PhD Research Project

Vacancy Reference Number
University of York & University of Leeds
Closing Date
15 Apr 2021
Fully funded for 3 years with a tax-free annual stipend (UK students only) at the standard Research Council rate (£15,609 for 2021-22), tuition fees and consumables
The PhD will be based at the University of York, Department of Chemistry (Prof. Dessent). Some work may also be carried out in the laboratory of the co-supervisor at the University of Leeds, School of Molecular and Cellular Biology (Prof. Sobott).
3 years

Mapping the Photophysics of Phycobilin Chromophores via Photo Mass-Spectrometry

Background and Objectives

Bilin-binding photoreceptors are light-signalling proteins that mediate a wide range of physiological processes from phototaxis to photosynthesis. They are also promising tunable optical agents for use in optogenetics and super-resolution microscopy, due to the fact that they can exhibit extremely diverse spectral properties covering regions from the near ultraviolet to the far red. The primary photochemical reaction involves photoisomerization of the central C=C double bond in the covalently linked linear tetrapyrole chromophore. However, it is not well understood how the phycobilin architecture affects its photophysical behaviour, and the extent to which an attached protein framework facilitates the bilin photoisomerization dynamics. In this project, we will take a bottom up approach to characterize the intrinsic photophysical properties of phycobilins, as a function of charge state, molecular conformation and domain size, through studying a series of phycobilins as isolated molecular systems in the gas-phase. We will then explore how the protein environment affects the bilin photophysics by studying a series of bilin-binding photoreceptors.

Over recent years, gas-phase studies of photoactive biological molecules including fluorescent proteins and flavins have provided key experimental data on the intrinsic photophysics of such molecules. The Dessent group have developed a series of novel laser-interfaced mass spectrometers for performing such photochemical measurements, allowing photochemical interrogation of mass-selected precursors. This project will offer the student the opportunity to further develop this approach by performing new experiments combining laser photolysis with ion-mobility mass spectrometry, through collaboration with Prof. Frank Sobott, Astbury Centre, University of Leeds.

Experimental Approach

In the first stage of the project, absorption spectra and wavelength dependent photofragments will be acquired using laser-interfaced mass spectrometry within a custom adapted ion-trap mass spectrometer (Bruker Amazon). Ion-mobility mass spectrometry will be used as a complementary technique to characterise the conformational structure of the various phytochromophores. On-line photolysis will be employed to probe solution-phase photoisomerization as a function of phytochrome structure. In the second stage, the ion-mobility mass spectrometer, IM-MS (Waters Synapt) will be adapted to allow photolysis within the trap, traveling wave cell, or transfer cell using a diode laser, allowing the measurement of photodynamics associated with individual conformational isomers of the phytochromophores. This will provide a directly link to the measurements made in the laser-interfaced mass spectrometer, clarifying the extent to which these results are complicated by the presence of multiple isomers. In the final stage, the experiments will be extended to bilin-binding photoreceptors, to probe the extent to which the photophysics changes when the chromophores are associated with a protein. Depending on progress, there will also be an opportunity for the student to conduct experiments in the Photochemistry Laboratory through collaboration with the Hunt group.


The proposed work will be the first gas-phase measurements of phycobillin chromophores, and will therefore provide the first measurements of their intrinsic spectroscopy and photophysics away from the complications of the bulk environment. The later-stage measurements of the phycobilin tethered to protein will provide direct insight into the critical role of the protein environment in defining the bilin photophysics. The experiments will exploit highly novel photo mass-spectrometry techniques, including laser-interfaced mass spectrometry, on-line photolysis mass spectrometry and on-line mass spectrometry coupled to ion mobility mass spectrometry.


The student will be trained in a wide range of mass spectrometry skills, as well as gaining experience with pulsed lasers and diode photolysis. The project will also offer opportunities for the student to gain experience in computational chemistry (molecular mechanics, ab initio and time-dependent density functional theory), depending on the interest of the student. 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:

Further Information

Candidate selection process:
• You should hold or expect to receive at least an upper second class degree in chemistry or a chemical sciences related subject
• Applicants should submit a PhD application to the University of York by 15 April 2021. Please note you will be unable to submit an application 6-12 April due to essential maintenance of the application system
• Supervisors may contact candidates either by email, telephone or web-chat
• Supervisors can nominate up to 2 candidates to be interviewed for the project
• The interview panel will shortlist candidates for interview from all those nominated
• Shortlisted candidates will be invited to a remote panel interview on 18 or 19 May
• The awarding committee will award studentships following the panel interviews
• Candidates will be notified of the outcome of the panel’s decision by email

Contact Details

For more information about the project, please contact Prof. Dessent at York (caroline.dessent AT or Prof. Sobott at Leeds (f.sobott AT

This PhD will formally start on 1 October 2021. Induction activities will start on 27 September.

To apply for this project, submit an online PhD in Chemistry application: