Dr Gary Thompson

NMR Facility Manager

About

Gary Thompson graduated in Chemistry from the University of York in 1981 and completed his PhD on complexes between sugars and Actinides at the University of Reading with Prof David Rice in 1984. Following his PhD he helped run the UK High Field NMR Facility at the University of Warwick. Between 1995 and 2000 he worked with Prof. Sheena Radford on the structure and folding of the single electron transfer blue copper protein pseudoazurin using NMR. Following a period as a postdoc with Prof Steve Homans at the University of Leeds using NMR to study vATPase, mouse urinary protein and MS2 bacteriophage, he became a staff member of the NMR Facility at the University of Leeds. During this time he was closely involved in the running and maintenance of the NMR Facility, helped found the Reson8 NMR managers group and worked on a wide range of projects using NMR to study the large protein complex FusB:EFG, the ion channel P7 from Hepatitis C, and the amyloid proteins from the ß2m system including the pathway of amyloid formation.
In 2017 Gary joined the University of Kent as NMR Facility Manager where he is in charge of the day to day running of the Facility, development of new techniques and training of users. Gary is also currently a member of the CCPN (combined Collaborative Computing Project for NMR) executive committee which guides the provision of software and teaching.
ORCID ID: 0000-0001-9399-7636

Research interests

Gary's research interests fall in 4 main strands;  
NMR Structure calculation and sparse restraints. NMR is one of the three main structural tools used to understand the structure and dynamics of molecules. Gary has a wide ranging interest in using NMR and integrated structural biology techniques used to understand protein-protein and protein-ligand interactions. These include a focus on the use of sparse restraints when calculating NMR structures and led to the development of the XCamshift implementation of the Camshift forcefield in xplor-nih (https://github.com/locsmith/xcamshift). Gary has used sparse restraints (RDCs, PREs, sPRES & chemical shifts) to calculate the structure of the 70kDa FusB:EFG complex and hidden states of the ß2m amyloid system.
Software tools. Gary is experienced in software development and has built a very fast chemical shift forcefield in python/cython that works with xplor-nih (https://github.com/locsmith/xcamshift). Currently he is collaborating with the CCPN software group to implement a modernised version of the CCPN data-model (https://www2.ccpn.ac.uk/api-documentation/ccpnmr/ccpnmr2.2/python/doc/api.html) and its toolchain using the XTEND computer language (https://www.eclipse.org/xtend/) and eclipse / papyrus uml model and tool chain (https://www.eclipse.org/papyrus/). Gary also has an interest in the use of diagrammatic representations of product operators (a fundamental tool use for the understanding of NMR pulse sequences) and there integration with symbolic maths programs programmed in python.
Structure and Dynamics of the protein PCTA. PCTA is a trans membrane protein from pseudomonas aureginosa that detects food sources (amino acids) and activates the CHE pathway which causes chemotaxis towards food sources. The mode of trans membrane signalling in the PCTA system is still not clearly understood and we are using NMR dynamics measurements (1H-15N) and RDCs to study the sensor domain of the protein (29kDa) in solution. (Collaboration with Jose Ortega Roldan)
Metabolomics There is a strong interest in the use of metabolomics and lipidomics in the School and Gary is collaborating with Jose Orteg-Roldan, Mark Shepherd and Anastasios Tsaousis to implement both current and novel metabolomics and lipidomics methodologies. This includes an interest in the use of 13C NMR and labelling in lipidomics and metabolomics studies.

Collaborations By the nature of his research Gary collaborates with a wide range of groups, current collaborators include; 
Jose Ortega-Roldan, University of Kent Ben Goult, University of Kent Anastasios Tsaousis, University of Kent Andrew Lawrence / Warren Group, University of Kent Richard Williamson, University of Kent Arnout Kalverda, University of Leeds Stephan Kerpinski, Univsersity of Leeds Jennifer Tomlinson, University of Leeds Stephan Kepinski, University of Leeds Wael Houssan, University of Aberdeen Ed Brooksbank / Geetern Vuister, University of Leicester / CCPN

Teaching

Gary teaches advanced NMR theory at the Reson8 NMR week on an annual basis.

Supervision

MSc-R project available for 2021

MSc Fast protein structure assignment and validation

An MSc in structural biology using NMR is available shared between the NMR Facility and the Laboratory of Jose Ortega Roldan. New structure prediction algorithms such as alpha fold from deep mind offer the possibility of very fast validation and refinement of predicted protein structures  using NMR based experimental restraints. The project will build a protocol to quickly validate protein structures using automatically assigned protein backbone and sidechain shifts [including 4D experiments], residual dipolar couplings and un-labelling approaches. The project will offer both an opportunity to learn how to carry out protein NMR experiments and a thorough grounding in python programming and structural biology. No previous programming experience is required.

MSc Docking of large protein complexes using sparse NMR Restraints

An MSc in structural biology using NMR is available shared between the NMR Facility and the Laboratory of Jose Ortega Roldan. The calculation of the structures of protein complexes by NMR remains an important area of research. This project will aim to improve protein-protein docking methodologies by using chemical shifts to restrain the proteins during docking so as to achieve a more natural soft docked structure. The project will examine two test systems a large protein-protein complex involved in antibiotic resistance (FusB-EFG) and a large multimeric protein multimer using solid state NMR data. The project will offer both an opportunity to learn how to carry out protein NMR experiments and a thorough grounding in python programming and structural biology. No previous programming experience is required.

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