The Project

A defining characteristic of life is the requirement of energy from an external source; we eat, plants absorb light. To maximize the energy gained from the food that we and all oxygen-breathing organisms consume, oxygen is converted to water as a final step and carbon dioxide is released. The oxygen in this equation arises from plants as they convert water, carbon dioxide and light, into oxygen and fuel. This cycle is not merely an auspicious result of billions of years of evolution. The molecular events that allow the processes of respiration and photosynthesis to happen are connected in deep ways, down to shared structures, molecules, and mechanisms.

Natural modular oxidoreductases support electron transfer over long distances and catalysis

At their most basic, respiration and photosynthesis are Nature’s way to capture and convert energy from one form to another. To do this, Nature has evolved complex structures, termed oxidoreductases, that bind molecules that aid in this conversion. These molecules can both absorb light, imparting plants with their colours, and take and give electrons. The oxidoreductases have evolved to take energy from external sources and convert it into forms that can be used by living organisms to grow and survive. The evident complexity of this process belies a central feature of the oxidoreductases involved: evolution has yielded structures that are built from repeats of relatively simple modules. All of respiration and photosynthesis are built on these repeating modules. But despite nearly a century of investigation, where we have outlined how respiration and photosynthesis work in fine detail, we remain unable to construct our own models of these processes. This naturally leads to a question of whether we really understand how these processes occur.

Here we have assembled a team of researchers from multiple academic institutions and disciplines to address deficiencies in our knowledge, with the unified target of building completely new oxidoreductases from scratch. Through this work we will fill holes in our understanding of how Nature captures and converts energy.

Our work begins by combining powerful computational techniques that allow us to design and construct oxidoreductases with tailor made functions. Within a virtual reality framework that we are developing for this project, we will work together in a shared digital space to construct molecular binding sites, alter how molecules take and give electrons or catalyse reactions, and create oxidoreductase modules that, taking inspiration from Nature, we will join to produce more complex functions. With these designs, we will use an iterative ‘build-test-learn’ approach to construct new oxidoreductases that match the activities and actions of those Nature uses in respiration and photosynthesis. By pulling together our expertise in computational biophysical methods, oxidoreductase engineering, modular structure creation, molecular binding site assembly and their chemistry, and the analysis of very fast oxidoreductase functions, our team stands to make a substantial leap in our understanding of how to construct new oxidoreductases that has, so far, remained beyond our grasp.

The principles we establish through this work will help us to better understand the oxidoreductases of respiration and photosynthesis, finally clarifying architectural features that are essential for their assembly and function that have remained opaque for over a century. With our new sets of design principles, we will be able to create oxidoreductases that fulfil our needs in bioscience and biotechnology, from the creation of single structures that produce fuels from light, water and carbon dioxide akin to photosynthesis to biosensors that detect toxins in the environment or signs of disease.

The Team

University of Bristol

J. L. Ross Anderson
Project Lead, and PI
Adrian J. Mulholland
Protein Dynamics Lead, and Co-I
Paul Curnow
Membrane Protein Design Lead, and Co-I
Thomas A. A. Oliver
Multi-dimentional Spectroscopy Lead, and Co-I
Fabio Parmeggiani
Computational Design Lead, and Co-I
Sofia Oliveira
Computational Protein Analysis, and Res-Co-I

University of Portsmouth

Bruce R. Lichtenstein
Protein Chemistry and Design Lead, and Co-I

University of East Anglia

Julea Butt
Electron Transport Lead, and Co-I

University College London/Birkbeck

Amadine Marechal
PCET Lead, and Co-I

The Positions

University of Bristol

Postdoctoral Research Associate #1 — Protein Design Group (Ross Anderson Lead)

The Role:
A postdoctoral research position in de novo protein and enzyme design is available for 36 months in the School of Biochemistry at the University of Bristol, supported by the BBSRC Grant BB/W003449/1, Creating and comprehending the circuitry of life: precise biomolecular design of multi-centre redox enzymes for a synthetic metabolism.

The postdoctoral research associate will work on designing soluble redox proteins and assemblies for electron transfer, light harvesting and catalysis, and will initially focus on the construction of discrete cofactor-binding modules to serve as a platform for more complex binary and chain-containing architectures. They will also work closely with other researchers on the project, combining expertise in membrane protein design, biomolecular simulation, chemical synthesis and spectroscopy towards the construction of artificial respiratory complexes and functional components for bionanotechnology.

More information on Ross Anderson’s group can be found at: https://theandersonlab.com

What will you be doing?
You will work on the de novo design and experimental characterisation of soluble redox and light harvesting proteins and enzymes in the School of Biochemistry at the University of Bristol, collaborating closely with the multidisciplinary consortium across four institutions. You will apply a modular, computational approach to design and assemble soluble single and multi-centre redox proteins and enzymes for long range electron and energy transfer, catalysis and broadband light harvesting. You will use computational tools to design functional modules (e.g. Rosetta, Molecular Dynamics, Continuum Electrostatics Calculations), standard molecular biology techniques to express and purify your designs, and an array of biophysical techniques to verify and study structure and function (e.g. visible/CD/fluorescence/NMR spectroscopies, protein electrochemistry, stopped flow spectrophotometry, X-ray crystallography, cryo-EM microscopy, mass spec).

