1
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Lane BJ, Ma Y, Yan N, Wang B, Ackermann K, Karamanos TK, Bode BE, Pliotas C. Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension. Structure 2024:S0969-2126(24)00080-7. [PMID: 38521071 DOI: 10.1016/j.str.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Membrane forces shift the equilibria of mechanosensitive channels enabling them to convert mechanical cues into electrical signals. Molecular tools to stabilize and methods to capture their highly dynamic states are lacking. Cyclodextrins can mimic tension through the sequestering of lipids from membranes. Here we probe the conformational ensemble of MscS by EPR spectroscopy, the lipid environment with NMR, and function with electrophysiology under cyclodextrin-induced tension. We show the extent of MscS activation depends on the cyclodextrin-to-lipid ratio, and that lipids are depleted slower when MscS is present. This has implications in MscS' activation kinetics when distinct membrane scaffolds such as nanodiscs or liposomes are used. We find MscS transits from closed to sub-conducting state(s) before it desensitizes, due to the lack of lipid availability in its vicinity required for closure. Our approach allows for monitoring tension-sensitive states in membrane proteins and screening molecules capable of inducing molecular tension in bilayers.
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Affiliation(s)
- Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yue Ma
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Bolin Wang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Theodoros K Karamanos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
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2
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Ackermann K, Heubach CA, Schiemann O, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Distance Measurements at Low Nanomolar Concentrations: The Cu II-Trityl Case. J Phys Chem Lett 2024; 15:1455-1461. [PMID: 38294197 PMCID: PMC10860127 DOI: 10.1021/acs.jpclett.3c03311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Recent sensitivity enhancements in pulse dipolar electron paramagnetic resonance spectroscopy (PDS) have afforded distance measurements at submicromolar spin concentrations. This development opens the path for new science as more biomolecular systems can be investigated at their respective physiological concentrations. Here, we demonstrate that the combination of orthogonal spin-labeling using CuII ions and trityl yields a >3-fold increase in sensitivity compared to that of the established CuII-nitroxide labeling strategy. Application of the recently developed variable-time relaxation-induced dipolar modulation enhancement (RIDME) method yields a further ∼2.5-fold increase compared to the commonly used constant-time RIDME. This overall increase in sensitivity of almost an order of magnitude makes distance measurements in the range of 3 nm with protein concentrations as low as 10 nM feasible, >2 times lower than the previously reported concentration. We expect that experiments at single-digit nanomolar concentrations are imminent, which have the potential to transform biological PDS applications.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
| | - Caspar A. Heubach
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
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3
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Simpson M, Harding CJ, Czekster RM, Remmel L, Bode BE, Czekster CM. Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Biochemistry 2023; 62:3188-3205. [PMID: 37924287 PMCID: PMC10666288 DOI: 10.1021/acs.biochem.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Intracellular leucine aminopeptidases (PepA) are metalloproteases from the family M17. These enzymes catalyze peptide bond cleavage, removing N-terminal residues from peptide and protein substrates, with consequences for protein homeostasis and quality control. While general mechanistic studies using model substrates have been conducted on PepA enzymes from various organisms, specific information about their substrate preferences and promiscuity, choice of metal, activation mechanisms, and the steps that limit steady-state turnover remain unexplored. Here, we dissected the catalytic and chemical mechanisms of PaPepA: a leucine aminopeptidase from Pseudomonas aeruginosa. Cleavage assays using peptides and small-molecule substrate mimics allowed us to propose a mechanism for catalysis. Steady-state and pre-steady-state kinetics, pH rate profiles, solvent kinetic isotope effects, and biophysical techniques were used to evaluate metal binding and activation. This revealed that metal binding to a tight affinity site is insufficient for enzyme activity; binding to a weaker affinity site is essential for catalysis. Progress curves for peptide hydrolysis and crystal structures of free and inhibitor-bound PaPepA revealed that PaPepA cleaves peptide substrates in a processive manner. We propose three distinct modes for activity regulation: tight packing of PaPepA in a hexameric assembly controls substrate length and reaction processivity; the product leucine acts as an inhibitor, and the high concentration of metal ions required for activation limits catalytic turnover. Our work uncovers catalysis by a metalloaminopeptidase, revealing the intricacies of metal activation and substrate selection. This will pave the way for a deeper understanding of metalloenzymes and processive peptidases/proteases.
