Search Results

You searched for all publications:

with publication states 'Published (Approved)'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

8 items found (0 items not approved), displaying all items.1

Instruments / Technical Area	Publication Details	Published
B21-High Throughput SAXS	Exploring Calbindin-IMPase fusion proteins structure and activity James Noble , John R. Atack Biochemistry And Biophysics Reports 30 DOI: 10.1016/j.bbrep.2022.101266 Diamond Proposal Number(s): [14891] Open Access Show Abstract ▼ Abstract: Calbindin-D28k is a calcium binding protein that is highly expressed in the mammalian central nervous system. It has been reported that calbindin-D28k binds to and increases the activity of inositol Monophosphatase (IMPase). This is an enzyme that is involved in the homeostasis of the Inositol trisphosphate signalling cascade by catalysing the final dephosphorylation of inositol and has been implicated in the therapeutic mechanism of lithium treatment of bipolar disorder. Previously studies have shown that calbindin-D28k can increase IMPase activity by up to 250 hundred-fold. A preliminary in silico model was proposed for the interaction. Here, we aimed at exploring the shape and properties of the calbindin-IMPase complex to gain new insights on this biologically important interaction. We created several fusion constructs of calbindin-D28k and IMPase, connected by flexible amino acid linkers of different lengths and orientations to fuse the termini of the two proteins together. The resulting fusion proteins have activities 200%–400% higher the isolated wild-type IMPase. The constructs were characterized by small angle X-ray scattering to gain information on the overall shape of the complexes and validate the previous model. The fusion proteins form a V-shaped, elongated and less compact complex as compared to the model. Our results shed new light into this protein-protein interaction.	Jul 2022
I04-1-Macromolecular Crystallography (fixed wavelength)	Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase Chloe R. Koulouris , Sian E. Gardiner , Tessa K. Harris , Karen T. Elvers , S. Mark Roe , Jason A. Gillespie , Simon E. Ward , Olivera Grubisha , Robert A. Nicholls , John R. Atack , Benjamin D. Bax Communications Biology 5 DOI: 10.1038/s42003-022-03264-5 Diamond Proposal Number(s): [19990] Open Access Show Abstract ▼ Abstract: Human serine racemase (hSR) catalyses racemisation of L-serine to D-serine, the latter of which is a co-agonist of the NMDA subtype of glutamate receptors that are important in synaptic plasticity, learning and memory. In a ‘closed’ hSR structure containing the allosteric activator ATP, the inhibitor malonate is enclosed between the large and small domains while ATP is distal to the active site, residing at the dimer interface with the Tyr121 hydroxyl group contacting the α-phosphate of ATP. In contrast, in ‘open’ hSR structures, Tyr121 sits in the core of the small domain with its hydroxyl contacting the key catalytic residue Ser84. The ability to regulate SR activity by flipping Tyr121 from the core of the small domain to the dimer interface appears to have evolved in animals with a CNS. Multiple X-ray crystallographic enzyme-fragment structures show Tyr121 flipped out of its pocket in the core of the small domain. Data suggest that this ligandable pocket could be targeted by molecules that inhibit enzyme activity.	Apr 2022
I04-1-Macromolecular Crystallography (fixed wavelength)	Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase Gareth D. Fenn , Helen Waller-Evans , John R. Atack , Benjamin D. Bax Acta Crystallographica Section F Structural Biology Communications 76 DOI: 10.1107/S2053230X20011310 Diamond Proposal Number(s): [20147] Open Access Show Abstract ▼ Abstract: Inositol monophosphatase (IMPase) is inhibited by lithium, which is the most efficacious treatment for bipolar disorder. Several therapies have been approved, or are going through clinical trials, aimed at the replacement of lithium in the treatment of bipolar disorder. One candidate small molecule is ebselen, a selenium-containing antioxidant, which has been demonstrated to produce lithium-like effects both in a murine model and in clinical trials. Here, the crystallization and the first structure