Deuteration Initiative for Neutron Scattering and NMR Studies of Biological Molecules
Lead Research Organisation:
Keele University
Department Name: Sch of Chemistry & Physics
Abstract
This proposal requests EPSRC support for a consortium of UK scientists for research projects of high biological interest. All will use sophisticated methods that enable parts of biomolecules to have their hydrogen atoms replaced by its heavier 'isotope' deuterium. This allows novel neutron scattering and NMR work in which these parts are highlighted, providing important information on structure and movement that is not available by other methods. This 'deuteration' or 'labelling' requires innovative approaches that have been developed at the Grenoble Deuteration Laboratory at the Institut Laue Langevin (the ILL is 33% UK-owned/funded). The laboratory was built with funding from a previous EPSRC grant that equipped it and initiated UK-driven scientific activity. It is now a unique facility in the world, with a flourishing in-house and user programme. Located on a remarkable science campus, the UK-based projects described below will also benefit from other powerful platforms available.1. Neutron studies of T-tract sequences of DNA (Keele)'T-tracts' are regions of DNA with repetitive runs of thymine. They have been implicated in regulatory processes. Deuteration will be used to highlight each of the two DNA strands in studies aimed at understanding these sequences and how they may be related to function.2. Structure and dynamics in filamentous viruses (Cambridge, Keele) Filamentous viruses are unique models for fundamental processes inbiology, and also have important technological uses in drug discovery and vaccine design. We will use deuteration methods to study structure and movement within the virus3. NMR/neutron studies of a mechanosensitive channel protein (Oxford) We will study a 'mechanosensitive' protein from membranes that controls cell shape and size in different environments. We have made a breakthrough in producing deuterated samples so that we can obtain important information that may be relevant to diseases and their treatment.4. Neutron scattering studies of a multienzyme complex (Glasgow)We will study how a particular set of proteins is put together to make a specialised 'molecular machine' of medical importance that controls a key step in the pathway that converts glucose into energy.5. Studies of bacterial protein-DNA complexes (Portsmouth)All bacterial species have an 'immune system', whereby their own DNA can be distinguished from foreign DNA. Deuteration will allow studies that will be important in understanding how bacterial defences can be overcome.6. Studies of the 'IMPase' enzyme, in relation to bipolar disorder (Southampton)Bipolar disorder is a mental illness. It is often treated with lithium, which interacts with the IMPase enzyme. We will study its interaction with lithium in order to understand the nature of lithium therapy, side effects, and potential alternative therapies.7. Neutron diffraction studies of DNA and drug-DNA complexes (Reading)DNA is not always the beautiful double helix of popular imagination. It forms many 'hydrogen-bonding' interactions that are not properly understood. Anticancer and other DNA-binding drugs interfere with these interactions. Deuteration will allow these effects to be seen for the first time.8. NMR and neutron studies of chromatin structure (Cambridge)DNA within the cell is packaged into bundles with proteins to give a structure called chromatin. Deuteration will be used to study how key protein complexes work to regulate the formation of chromatin structure, and which genes are expressed (transcribed into RNA and protein).9. Structural studies of human ferroportin (King's College London)Ferroportin is a protein that is involved in transferring dietary iron from intestines to blood. It is a prime target for therapeutic intervention in the illnesses haemachromatosis and thalassaemia. Deuteration will be used to provide information that will help drug design.
Publications
Obarska-Kosinska A
(2008)
HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling
in Journal of Molecular Biology
Fichou Y
(2015)
Hydration water mobility is enhanced around tau amyloid fibers.
in Proceedings of the National Academy of Sciences of the United States of America
Kovalevsky AY
(2011)
Identification of the elusive hydronium ion exchanging roles with a proton in an enzyme at lower pH values.
in Angewandte Chemie (International ed. in English)
Yee A
(2016)
Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses
in Angewandte Chemie
Yee AW
(2016)
Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses.
in Angewandte Chemie (International ed. in English)
Foglia F
(2019)
In Vivo Water Dynamics in Shewanella oneidensis Bacteria at High Pressure.
in Scientific reports
Kovalevsky A
(2012)
Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.
in Acta crystallographica. Section D, Biological crystallography
Cowsill BJ
(2014)
Interfacial structure of immobilized antibodies and perdeuterated HSA in model pregnancy tests measured with neutron reflectivity.
in Langmuir : the ACS journal of surfaces and colloids
Blanc M
(2014)
Intrinsic disorder within the erythrocyte binding-like proteins from Plasmodium falciparum.
in Biochimica et biophysica acta
Waldie S
(2020)
Lipoprotein ability to exchange and remove lipids from model membranes as a function of fatty acid saturation and presence of cholesterol.
in Biochimica et biophysica acta. Molecular and cell biology of lipids
Dunne O
(2017)
Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures.
in European biophysics journal : EBJ
Kovalevsky AY
(2010)
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
in Structure (London, England : 1993)
Drago VN
(2022)
Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction.
in NPJ microgravity
Misuraca L
(2017)
Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study
in Life
Gerelli Y
(2014)
Multi-lamellar organization of fully deuterated lipid extracts of yeast membranes.
in Acta crystallographica. Section D, Biological crystallography
Ahmadi D
(2022)
Nanoscale Structure and Dynamics of Model Membrane Lipid Raft Systems, Studied by Neutron Scattering Methods
in Frontiers in Physics
Cuypers MG
(2013)
Near-atomic resolution neutron crystallography on perdeuterated Pyrococcus furiosus rubredoxin: implication of hydronium ions and protonation state equilibria in redox changes.
in Angewandte Chemie (International ed. in English)
Gajdos L
(2022)
Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.
in Nature communications
Tiggelaar SM
(2011)
Neutron fibre diffraction studies of amyloid using H2O/D2O isotopic replacement.
in Acta crystallographica. Section F, Structural biology and crystallization communications
Wacklin HP
(2016)
Neutron reflection study of the interaction of the eukaryotic pore-forming actinoporin equinatoxin II with lipid membranes reveals intermediate states in pore formation.
in Biochimica et biophysica acta
Howard EI
(2011)
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.
in Journal of molecular recognition : JMR
Zaccai G
(2016)
Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane.
in Scientific reports
Varga K
(2007)
NMR crystallography: the effect of deuteration on high resolution 13C solid state NMR spectra of a 7-TM protein.
in Biochimica et biophysica acta
Moulin M
(2018)
Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris.
in Chemistry and physics of lipids