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Affiliation(s)
- Martha
Clementine Simpson
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
| | - Christopher John Harding
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
| | - Ricardo Melo Czekster
- School
of Computer Science and Digital Technologies, Department of Software
Engineering and Cybersecurity, Aston University, B4 7ET, Birmingham,United Kingdom
| | - Laura Remmel
- School
of Chemistry, University of St Andrews, North Haugh, Purdie Building, KY16 9ST, Saint Andrews , United Kingdom
| | - Bela E. Bode
- School
of Chemistry, University of St Andrews, North Haugh, Purdie Building, KY16 9ST, Saint Andrews , United Kingdom
| | - Clarissa Melo Czekster
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
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4
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McQuarrie S, Athukoralage JS, McMahon SA, Graham S, Ackermann K, Bode BE, White MF, Gloster TM. Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open. Nucleic Acids Res 2023; 51:10590-10605. [PMID: 37747760 DOI: 10.1093/nar/gkad739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
Type III CRISPR systems synthesize cyclic oligoadenylate (cOA) second messengers as part of a multi-faceted immune response against invading mobile genetic elements (MGEs). cOA activates non-specific CRISPR ancillary defence nucleases to create a hostile environment for MGE replication. Csm6 ribonucleases bind cOA using a CARF (CRISPR-associated Rossmann Fold) domain, resulting in activation of a fused HEPN (Higher Eukaryotes and Prokaryotes Nucleotide binding) ribonuclease domain. Csm6 enzymes are widely used in a new generation of diagnostic assays for the detection of specific nucleic acid species. However, the activation mechanism is not fully understood. Here we characterised the cyclic hexa-adenylate (cA6) activated Csm6' ribonuclease from the industrially important bacterium Streptococcus thermophilus. Crystal structures of Csm6' in the inactive and cA6 bound active states illuminate the conformational changes which trigger mRNA destruction. Upon binding of cA6, there is a close to 60° rotation between the CARF and HEPN domains, which causes the 'jaws' of the HEPN domain to open and reposition active site residues. Key to this transition is the 6H domain, a right-handed solenoid domain connecting the CARF and HEPN domains, which transmits the conformational changes for activation.
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Affiliation(s)
- Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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5
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Vitali V, Ackermann K, Hagelueken G, Bode BE. Spectroscopically Orthogonal Labelling to Disentangle Site-Specific Nitroxide Label Distributions. Appl Magn Reson 2023; 55:187-205. [PMID: 38357007 PMCID: PMC10861635 DOI: 10.1007/s00723-023-01611-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 02/16/2024]
Abstract
Biomolecular applications of pulse dipolar electron paramagnetic resonance spectroscopy (PDS) are becoming increasingly valuable in structural biology. Site-directed spin labelling of proteins is routinely performed using nitroxides, with paramagnetic metal ions and other organic radicals gaining popularity as alternative spin centres. Spectroscopically orthogonal spin labelling using different types of labels potentially increases the information content available from a single sample. When analysing experimental distance distributions between two nitroxide spin labels, the site-specific rotamer information has been projected into the distance and is not readily available, and the contributions of individual labelling sites to the width of the distance distribution are not obvious from the PDS data. Here, we exploit the exquisite precision of labelling double-histidine (dHis) motifs with CuII chelate complexes. The contribution of this label to the distance distribution widths in model protein GB1 has been shown to be negligible. By combining a dHis CuII labelling site with cysteine-specific nitroxide labelling, we gather insights on the label rotamers at two distinct sites, comparing their contributions to distance distributions based on different in silico modelling approaches and structural models. From this study, it seems advisable to consider discrepancies between different in silico modelling approaches when selecting labelling sites for PDS studies. Supplementary Information The online version contains supplementary material available at 10.1007/s00723-023-01611-1.