of human IMPase covalently complexed with ebselen, a 1.47 Å resolution crystal structure (PDB entry 6zk0), are presented. In the complex with human IMPase, ebselen in a ring-opened conformation is covalently attached to Cys141, a residue located away from the active site. IMPase is a dimeric enzyme and in the crystal structure two adjacent dimers share four ebselen molecules, creating a tetramer with approximate 222 symmetry. In the crystal structure presented in this publication, the active site in the tetramer is still accessible, suggesting that ebselen may function as an allosteric inhibitor or may block the binding of partner proteins.	Oct 2020
I03-Macromolecular Crystallography	Conformational flexibility within the small domain of human serine racemase Chloe R. Koulouris , Benjamin D. Bax , John R. Atack , S. Mark Roe Acta Crystallographica Section F Structural Biology Communications 76, 65 - 73 DOI: 10.1107/S2053230X20001193 Diamond Proposal Number(s): [14891] Show Abstract ▼ Abstract: Serine racemase (SR) is a pyridoxal 5′-phosphate (PLP)-containing enzyme that converts L-serine to D-serine, an endogenous co-agonist for the N-methyl-D-aspartate receptor (NMDAR) subtype of glutamate ion channels. SR regulates D-serine levels by the reversible racemization of L-serine to D-serine, as well as the catabolism of serine by α,β-elimination to produce pyruvate. The modulation of SR activity is therefore an attractive therapeutic approach to disorders associated with abnormal glutamatergic signalling since it allows an indirect modulation of NMDAR function. In the present study, a 1.89 Å resolution crystal structure of the human SR holoenzyme (including the PLP cofactor) with four subunits in the asymmetric unit is described. Comparison of this new structure with the crystal structure of human SR with malonate (PDB entry 3l6b) shows an interdomain cleft that is open in the holo structure but which disappears when the inhibitor malonate binds and is enclosed. This is owing to a shift of the small domain (residues 78–155) in human SR similar to that previously described for the rat enzyme. This domain movement is accompanied by changes within the twist of the central four-stranded β-sheet of the small domain, including changes in the φ–ψ angles of all three residues in the C-terminal β-strand (residues 149–151). In the malonate-bound structure, Ser84 (a catalytic residue) points its side chain at the malonate and is preceded by a six-residue β-strand (residues 78–83), but in the holoenzyme the β-strand is only four residues (78–81) and His82 has φ–ψ values in the α-helical region of the Ramachandran plot. These data therefore represent a crystallographic platform that enables the structure-guided design of small-molecule modulators for this important but to date undrugged target.	Feb 2020
B21-High Throughput SAXS	The molecular basis for apolipoprotein E4 as the major risk factor for late-onset Alzheimer's disease Ana-Caroline Raulin , Lucas Kraft , Youssra K. Al-Hilaly , Wei-Feng Xue , John E. Mcgeehan , John R. Atack , Louise Serpell Journal Of Molecular Biology DOI: 10.1016/j.jmb.2019.04.019 Diamond Proposal Number(s): [14891] Open Access Show Abstract ▼ Abstract: Apolipoprotein E4 (ApoE4) is one of three (E2, E3 and E4) human isoforms of an α-helical, 299-amino-acid protein. Homozygosity for the ε4 allele is the major genetic risk factor for developing late-onset Alzheimer's disease (AD). ApoE2, ApoE3 and ApoE4 differ at amino acid positions 112 and 158, and these sequence variations may confer conformational differences that underlie their participation in the risk of developing AD. Here, we compared the shape, oligomerization state, conformation and stability of ApoE isoforms using a range of complementary biophysical methods including small-angle x-ray scattering, analytical ultracentrifugation, circular dichroism, x-ray fiber diffraction and transmission electron microscopy We provide an in-depth and definitive study demonstrating that all three proteins are similar in stability and conformation. However, we show that ApoE4 has a propensity to polymerize to form wavy filaments, which do not share the characteristics of cross-β amyloid fibrils. Moreover, we provide evidence for the inhibition of ApoE4 fibril formation by ApoE3. This study shows that recombinant ApoE isoforms show no significant differences at the structural or conformational level. However, self-assembly of the ApoE4 isoform may play a role in pathogenesis, and these results open opportunities for uncovering new triggers for AD onset.	Apr 2019
