Overview

Enzyme cascades and their applications

Enzymes are nature’s catalysts. They are molecules that make reactions in biology work faster. All the chemical changes needed in living systems rely on enzymes speeding up reactions at the right time. Our work seeks to understand sets of enzymes working together – a “cascade” – to drive desirable reactions. We engineer some enzymes using evolutionary methods. We then apply this understanding to practical problems. Our key examples are: the production of sugars for use in vaccines against bacteria; and chemical transformations for drug manufacture. Our work will help to deliver vaccines or drugs at scale using fewer resources and producing less waste. It will help both with overcoming antimicrobial resistance, and achieving a green future.

Time-resolved structural studies of enzymes

The key steps in enzyme catalysis occur quickly in rare events on a molecular timescale. To gain deeper understanding of how enzymes work, we want to determine the structure of enzymes as they move through the catalytic cycle. Achieving this requires the latest structural biology innovations. We aim to use our well-characterised systems from the enzyme cascade projects to work with synchrotron experts to catch enzymes in the act of catalysis and better understand how enzymes achieve their amazing speeding up of reactions.

Research Team

Anil Jamithireddy (Postdoc)

Courtney Tremlett (PhD)

William Stuart (PhD)

Freddie Moore (PhD)

I am a member of the Biochemistry, Chemical Biology and Structural Biology and Microbes and Disease research groups.

Qualifications

Biography

Prof. Harmer trained for his PhD in X-ray crystallography in the laboratory of Prof. Sir Tom Blundell at the University of Cambridge. He spent three further years in Cambridge as a postdoctoral research associate working on growth factors and enzymes, and learning biophysical techniques. He then worked for AstraZeneca in Mölndal, Sweden as a structural biologist for one year to gain an understanding of industry. He joined the University of Exeter in 2007 and established a research programme on the structure and function of enzymes in biological cascades. In 2017 he was amongst the first PIs to join the Living Systems Institute.

Qualifications

2000-2004 PhD Biochemistry, University of Cambridge
1999-2000 MSci Natural Sciences, University of Cambridge
1996-2000 2003 MA Natural Sciences, University of Cambridge

Career

2018-present Associate Professor in Biochemistry, Living Systems Institute, University of Exeter, UK

2012-2018 Senior Lecturer in Structural Biochemistry, School of Biosciences, University of Exeter, UK
2007-2012 Lecturer in Structural Biochemistry, School of Biosciences, University of Exeter, UK
2006-2007 Senior Scientist, AstraZeneca R&D Molndal, Sweden
2003-2006 Research Associate, Department of Biochemistry, University of Cambridge, UK

Links

• My research page at the Living Systems Institute

Research group links

• Microbial Evolutionary Ecology
• Biochemistry and Molecular Microbiology

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Research

Research interests

Enzyme cascades and their applications

Our work aims to understand enzymes as biological catalysts. We seek to understand enzymes individually from a structure-function perspective: we determine the structure of enzymes and align this to function using enzyme assays and complementary methods. Our aim is to understand how enzymes achieve rate enhancement, and how this can be modulated for different functions. Where necessary, we are engineering enzymes using ancestral sequence reconstruction to obtain proteins with novel properties. Key example enzymes are carbohydrate active enzymes, carboxylic acid reductases and prolyl-peptidyl isomerases.

Alongside our studies of individual enzymes, we also aim to understand how groups of enzymes work together to achieve larger transformations. Our particular interest is in modelling groups of enzymes to see whether their individual properties explain their behaviour as a group. Building faithful models of enzyme activity is essential for process upscaling to the quantities required for production levels. We use Python, Matlab or R as appropriate to the experimental problem.

