Quantum Biology to Enhance CO2 Fixation

Despite the billions of tonnes of CO2 photosynthetic organisms fix every year, they do not have the capacity to absorb the quantities released into the atmosphere from human combustion of fossil fuels for energy. Progress must be made to assist carbon fixing autotrophs. One potential method could be the creation novel fixation pathways which, with further manipulation, could produce value-added multi-carbon products using CO2 as the feedstock. This would be a huge step towards a true sustainable, circular economy.

RuBisCo, the most abundant enzyme on the planet, is the carbon fixing enzyme in the Calvin-Benson cycle and fixes the majority of CO2. It allows plants to synthesise the multimeric carbon molecules they need for growth using carbon dioxide as the most basic building block. Unfortunately, reaction rates are very low and are further hampered by a side reaction with O2.

In a bid to speed up the carbon fixation process, Schwander et al., developed the CETCH cycle: the first synthetic carbon fixing cycle based around a recently discovered class of carboxylases which have the fastest reaction rates of all known carboxylases. Using this cycle, CO2 can be fixed up to 40 times faster than by using the Calvin-Benson cycle. To achieve this, some of the enzymes have been engineered to ensure continuous cycling and eliminate deleterious side products. We propose to build on this work by analysing the enzymes in the cycle and rationally improving them using machine learning.

Innovations such as these could be useful to the bioeconomy providing technology to use CO2 as a feedstock to produce useful chemicals. Combining the cycle with a photosynthetic energy source means that the whole process could be solar powered; a prototype has been demonstrated to have potential by Miller et al.

Proposed solution and methodology
We propose to develop a systematic workflow to characterise enzymes, glean insights into their mechanisms and then apply machine learning to suggest beneficial mutations in a data-driven manner. This workflow will be developed and tested using enzymes from the CETCH cycle in the hopes of contributing to the field of carbon fixation.

Characterising the target enzyme will give insights into the mechanism which will assist with the enhancement of enzymes by rational design. This can be achieved with a combination of molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) methods which predict what conformations are sampled by the enzymes and where interactions occur.

To assess the contribution of co-factors and the surrounding environment to reactivity and stability MD simulations will be performed. Quantum chemical models will be used to determine the feasibility of the reaction independently providing a baseline for how the reaction is likely to progress. These calculations also allow interrogation of the active site particularly in terms of bonds breaking and forming and how specific residues contribute to the mechanism.

The hybrid QM/MM model will allow for a deeper exploration of the reaction in the context of the entire enzyme. Reactivity descriptors will be derived from this model to provide metrics that will be used to develop an artificial intelligence model for the prediction of directed changes to improve enzyme function. The resultant mutants can then be subjected to the same methods as the wild type protein to assess stability and changes to enzyme efficiency.

Success will provide a novel method to design enzymes in silico for any challenge. Leaving the rational design for a computer to discover may throw up curious, previously unconsidered proposals. As a model system, the CETCH cycle for carbon fixation will be used as an enzyme source due to its importance to synthetic carbon fixation progress and potential applications in the bioeconomy.

This CDT will deliver impact aligned to the following agendas:

People
A2P will provide over 60 PhD graduates with the skill sets required to deliver innovative sustainable products and processes into the UK chemicals manufacturing industry. A2P will inspire and develop leaders who will:
- understand the needs of industrial end-users;
- embed sustainability across a range of sectors; and
- catalyse the transition to a more productive and resilient UK economy.

Economy
A2P will promote a step change towards a circular economy that embraces resilience and efficiency in terms of atoms and energy. The benefits of adopting more sustainable design principles and smarter production are clear. For example, the global production of active pharmaceutical ingredients (APIs) has been estimated at 65,000-100,000 tonnes per annum. The scale of associated waste is > 10 million tonnes per annum with a disposal cost of more than £15 billion. Consequently, even a modest efficiency increase by applying new, more sustainable chemical processes would deliver substantial economic savings and environmental wins. A2P will seek and deliver systematic gains across all sectors of the chemicals manufacturing industry. Our goals of providing cross-scale training in chemical sciences with economic and life- cycle awareness will drive uptake of sustainable best practice in UK industry, leading to improved economic competitiveness.

Knowledge
This CDT will deliver significant new knowledge in the development of more sustainable processes and products. It will integrate the philosophy of sustainability with catalysis, synthetic methodology, process engineering, and scale-up. Critical concepts such as energy/resource efficiency, life cycle analysis, recycling, and sustainability metrics will become seamlessly joined to what is considered a 'normal' approach to new molecular products. This knowledge and experience will be shared through publications, conferences and other engagement activities. A2P partners will provide efficient routes to market ensuring the efficient translation and transferal of new technologies is realised, ensuring impact is achieved.

Society
The chemistry-using industries manufacture a rich portfolio of products that are critical in maintaining a high quality of life in the UK. A2P will provide highly trained people and new knowledge to develop smarter, better products, whilst increasing the efficiency and sustainability of chemicals manufacture.
To amplify the impacts of our CDT, effective public engagement and technology transfer will become crucially important. As a general comment, 'sustainability' styled research is often regarded in a positive light by society, however, the science that underpins its effective implementation is often poorly appreciated. The University of Nottingham has developed an effective communication portfolio (with dedicated outreach staff) to tackle this issue. In addition to more traditional routes of scientific communication and dissemination, A2P will develop a portfolio of engagement and outreach activities including blogs, webpages, public outreach events, and contribution of material to our award-winning YouTube channel, www.periodicvideos.com.

A2P will build on our successful Sustainable Chemicals and Processes Industry Forum (SCIF), which will provide entry to networks with a wide range of chemical science end-users (spanning multinationals through to speciality SMEs), policy makers and regulators. We will share new scientific developments and best practice with leaders in these areas, to help realise the full impact of our CDT. Annual showcase events will provide a forum where knowledge may be disseminated to partners, we will broaden these events to include participants from thematically linked CDTs from across the UK, we will build on our track record of delivering hi-impact inter-CDT events with complementary centres hosted by the Universities of Bath and Bristol.