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Affiliation(s)
- Valentina Vitali
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
| | - Gregor Hagelueken
- Institute of Structural Biology, Biomedical Center, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland
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6
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Wort JL, Ackermann K, Giannoulis A, Bode BE. Enhanced sensitivity for pulse dipolar EPR spectroscopy using variable-time RIDME. J Magn Reson 2023; 352:107460. [PMID: 37167826 DOI: 10.1016/j.jmr.2023.107460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/03/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Pulse dipolar EPR spectroscopy (PDS) measurements are an important complementary tool in structural biology and are increasingly applied to macromolecular assemblies implicated in human health and disease at physiological concentrations. This requires ever higher sensitivity, and recent advances have driven PDS measurements into the mid-nanomolar concentration regime, though optimization and acquisition of such measurements remains experimentally demanding and time expensive. One important consideration is that constant-time acquisition represents a hard limit for measurement sensitivity, depending on the maximum measured distance. Determining this distance a priori has been facilitated by machine-learning structure prediction (AlphaFold2 and RoseTTAFold) but is often confounded by non-representative behaviour in frozen solution that may mandate multiple rounds of optimization and acquisition. Herein, we endeavour to simultaneously enhance sensitivity and streamline PDS measurement optimization to one-step by benchmarking a variable-time acquisition RIDME experiment applied to CuII-nitroxide and CuII-CuII model systems. Results demonstrate marked sensitivity improvements of both 5- and 6-pulse variable-time RIDME of between 2- and 5-fold over the constant-time analogues.
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Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Angeliki Giannoulis
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland.
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7
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Ackermann K, Khazaipoul S, Wort JL, Sobczak AIS, Mkami HE, Stewart AJ, Bode BE. Investigating Native Metal Ion Binding Sites in Mammalian Histidine-Rich Glycoprotein. J Am Chem Soc 2023; 145:8064-8072. [PMID: 37001144 PMCID: PMC10103162 DOI: 10.1021/jacs.3c00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Mammalian histidine-rich glycoprotein (HRG) is a highly versatile and abundant blood plasma glycoprotein with a diverse range of ligands that is involved in regulating many essential biological processes, including coagulation, cell adhesion, and angiogenesis. Despite its biomedical importance, structural information on the multi-domain protein is sparse, not least due to intrinsically disordered regions that elude high-resolution structural characterization. Binding of divalent metal ions, particularly ZnII, to multiple sites within the HRG protein is of critical functional importance and exerts a regulatory role. However, characterization of the ZnII binding sites of HRG is a challenge; their number and composition as well as their affinities and stoichiometries of binding are currently not fully understood. In this study, we explored modern electron paramagnetic resonance (EPR) spectroscopy methods supported by protein secondary and tertiary structure prediction to assemble a holistic picture of native HRG and its interaction with metal ions. To the best of our knowledge, this is the first time that this suite of EPR techniques has been applied to count and characterize endogenous metal ion binding sites in a native mammalian protein of unknown structure.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
| | - Siavash Khazaipoul
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Joshua L. Wort
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
| | - Amélie I. S. Sobczak
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Hassane El Mkami
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, Scotland
| | - Alan J. Stewart
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Bela E. Bode
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
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8
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Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G. Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 2023; 614:168-174. [PMID: 36423657 DOI: 10.1038/s41586-022-05571-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
CRISPR defence systems such as the well-known DNA-targeting Cas9 and the RNA-targeting type III systems are widespread in prokaryotes1,2. The latter orchestrates a complex antiviral response that is initiated through the synthesis of cyclic oligoadenylates after recognition of foreign RNA3-5. Among the large set of proteins that are linked to type III systems and predicted to bind cyclic oligoadenylates6,7, a CRISPR-associated Lon protease (CalpL) stood out to us. CalpL contains a sensor domain of the SAVED family7 fused to a Lon protease effector domain. However, the mode of action of this effector is unknown. Here we report the structure and function of CalpL and show that this soluble protein forms a stable tripartite complex with two other proteins, CalpT and CalpS, that are encoded on the same operon. After activation by cyclic tetra-adenylate (cA4), CalpL oligomerizes and specifically cleaves the MazF homologue CalpT, which releases the extracytoplasmic function σ factor CalpS from the complex. Our data provide a direct connection between CRISPR-based detection of foreign nucleic acids and transcriptional regulation. Furthermore, the presence of a SAVED domain that binds cyclic tetra-adenylate in a CRISPR effector reveals a link to the cyclic-oligonucleotide-based antiphage signalling system.
