Dr Patricia Rodriguez-Macia

Supervisor Details

Contact Details

School of Chemistry, University of Leicester

Scientific Background

Research Interests

Our research focuses on biocatalysis, to learn from and mimic nature at the intersection of chemistry, biology and materials science. The overall goal is to establish fundamental chemical insight for supporting future renewable energy technologies, i.e. to develop efficient catalysts and new catalytic routes for energy conversion reactions based on abundant and cheap metals. Energy converting enzymes are capable of using earth-abundant metals in their active site to perform key chemical reactions (e.g. reduction of nitrogen to ammonia, oxidation/production of H2, and reduction of CO2 to CO and formate) in a very efficient manner. These reactions still represent big challenges for chemistry, and it is often difficult to synthesise catalysts with efficiencies similar to the natural enzymes for these energy conversion reactions.

Our research combines the fields of biology, synthetic chemistry and physical chemistry to study energy converting metalloenzymes and understand the chemistry at their active site and the interplay between active site and protein matrix at the molecular level. Solutions to the energy problem require a fundamental understanding of how energy conversion processes happen in nature and of what it takes to make catalytic systems with performances and efficiencies as high as the systems existing in nature (i.e. energy converting metalloenzymes), while maintaining the relative simplicity of a molecular catalyst or catalytic material. Thus, our lines of research are dedicated to translating the understanding of complex biocatalytic processes into catalyst design for technological applications.

Metalloenzymes for energy conversion: study and exploitation of natural catalytic systems. This line of research focused mainly on hydrogenases ([FeFe] hydrogenases, but also [NiFe] hydrogenases) and CO dehydrogenases (CODHs). Hydrogenases are the most efficient H2 conversion catalysts in nature. They are able to reversibly interconvert H2 with protons and electrons at very high rates, under ambient conditions and without energy waste by utilising earth-abundant metals like Ni and/or Fe in their active site. On the other hand, CODHs catalyse the reversible interconversion of CO2 and CO in nature at very high rates, with minimal energy waste and using a Ni-Fe active site. To study the catalytic mechanism and the secondary-sphere interactions in these fascinating metalloenzymes, we apply complementary spectroscopic techniques alongside electrochemistry.
Semi-synthetic hydrogenases. This second line of research combines synthetic chemistry with molecular biology. [FeFe] hydrogenases from various organism are recombinantly produced in E. coli as pro-enzymes in high yields (i.e. apo-enzyme lacking the active site). By using engineered affinity tags, high purity is achieved in just 1-purification step. The active holo-hydrogenase is then generated by mixing the pro-enzyme with synthetic active-site mimics. The high yield and purity in which these semi-synthetic enzymes can be produced facilitate advanced spectroscopic and spectroelectrochemical studies. We are interested in using new cofactor precursors to generate chemically altered active-site variants to fine-tune the active-site chemistry and the catalytic properties of the enzyme. This approach can be also used for rapid screening of mutant libraries to generate semi-synthetic hydrogenases with desirable features such as oxygen tolerance, enhanced catalytic performance, or enhanced temperature sensitivity.

Supervision Style

In three words or phrases: Technique-orientated, supportive, guiding.

Provision of Training

As an early career researcher, I like to be in the lab and train the students myself. I first focus on giving detailed training on the techniques we are going to use and on introducing the targeted system/s. In this way, together with the student, a research plan is developed, leading to more independence later but always under my guidance.

Progression Monitoring and Management

I like to be kept up to date. We will have weekly progress meetings to discuss project progress, identify challenges and troubleshoot problems. I am always available to help the student and to answer any questions. I like to give flexibility and I am always open to the student’s suggestions.

Communication

I am very approachable and have an open-door policy. I work flexibly and sometimes I email out of hours, however, I do not expect my students to reply immediately. I encourage them to have a healthy work/life balance and I am always happy to discuss any issues and to provide scientific and pastoral support.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD study

At least once per week

In year 2 of PhD study

At least once per week

In year 3 of PhD study

At least once per week

The meetings will be face to face and I am usually contactable for an instant response (if required) on every working day.

Working Pattern

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings), I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 week’s notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

New Approaches to Investigate Substrate Binding and Reaction Mechanism of CO2-reducing Enzymes

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

New Approaches to Investigate Substrate Binding and Reaction Mechanism of CO2-reducing Enzymes

Secondary Supervisor(s): Dr Emma L Hesketh

University of Registration: University of Leicester

BBSRC Research Themes: Renewable Resources and Clean Growth (Bio-energy, Industrial Biotechnology)

Project Outline

Global warming caused by rising levels of greenhouse gases, especially CO₂ is a major global concern. Sequestration and reduction of atmospheric CO₂ is central for limiting global warming and providing a non-petrochemical route to chemical building blocks such as CO, a key feedstock for use in downstream industrial applications. Therefore, it is essential to develop eco-friendly and cost-effective catalysts for CO₂ conversion into chemical feedstocks, i.e. catalysts based on abundant and cheap metals. Nevertheless, catalysts for CO₂ reduction, particularly in aqueous media, remain a major challenge to design mainly due to selectivity problems. To help design and develop efficient and selective catalysts for CO₂ conversion, a fundamental understanding of how CO₂ fixation happens in nature is required in order to understand how we can make synthetic catalytic systems with activities, selectivity and efficiencies as high as the biocatalysts. As such, studying biocatalytic CO₂ reduction offers enormous potential for guiding the design of novel catalysts needed for a sustainable circular energy economy to help close the CO₂ cycle.

Only two enzymes are known to catalyse the direct reduction of CO₂ in nature: CO dehydrogenases (CODH), which catalyse the reduction of CO₂ to CO and formate dehydrogenases (FDH), which catalyse the reduction of CO₂ to formate (HCOO^-).Both of these enzymes participate in the Wood-Ljungdahl pathway, a major circular CO₂ fixation pathway in anaerobic organisms, and work under physiological conditions with very high activities, selectivity and reversibility/efficiency. Ni-containing CODHs contain a unique [Ni–4Fe–4S] active site, while metal-dependent (Mo- or W-containing) FDHs active site contains a hexacoordinated metal ion (Mo or W) in a distorted triangular prismatic geometry with two dithiolene ligands, a cysteine (Cys) or selenocysteine (SeCys) residue and an inorganic sulfide that is necessary for activity. Apart from the active site, both enzymes contain gas channels for the substrates (i.e. CO₂ and CO) to diffuse in and out the active site, proton pathways and iron-sulfur clusters as electron relays.

Objectives

This exciting project will focus on the structural and biophysical characterisation of natural CO₂-reducing enzymes, CODH and FDH enzymes, by developing new approaches to study substrate binding at the active site and its mechanism of conversion. Structural characterisation under different conditions will be achieved via cryo-EM. New approaches for cryo-EM grid preparation under anaerobic and substrate-controlled conditions will be developed with the long-term goal of coupling cryo-EM with electrochemical control to poise the enzymes into well-defined catalytic states in the presence/absence of the substrate. Cryo-EM will be complemented with electrochemistry and spectroscopic and computational methods to gain a holistic understanding of how CO₂ binds at the active site of these enzymes and is converted to C1-products.

This is an interdisciplinary project encompassing molecular and structural biology, chemistry and biophysics. Novel methodologies and approaches will be developed to provide crucial insights into these fascinating CO₂-reducing enzymes, and to reveal design principles toward the development of (bio)hybrid catalysts for CO₂ reduction.

Methodology

Molecular biology will be used to introduce the CODH and FDH genes into E. coli to recombinantly produce and isolate the desire enzymes. Biochemical characterisation will be performed in parallel to structural characterisation via cryo-EM. The enzymes will be prepared in different catalytic states in the presence and absence of the substrate and their cryo-EM structures will be solved. The catalytic activity of the produced enzymes will be assessed using coupled assays and electrochemistry. To stabilise the substrate-bound state, the enzymes will be engineered by site-directed mutagenesis.

Techniques

Techniques that will be undertaken during the project:

Molecular biology techniques (this includes heterologous protein expression in E. coli, protein purification, genetic modification via site-directed mutagenesis, subcloning, in vitro reconstitution of proteins)

Spectroscopy: infrared (IR) spectroscopy and electron paramagnetic resonance (EPR)

Analytical techniques: Electrochemistry

Structural biology: crystallisation, Cryo-EM, ab initio structure prediction

References

Y. Basak et al., Angew Chem Int Ed Engl 2023, 62, 32, e202305341.

Y. Basak et al., ACS Catal. 2022, 12, 20, 12711–12719.

J. Park et al., Scientific Reports 2024, 14, 3819.

Previous Projects (2024-25)

Primary supervisor for:

Exploring natural and de novo protein scaffolds for the development of new semi-synthetic and artificial metalloenzymes for sustainable chemistry

Previous Projects (2023-24)

Primary supervisor for:

Dual approach to develop new catalytic systems for energy conversion: exploring natural and de novo protein scaffolds combined with synthetic cofactors