B21-High Throughput SAXS I03-Macromolecular Crystallography I23-Long wavelength MX	The X-ray structure of human calbindin-D28K: an improved model James W. Noble , Rehab Almalki , S. Mark Roe , Armin Wagner , Ramona Duman , John Atack Acta Crystallographica Section D Structural Biology 74, 1008 - 1014 DOI: 10.1107/S2059798318011610 Diamond Proposal Number(s): [14891, 11175] Open Access Show Abstract ▼ Abstract: Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D28K are of therapeutic interest: for example, inositol monophosphatase, the putative target of lithium therapy in bipolar disorder. Presented here is the first crystal structure of human calbindin-D28K. There are significant deviations in the tertiary structure when compared with the NMR structure of rat calbindin-D28K (PDB entry 2g9b), despite 98% sequence identity. Small-angle X-ray scattering (SAXS) indicates that the crystal structure better predicts the properties of calbindin-D28K in solution compared with the NMR structure. Here, the first direct visualization of the calcium-binding properties of calbindin-D28K is presented. Four of the six EF-hands that make up the secondary structure of the protein contain a calcium-binding site. Two distinct conformations of the N-terminal EF-hand calcium-binding site were identified using long-wavelength calcium single-wavelength anomalous dispersion (SAD). This flexible region has previously been recognized as a protein–protein interaction interface. SAXS data collected in both the presence and absence of calcium indicate that there are no large structural differences in the globular structure of calbindin-D28K between the calcium-loaded and unloaded proteins.	Oct 2018
I02-Macromolecular Crystallography I04-Macromolecular Crystallography	Co-crystallization of human inositol monophosphatase with the lithium mimetic L-690,330 Lucas Kraft , Mark Roe , Raj Gill , John Atack Acta Crystallographica Section D Structural Biology 74, 973 - 978 DOI: 10.1107/S2059798318010380 Show Abstract ▼ Abstract: Lithium, which is still the gold standard in the treatment of bipolar disorder, has been proposed to inhibit inositol monophosphatase (IMPase) and is hypothesized to exert its therapeutic effects by attenuating phosphatidylinositol (PI) cell signalling. Drug-discovery efforts have focused on small-molecule lithium mimetics that would specifically inhibit IMPase without exhibiting the undesired side effects of lithium. L-690,330 is a potent bisphosphonate substrate-based inhibitor developed by Merck Sharp & Dohme. To aid future structure-based inhibitor design, determination of the exact binding mechanism of L-690,330 to IMPase was of interest. Here, the high-resolution X-ray structure of human IMPase in complex with L690,330 and manganese ions determined at 1.39 Å resolution is reported.	Oct 2018
I04-Macromolecular Crystallography	Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2 Peter Hornyak , T. Askwith , S. Walker , E. Komulainen , M. Paradowski , L. E. Pennicott , E. J. Bartlett , Nigel Brissett , A. Raoof , M. Watson , A. M. Jordan , D. J. Ogilvie , S. E. Ward , J. R. Atack , Laurence Pearl , K. W. Caldecott , Antony W. Oliver Biochemical Journal 473, 1869 - 1879 DOI: 10.1042/BCJ20160180 Diamond Proposal Number(s): [10088] Open Access Show Abstract ▼ Abstract: TDP2 is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II. TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful concentrations, but their mode of action was uncertain. We have confirmed that the deazaflavin series inhibits TDP2 enzyme activity in a fluorescence-based assay, suitable for HTS-screening. We have gone on to determine crystal structures of these compounds bound to a 'humanised' form of murine TDP2. The structures reveal their novel mode of action as competitive ligands for the binding site of an incoming DNA substrate, and point the way to generating novel and potent inhibitors of TDP2.	Jun 2016

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User