstract Binding protein to enzyme Jackson Clifton

 

It’s out! Our Nature Chemical Biology paper “Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein” is now online. 

How do new enzymes evolve from proteins that were initially specialised for binding? In this work, we use ancestral protein reconstruction to calculate and characterise the evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme–substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations.