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AI-assisted approaches to developing a ‘nylonase’ enzyme for recycling waste plastics

   Department of Chemistry

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  Dr Andrew Carnell, Prof D J Rigden  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Applications will be accepted until a suitable candidate is appointed, early applications are therefore encouraged.  

A fully funded PhD studentship is available to work on a multidisciplinary project led by Dr Andrew Carnell to tackle global waste plastic issues by designing novel enzymes for their degradation and recycling. Moving towards a circular economy requires rapid progress to develop energy efficient new technologies for recycling waste plastics. In this project we take a new approach to develop enzymes for nylon degradation, using a combination of computational biology and directed evolution. Using primary protein sequence data we will build and screen cutting edge 3D-computational models (AlphaFold2) of known and previously unexplored hydrolase enzymes for appropriate substrate binding sites and catalytic architecture. Docking of nylon oligomers with these models will allow identification of the best starting points for new enzymes that bind nylon and stabilise the transition state for amide bond cleavage. Molecular dynamics simulations will help assess substrate binding and the spatial arrangement for key interactions in the active site to facilitate efficient catalysis. The predicted enzymes will be expressed and tested on model polyamides and on post-consumer nylon to provide validation and further refinement of the models. Successful variants will identify key residues that may be further mutated to find optimal combinations of mutations to provide the required ‘nylonase’ activity. 

This highly multi-disciplinary project will combine biocatalysis, molecular biology and computational biology. You will receive training in all aspects of the project in world class research environment with access to state-of-the-art facilities for biocatalysis (Dr Carnell, Department of Chemistry), computational Biology (Professor Daniel Rigden, Institute of Systems, Molecular and Integrative Biology) and gene synthesis and screening (Liverpool GeneMill). You will work within a highly motivated group engaged in the development of enzymes for industrial biotechnology and to address current challenges presented by the global waste plastics issue. You will present your work at regular interdisciplinary research group meetings and at national or international conferences.

You should hold or expect to hold a first class or high 2:1 or equivalent in chemistry (MChem), biochemistry, molecular biology or a related subject (Masters or BSc). Experience of lab work in molecular biology, protein biochemistry or computational biology would be an advantage but not a pre-requisite. 

Informal enquiries can be made to Dr Andrew Carnell ([Email Address Removed]).

To apply for this opportunity, please visit:  and click on the 'Ready to apply? Apply online' button, to start your application.  Please ensure you note the subject title AI-assisted approaches to developing a ‘nylonase’ enzyme for recycling waste plastics, and reference CCPR044 on your online application form.

This position is available from 1st October 2022  

Funding Notes

The funding for this position is from an EPSRC DTP studentship. The eligibility details of both are below.
EPSRC eligibility: Applications from candidates meeting the eligibility requirements of the EPSRC are welcome – please refer to the EPSRC website:
The award will pay full tuition fees and a maintenance grant for 3.5 years. The maintenance grant is £15,609 pa for 2022/23, with the possibility of an increase for 2023/24


Recent publications from our group in the Industrial Biotechnology/Bioplastics area:
1. “Carboxyl Methyltransferases: Natural Functions and Potential Applications in Industrial Biotechnology” L. C. Ward,* H.V. McCue, A.J. Carnell,* ChemCatChem 2021, 13, 121–128.
2. “PET hydrolysing enzymes catalyse bioplastics precursor synthesis under aqueous conditions” D. Parisi, C. Riley, A. S. Srivastava, H. V. McCue, J. R. Johnson, A. J. Carnell,* Green Chem. 2019, 21, 3827–3833.
3. "The continuous oxidation of HMF to FDCA and the immobilisation and stabilisation of periplasmic aldehyde oxidase (PaoABC)", S. M. McKenna, P. Mines, P. Law, K. Kovacs-Schreiner, W. R. Birmingham, N.J. Turner, S. Leimkühler, A. J. Carnell,* Green Chem., 2017, 19, 4660-4665.
4. “Enzyme Cascade Reactions: Synthesis of Furandicarboxylic Acid (FDCA) and Carboxylic Acids using Oxidases in Tandem” S. McKenna, S. Leimkühler, S. Herter, N. J. Turner,* A. J. Carnell,* Green Chem. 2015, 17, 3271-3275.
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