Our enzyme studies are being applied to important problems in life and molecular sciences. Current main projects for the group are the biosynthesis of the Coxiella burnetii O-antigen, and enzyme cascades based around carboxylic acid reductases. Coxiella burnetii infects sheep, goats and cattle across the world, causing abortions and stillbirths, and causes a disease called Q fever in humans. We aim to use our understanding of the O-antigen biosynthesis to help develop a vaccine (funding: BBSRC, Dstl). We are also developing enzyme cascades that can be used to synthesise chiral building blocks for drug manufacture with reduced resources and waste streams (funding: BBSRC, GSK).

Research projects

Current key projects include:

1. Coxiella burnetii O-antigen
Q fever is a disease of ruminant domestic animals, and only a few bacteria are necessary to infect humans. The pathogen is found globally, and is economically important as it can cause abortions in domestic animals. My group is investigating the biosynthesis of the O-antigen of C. burnetii. This is the only polysaccharide of this organism, and is an excellent candidate for novel vaccines. This work is undertaken in collaboration with Prof. Rick Titball (Exeter), Dr. Joann Prior (Dstl), Prof. Brendan Wren and Dr. Jon Cuccui (London School of Hygiene and Tropical Medicine), and Prof. Rob Field (John Innes Centre). This work is funded by BBSRC and Dstl.

2. Enzyme cascades for green chemistry

There is an increasing desire to replace organic chemistry methods with enzymes where possible. This reduces the use of polluting chemicals and solvents. Enzymes also offer the opportunity to generate chiral products with high purity. Using a cascade of enzymes offers further opportunities to reduce side reactions, or to minimise the concentrations of less stable intermediates. We are working on cascades based on the carboxylic acid reductases (CAR). These enzymes reduce acid to aldehydes, producing a reactive substrate for further enzymes. We have developed the most thermostable CAR available to date and aim to use this for biocatalysis at higher temperatures. This work is being undertaken in collaboration with Prof. Jenny Littlechild (Exeter) and Dr. Richard Lloyd (GSK), and is funded by GSK and BBSRC.

3. Chaperones of B. pseudomallei. 
Chaperones are essential for the correct folding of many proteins in all organisms, and as such they inevitably contribute to the viability and infectivity of micro-organisms. Moreover, chaperones of the FK-506 binding protein family have been identified as significant virulence factors in a range of micro-organisms. My group is aiming to understand the contribution of chaperones to B. pseudomallei infectivity, and determine the potential for novel antimicrobials. This project is being undertaken in collaboration with Dr. Andy Scott (Dstl), Dr. Mitali Sarkar-Tyson (University of Western Australia) and Prof. Ulrike Holzgrabe (University of Würzburg), and is funded by Dstl. It has received further funding from Interreg.

Research grants:

BBSRC - Glycoengineering of Veterinary Vaccines (CoI, Exeter co-PI)

BBSRC/Dstl - Defining the O-antigen biosynthetic pathways in zoonotic Coxiella burnetii (PI)

BBSRC/GSK - Synthetic biology for green chemistry: Building in vivo enzymatic cascades using Carboxylic acid reductases (CARs) – (PI)

BBSRC/ERAnet - HotSolute - Thermophilic bacteria and archaeal chassis for extremolyte production (CoI with Jenny Littlechild)

Research networks

Current external collaborators include Dr. Joann Prior, Dr. Andy Scott (Dstl); Professor Rob Field (University of Manchester); Prof. Brendan Wren and Dr. Jon Cuccui (London School of Hygiene and Tropical Medicine); Prof. Ulrike Holzgrabe (University of Würzburg); Dr. Mitali Sarkar-Tyson (University of Western Australia); Dr. Jiayun Pang (University of Greenwich); Dr. Richard Lloyd (GSK Stevenage).

Links

• ResearchGate profile

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Publications

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External Engagement and Impact

Committee/panel activities

Research Council Committees

BBSRC Panel D Core Member (since 2015)
BBSRC Pool of Experts (2014-2015)

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Teaching

Modules

2023/24

Information not currently available

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Supervision / Group

Postdoctoral researchers

Postgraduate researchers

Alumni

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