You should apply if:
This position would best suit a talented and motivated early career researcher with a PhD in Biochemistry or Chemistry, and, in particular, those with experience in de novo protein design or protein engineering using computational methods. Some or all of the following skills would be an advantage: experience running Molecular Dynamics simulations and/or Rosetta protein design software; demonstrated skills in molecular biology, protein expression/purification, and structural and biophysical protein analysis; knowledge of, or experience with, cofactor-containing proteins and enzymes; ability to communicate complex information clearly and accurately in English, both in written and oral forms; ability to work independently and as part of a team.

Informal Inquiries for PDRA #1 can be directed to: ross.anderson@bristol.ac.uk

Postdoctoral Research Associate #2 — Membrane Protein Design Group (Paul Curnow Lead)

The Role:
A postdoctoral research position in de novo membrane protein design is available for 36 months in the School of Biochemistry at the University of Bristol, supported by the BBSRC Grant BB/W003449/1, Creating and comprehending the circuitry of life: precise biomolecular design of multi-centre redox enzymes for a synthetic metabolism.

The postdoctoral research associate will work on designing cofactor-binding membrane proteins and assemblies for electron transfer, light harvesting and catalysis. The ambition is to establish a suite of modular designs that can interact with soluble enzymes to create more complex binary and chain-containing architectures. They will also work closely with other researchers on the project, combining expertise in membrane protein design, biomolecular simulation, chemical synthesis and spectroscopy towards the construction of artificial respiratory complexes and functional components for bionanotechnology and bioengineering.

More information on Paul Curnow’s research can be found at https://tinyurl.com/pcurnow.

What will you be doing?
The postdoctoral researcher will use computational methods, specifically the membrane extension of Rosetta and Molecular Dynamics, to design a range of single and multi-centre membrane redox proteins that can be employed in long range electron and energy transfer, catalysis and broadband light harvesting. They will then use standard molecular biology techniques to express and purify their designs in recombinant cell systems. This will likely involve the screening of different solubilising detergents to obtain stable, soluble membrane proteins in vitro. An array of biophysical techniques will then be employed to verify and study structure and function (e.g. visible/CD/fluorescence/NMR spectroscopies, protein electrochemistry, stopped flow spectrophotometry, X-ray crystallography, cryo-EM microscopy, mass spectrometry).

You should apply if:
This position would best suit a talented and motivated early career researcher with a PhD in Biochemistry or Chemistry. Prior experience in computational membrane protein design (RosettaMP, Molecular Dynamics) would be an advantage as would knowledge of, or experience in, bioenergetics. The candidate should be able to demonstrate skills in molecular biology, protein expression/purification, and structural and biophysical protein analysis. Preferred candidates are likely to be familiar with applying these methods to integral membrane proteins, and relevant skill sets – for example, experience in detergent screening methods – would be advantageous. They should also have the ability to communicate complex information clearly and accurately in English, both in written and oral forms; and the ability to work both independently and as part of a research team.

Informal Inquiries for PDRA #2 can be directed to: p.curnow@bristol.ac.uk

Postdoctoral Research Associate #3 — Multi-dimentional Spectroscopy Group (Tom Oliver Lead)

The Role:
A postdoctoral research associate position in experimental studies of ultrafast photobiology is available in the School of Chemistry at the University of Bristol, supported by the BBSRC Grant BB/W003449/1, Creating and comprehending the circuitry of life: precise biomolecular design of multi-centre redox enzymes for a synthetic metabolism.

The postdoctoral research associate will work on the following objectives of the project: (i) assemble a new commercial ultrafast laser system to probe photoinduced dynamics spanning 100 femtoseconds to 1 millisecond; (ii) determine the rates of photoinduced electron transfer between multiple moieties in designer proteins; (iii) elucidate the ultrafast electronic energy transfer pathways between chromophores in specially tailored photoactive proteins using 2D electronic spectroscopy.

Further information on Tom Oliver’s group can be found at: www.taaoliver.com

What will you be doing?
The postdoctoral researcher will undertake ultrafast laser laboratory-based studies in the School of Chemistry at the University of Bristol, collaborating closely with the multidisciplinary consortium across four institutions. They will contribute to the construction of transient absorption and transient infrared experiments using a commercial dual-amplified ultrafast laser system and optical parametric amplifiers to probe dynamics between 100 fs and 1 ms. The appointee will also use an established 2D electronic spectroscopy experiment to monitor ultrafast energy transfer reactions occurring on 10 fs – 200 ps timescales. The rate constants determined from ultrafast studies for energy and electron transfer will be used to identify bottlenecks or potential deficiencies in the synthetic proteins and be provide critical feedback in the iterative protein design process. Other techniques will include: 2D electronic-vibrational spectroscopy and time-resolved fluorescence spectroscopy.

You should apply if:
The position would best suit a talented and motivated early career researcher with a PhD in Physical Chemistry or Physics and experience in experimental research using ultrafast laser spectroscopy. Some or all of the following skills and experience would be an advantage: use of ultrafast Yb:KGW or Ti:sapphire amplifiers and optical parametric amplifiers; knowledge of non-linear optics; development of Labview control software; experience with analysis of time-resolved spectra; handling photoactive proteins or biomolecules; ability to communicate complex information clearly and accurately in English, both in written and oral forms; ability to work independently and as part of a team.

Informal Inquiries for PDRA #3 can be directed to: tom.oliver@bristol.ac.uk

A PDRA at Portsmouth will be advertised soon!

Funding Provided By: