Repurposing metalloenzymes for the conversion of biomass

Background

The sustainable use of biomass is one of the great challenges of our age. For instance, the ability to generate bioethanol from non-food biomass, eg cellulose and some industry waste, would transform the use of biofuels. However, the issue is that these materials are hard to break down into the fermentable sugars, making their use difficult.

Several methods have been used to overcome the resistance of biomass to break down. These include gasification, pyrolysis and biochemical conversion using enzymes. Of these methods, the use of naturally-occurring enzymes is perhaps the most promising.  

Nature has developed a wide range of enzymes that are capable of deconstructing biomass. These include ligninases and cellulases. While most of these enzymes break down the polysaccharides using hydrolytic catalysis, some use an oxidative mechanism where oxygen from the atmosphere is activated to form a very reactive species capable of breaking the chemical bonds within biomass. Often these enzymes are metal-containing enzymes, usually with copper at their active sites. An example is the lytic polysaccharide monooxygenase (LPMO) class of enzymes.

Objectives

This project seeks to use enzymes in a wholly different way to break down lignocellulosic biomass. Building on the lab’s extensive experience of LPMO biochemistry, we seek to repurpose these enzymes not to break down biomass oxidatively, but to break it down reductively. This will be achieved by taking known LPMOs and performing site-directed-mutagenesis experiments on them, such that they will be able to coordinate a metal ion other than Cu at their active sites. The new metal will be able to activate reducing agents to cleave the bonds in biomass.

Experimental Approach

The key techniques used in the project will be: protein synthesis, site-directed-mutagenesis, evolution-directed-mutagenesis, EPR spectroscopy, protein structure determination using X-ray diffraction and activity analysis using both mass spectrometry and chromatographic techniques. Notably, the student will be expected to examine existing LPMO structures and then suggest mutants that could be prepared, such that the mutant would be capable of coordinating to a metal ion other than Cu. Accordingly, the student will also perform metal binding studies through the use of calorimetry and spectroscopy.

Novelty

While LPMOs are well-known in the world of biofuel production, the enzymes and the reductive methods proposed in this project are wholly new, and this approach to the break down of biomass has not been tried before.  

Training 

The principal training the student will receive will be in advanced biochemical techniques, including protein production using bacterial and eukaryotic expression systems. The student will also be trained in the determination of protein structure using X-ray diffraction and will therefore be trained in crystallisation techniques alongside training in protein structure solution and refinement. Necessarily, the student will also be trained in the basics of metal coordination chemistry, especially in the structures of metal complexes and their associated spectroscopy. The last of these includes EPR spectroscopy and X-ray absorption spectroscopy.  

All Chemistry research students have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills: https://www.york.ac.uk/chemistry/postgraduate/training/idtc/ 

The Department of Chemistry holds an Athena SWAN Gold Award and is committed to supporting equality and diversity for all staff and students. The Department strives to provide a working environment which allows all staff and students to contribute fully, to flourish, and to excel: https://www.york.ac.uk/chemistry/ed/  

For more information about the project, click on the supervisor's name above to email the supervisor. For more information about the application process or funding, please click on email institution

This PhD will formally start on 1 October 2023. Induction activities may start a few days earlier.

To apply for this project, submit an online PhD in Chemistry application: https://www.york.ac.uk/study/postgraduate/courses/apply?course=DRPCHESCHE3