CryoEM and biochemistry-led discovery of protein nanopores for biotechnology

This project will focus on Biochemical and Structural Biology (cryoEM) studies of natural pore-containing proteins and translating the research findings into applications in nanobiotechnology. During the last few years, proteins containing pores of 1-2nm in diameter have allowed to make rapid advances in nucleic acid sequencing, advancing the science and promising to revolutionise nanosensing technology to enable novel applications in healthcare, biosafety and forensic science. However, development and application of this technology is limited by the availability of different types of protein nanopores that are robust, easy to engineer and produce.

Portal proteins from large dsDNA viruses, such as bacteriophages as well as human and animal herpes viruses, are natural biological nanopores containing a channel through which the DNA genome is translocated into the preformed viral capsid during virus particle assembly [1]. The portal protein also serves as a central component of an ATP-driven DNA packaging machine, which is the most powerful biological motor found on our planet: it can work against a huge pressure (up to 10 x that contained in a champagne bottle) that builds up inside the capsid when DNA is packaged at crystalline density. Portal proteins from bacteriophages found at extreme environments, such as deep-sea vents or thermal springs, are intrinsically robust and resistant to the high temperature and pressures of the natural environment. These stable and tractable proteins are promising to significantly expand the variety of protein nanopores available, to create a toolbox of nanopore scaffolds with varying properties that can be ’tuned’ for different biotechnological applications [2,3].

This project provides a unique opportunity for an international interdisciplinary collaboration spanning molecular biology, protein biochemistry, structural biology and single molecule biophysics, at the interface of academic (University of York, UK) and industrial (Dreampore, Paris, France) research. Portal proteins from thermophillic viruses will be structurally (Cryo-EM) and biophysically (NanoDSF, NanoDLS) characterised at York to identify those that are stable and assemble with defined geometries. The geometric and physiochemical properties of the internal channel will be engineered for different sensing applications before characterisation as single molecule nanopore sensors, using sensitive, high band-width electronic detection equipment during an 8-month placement with Dreampore, an international leader in the development of peptide and protein biosensors. Due to the nature of unique collaboration, the project will provide opportunities for the student to work at the interface of highly competitive areas of research: structural biology using Cryo-EM, experiments at the single molecule level using nanopores, protein sequencing and detection of biomarkers.

You will work in a dynamic environment, with internationally recognized academics and entrepreneurs. Dreampore offers opportunities to learn to valorize the industrial potential of your research and to participate in cross-disciplinary collaboration from bench to bedside. At York, you will participate in a world class academic research program. You would gain invaluable experience for a research and development career in academia, industry or with a start-up company.

This prestigious Doctoral Training Partnership (DTP) brings together the very best molecular, chemical and cellular bioscience research across the White Rose Consortium of Universities (Leeds, Sheffield and York), which maps on to the research themes of the BBSRC. Students benefit from a regional PhD training programme that has interdisciplinary collaboration at its core. Students develop a range of research skills in biological and biochemical areas and are equiped with core mathematical, data analysis and generic professional skills that are necessary for bioscience research in the coming decades.

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/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/. This PhD project is available to study full-time or part-time (50%).

This PhD will formally start on 1 October 2020. Induction activities will start on 28 September.