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Affiliation(s)
- Christophe Rouillon
- Institute of Structural Biology, University of Bonn, Bonn, Germany.
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany.
| | | | - Haotian Chi
- School of Biology, University of St Andrews, St Andrews, UK
| | - Katja Blumenstock
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory (EMBL), Hamburg Site, Hamburg, Germany
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Wolfgang Boenigk
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany
| | - Reinhard Seifert
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, UK
| | - Jonathan L Schmid-Burgk
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Site, Hamburg, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
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9
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Bode BE, Fusco E, Nixon R, Buch CD, Weihe H, Piligkos S. Dipolar-Coupled Entangled Molecular 4f Qubits. J Am Chem Soc 2023; 145:2877-2883. [PMID: 36695706 PMCID: PMC9912257 DOI: 10.1021/jacs.2c10902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We demonstrate by use of continuous wave- and pulse-electron paramagnetic resonance spectroscopy on oriented single crystals of magnetically dilute YbIII ions in Yb0.01Lu0.99(trensal) that molecular entangled two-qubit systems can be constructed by exploiting dipolar interactions between neighboring YbIII centers. Furthermore, we show that the phase memory time and Rabi frequencies of these dipolar-interaction-coupled entangled two-qubit systems are comparable to the ones of the corresponding single qubits.
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Affiliation(s)
- Bela E. Bode
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.,
| | - Edoardo Fusco
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.
| | - Rachel Nixon
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.
| | - Christian D. Buch
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark
| | - Høgni Weihe
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark
| | - Stergios Piligkos
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark,
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10
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Giannoulis A, Ackermann K, Bogdanov A, Cordes DB, Higgins C, Ward J, Slawin AMZ, Taylor JE, Bode BE. Synthesis of mono-nitroxides and of bis-nitroxides with varying electronic through-bond communication. Org Biomol Chem 2023; 21:375-385. [PMID: 36524609 PMCID: PMC9811921 DOI: 10.1039/d2ob01863b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nitroxides are a unique class of persistent radicals finding a wide range of applications, from spin probes to polarizing agents, and recently bis-nitroxides have been used as proof-of-concept molecules for quantum information processing. Here we present the syntheses of pyrroline-based nitroxide (NO) radicals and give a comparision of two possible synthetic routes to form two key intermediates, namely 2,2,5,5-tetramethylpyrroline-1-oxyl-3-acetylene (TPA) and 1-oxyl-2,2,5,5-tetramethylpyrroline-3-carboxylic acid (TPC). TPC and TPA were then used as precursors for the synthesis of three model compounds featuring two distant NO groups with a variable degree of conjugation and thus electronic communication between them. Using relatively facile synthetic routes, we produced a number of mono- and bis-nitroxides with the structures of multiple compounds unambiguously characterized by X-ray crystallography, while Continuous Wave Electron Paramagnetic Resonance (CW-EPR) allowed us to quantify the electronic communication in the bis-nitroxides. Our study expands the repertoire of mono- and bis-nitroxides with possibilities of exploiting them for studying quantum coherence effects and as polarizing agents.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovot76100Israel,EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Alexey Bogdanov
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovot76100Israel
| | - David B. Cordes
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Catherine Higgins
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Joshua Ward
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Alexandra M. Z. Slawin
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - James E. Taylor
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK,Department of Chemistry, University of BathClaverton DownBathBA2 7AYUK
| | - Bela E. Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St AndrewsNorth HaughSt AndrewsKY16 9STUK
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11
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Oranges M, Wort JL, Fukushima M, Fusco E, Ackermann K, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Reveals Buffer-Modulated Cooperativity of Metal-Templated Protein Dimerization. J Phys Chem Lett 2022; 13:7847-7852. [PMID: 35976741 PMCID: PMC9421889 DOI: 10.1021/acs.jpclett.2c01719] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/10/2022] [Indexed: 05/26/2023]
Abstract
Self-assembly of protein monomers directed by metal ion coordination constitutes a promising strategy for designing supramolecular architectures complicated by the noncovalent interaction between monomers. Herein, two pulse dipolar electron paramagnetic resonance spectroscopy (PDS) techniques, pulse electron-electron double resonance and relaxation-induced dipolar modulation enhancement, were simultaneously employed to study the CuII-templated dimerization behavior of a model protein (Streptococcus sp. group G, protein G B1 domain) in both phosphate and Tris-HCl buffers. A cooperative binding model could simultaneously fit all data and demonstrate that the cooperativity of protein dimerization across α-helical double-histidine motifs in the presence of CuII is strongly modulated by the buffer, representing a platform for highly tunable buffer-switchable templated dimerization. Hence, PDS enriches the family of techniques for monitoring binding processes, supporting the development of novel strategies for bioengineering structures and stable architectures assembled by an initial metal-templated dimerization.
