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
Maric S
(2015)
Biosynthetic preparation of selectively deuterated phosphatidylcholine in genetically modified Escherichia coli.
in Applied microbiology and biotechnology
Masson S
(2009)
Central Domain of DivIB Caps the C-terminal Regions of the FtsL/DivIC Coiled-coil Rod
in Journal of Biological Chemistry
Misuraca L
(2017)
Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study.
in Life (Basel, Switzerland)
Mizuta R
(2018)
Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide.
in Nanoscale
Mossou E
(2014)
The self-assembling zwitterionic form of L-phenylalanine at neutral pH.
in Acta crystallographica. Section C, Structural chemistry
Moulin M
(2018)
Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris.
in Chemistry and physics of lipids
Moulin M
(2019)
Towards a molecular understanding of the water purification properties of Moringa seed proteins.
in Journal of colloid and interface science
Nitsche J
(2018)
Structural basis for activation of plasma-membrane Ca2+-ATPase by calmodulin.
in Communications biology
Obarska-Kosinska A
(2020)
Corrigendum to "HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling" [J. Mol. Biol. 376(2) 2008 Feb 15: 438-452.].
in Journal of molecular biology
Obarska-Kosinska A
(2008)
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.
in Journal of molecular biology
Parrot I
(2006)
X-rays and neutrons for the study of DNA structure, hydration, and transitions
in Physica B: Condensed Matter
Ramos J
(2021)
The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme.
in Acta crystallographica. Section D, Structural biology
Schirò G
(2015)
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.
in Nature communications
Schreiber F
(2022)
High-resolution Neutron Spectroscopy to Study Picosecond-nanosecond Dynamics of Proteins and Hydration Water
in Journal of Visualized Experiments
Sebastiani F
(2021)
Apolipoprotein E Binding Drives Structural and Compositional Rearrangement of mRNA-Containing Lipid Nanoparticles
in ACS Nano
Taylor J
(2024)
Correction: Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124INT
in PLOS ONE
Taylor JE
(2020)
Correction: Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124INT.
in PloS one
Taylor JE
(2012)
Structural and functional analysis of the symmetrical Type I restriction endonuclease R.EcoR124INT.
in PloS one
Taylor JEN
(2010)
Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124INT.
in Journal of molecular biology
Teixeira SC
(2010)
Sweet neutron crystallography.
in Acta crystallographica. Section D, Biological crystallography
Tiggelaar SM
(2011)
Neutron fibre diffraction studies of amyloid using H2O/D2O isotopic replacement.
in Acta crystallographica. Section F, Structural biology and crystallization communications
Varga K
(2008)
Advances towards resonance assignments for uniformly--13C, 15N enriched bacteriorhodopsin at 18.8 T in purple membranes.
in Journal of biomolecular NMR
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
Vijayakrishnan S
(2010)
Solution structure and characterisation of the human pyruvate dehydrogenase complex core assembly.
in Journal of molecular biology
Vijayakrishnan S
(2011)
Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly.
in The Biochemical journal
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
Waldie S
(2021)
ApoE and ApoE Nascent-Like HDL Particles at Model Cellular Membranes: Effect of Protein Isoform and Membrane Composition.
in Frontiers in chemistry
Waldie S
(2019)
The Production of Matchout-Deuterated Cholesterol and the Study of Bilayer-Cholesterol Interactions.
in Scientific reports
Waldie S
(2018)
Localization of Cholesterol within Supported Lipid Bilayers Made of a Natural Extract of Tailor-Deuterated Phosphatidylcholine.
in Langmuir : the ACS journal of surfaces and colloids
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
Wood K
(2013)
Protein surface and core dynamics show concerted hydration-dependent activation.
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
(2019)
A molecular mechanism for transthyretin amyloidogenesis.
in Nature communications
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)
Yee AW
(2017)
Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy.
in Journal of applied crystallography
Zaccai G
(2016)
Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane.
in Scientific reports
Zhu X
(2010)
Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations.
in Physical review. E, Statistical, nonlinear, and soft matter physics