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12
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Ackermann K, Wort JL, Bode BE. Correction: Pulse dipolar EPR for determining nanomolar binding affinities. Chem Commun (Camb) 2022; 58:9438. [PMID: 35942935 PMCID: PMC9387565 DOI: 10.1039/d2cc90293a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Correction for ‘Pulse dipolar EPR for determining nanomolar binding affinities’ by Katrin Ackermann et al., Chem. Commun., 2022, DOI: https://doi.org/10.1039/d2cc02360a.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
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13
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Abstract
Protein interaction studies often require very low concentrations and highly sensitive biophysical methods. Here, we demonstrate that pulse dipolar electron paramagnetic resonance spectroscopy allows measuring dissociation constants in the nanomolar range. This approach is appealing for concentration-limited biomolecular systems and medium-to-high-affinity binding studies, demonstrated here at 50 nanomolar protein concentration. CuII-nitroxide RIDME measurements at 100 nM protein concentration allow reliable extraction of dissociation constants and distances, while measurements at 50 nM protein concentration allow reliable extraction of dissociation constants only.![]()
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
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14
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Roemmele TL, Knight FR, Crawford E, Robertson SD, Bode BE, Buehl M, Slawin A, Woollins JD, Boeré R. Chalcogen controlled redox behaviour in peri-substituted S, Se and Te naphthalene derivatives. NEW J CHEM 2022. [DOI: 10.1039/d2nj04737c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cyclic and square wave voltammetry of (PhE)2 peri-disubstituted naphthalene[1,8-cd]dichalcoganyls and acenaphthene[5,6-diyl]dichalcoganyls (E = S,Se,Te, 12 compounds), is reported. Mixed E1 = Se,Te; E2 = Br,I) naphthalene[1,8-cd]halochalcoganyls were also investigated, as...
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15
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Ackermann K, Chapman A, Bode BE. A Comparison of Cysteine-Conjugated Nitroxide Spin Labels for Pulse Dipolar EPR Spectroscopy. Molecules 2021; 26:7534. [PMID: 34946616 PMCID: PMC8706713 DOI: 10.3390/molecules26247534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
The structure-function and materials paradigms drive research on the understanding of structures and structural heterogeneity of molecules and solids from materials science to structural biology. Functional insights into complex architectures are often gained from a suite of complementary physicochemical methods. In the context of biomacromolecular structures, the use of pulse dipolar electron paramagnetic resonance spectroscopy (PDS) has become increasingly popular. The main interest in PDS is providing long-range nanometre distance distributions that allow for identifying macromolecular topologies, validating structural models and conformational transitions as well as docking of quaternary complexes. Most commonly, cysteines are introduced into protein structures by site-directed mutagenesis and modified site-specifically to a spin-labelled side-chain such as a stable nitroxide radical. In this contribution, we investigate labelling by four different commercial labelling agents that react through different sulfur-specific reactions. Further, the distance distributions obtained are between spin-bearing moieties and need to be related to the protein structure via modelling approaches. Here, we compare two different approaches to modelling these distributions for all four side-chains. The results indicate that there are significant differences in the optimum labelling procedure. All four spin-labels show differences in the ease of labelling and purification. Further challenges arise from the different tether lengths and rotamers of spin-labelled side-chains; both influence the modelling and translation into structures. Our comparison indicates that the spin-label with the shortest tether in the spin-labelled side-group, (bis-(2,2,5,5-Tetramethyl-3-imidazoline-1-oxyl-4-yl) disulfide, may be underappreciated and could increase the resolution of structural studies by PDS if labelling conditions are optimised accordingly.
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Affiliation(s)
| | | | - Bela E. Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK; (K.A.); (A.C.)
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16
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Lozinska MM, Jamieson S, Verbraeken MC, Miller DN, Bode BE, Murray CA, Brandani S, Wright PA. Cation Ordering and Exsolution in Copper-Containing Forms of the Flexible Zeolite Rho (Cu,M-Rho; M=H, Na) and Their Consequences for CO 2 Adsorption. Chemistry 2021; 27:13029-13039. [PMID: 34213033 PMCID: PMC8518693 DOI: 10.1002/chem.202101664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Indexed: 11/06/2022]
Abstract
The flexibility of the zeolite Rho framework offers great potential for tunable molecular sieving. The fully copper-exchanged form of Rho and mixed Cu,H- and Cu,Na-forms have been prepared. EPR spectroscopy reveals that Cu2+ ions are present in the dehydrated forms and Rietveld refinement shows these prefer S6R sites, away from the d8r windows that control diffusion. Fully exchanged Cu-Rho remains in an open form upon dehydration, the d8r windows remain nearly circular and the occupancy of window sites is low, so that it adsorbs CO2 rapidly at room temperature. Breakthrough tests with 10 % CO2 /40 % CH4 mixtures show that Cu4.9 -Rho is able to produce pure methane, albeit with a relatively low capacity at this pCO2 due to the weak interaction of CO2 with Cu cations. This is in strong contrast to Na-Rho, where cations in narrow elliptical window sites enable CO2 to be adsorbed with high selectivity and uptake but too slowly to enable the production of pure methane in similar breakthrough experiments. A series of Cu,Na-Rho materials was prepared to improve uptake and selectivity compared to Cu-Rho, and kinetics compared to Na-Rho. Remarkably, Cu,Na-Rho with >2 Cu cations per unit cell exhibited exsolution, due to the preference of Na cations for narrow S8R sites in distorted Rho and of Cu cations for S6R sites in the centric, open form of Rho. The exsolved Cu,Na-Rho showed improved performance in CO2 /CH4 breakthrough tests, producing pure CH4 with improved uptake and CO2 /CH4 selectivity compared to that of Cu4.9 -Rho.
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Affiliation(s)
- Magdalena M. Lozinska
- EaStCHEM School of ChemistryUniversity of St. AndrewsPurdie Building, North HaughSt Andrews, FifeKY16 9STUK
| | - Sophie Jamieson
- EaStCHEM School of ChemistryUniversity of St. AndrewsPurdie Building, North HaughSt Andrews, FifeKY16 9STUK
| | - Maarten C. Verbraeken
- School of EngineeringUniversity of Edinburgh The King's BuildingsRobert Stevenson RoadEdinburghEH9 3FBUK
| | - David N. Miller
- EaStCHEM School of ChemistryUniversity of St. AndrewsPurdie Building, North HaughSt Andrews, FifeKY16 9STUK
| | - Bela E. Bode
- EaStCHEM School of ChemistryUniversity of St. AndrewsPurdie Building, North HaughSt Andrews, FifeKY16 9STUK
| | - Claire A. Murray
- Diamond Light Source Ltd.Harwell Science and Innovation CampusDidcot, OxfordshireOX11 0DEUK
| | - Stefano Brandani
- School of EngineeringUniversity of Edinburgh The King's BuildingsRobert Stevenson RoadEdinburghEH9 3FBUK
| | - Paul A. Wright
- EaStCHEM School of ChemistryUniversity of St. AndrewsPurdie Building, North HaughSt Andrews, FifeKY16 9STUK
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17
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Robertson J, Ungogo MA, Aldfer MM, Lemgruber L, McWhinnie FS, Bode BE, Jones KL, Watson AJB, de Koning HP, Burley GA. Direct, Late-Stage Mono-N-arylation of Pentamidine: Method Development, Mechanistic Insight, and Expedient Access to Novel Antiparastitics against Diamidine-Resistant Parasites. ChemMedChem 2021; 16:3396-3401. [PMID: 34357687 PMCID: PMC9291547 DOI: 10.1002/cmdc.202100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/16/2022]
Abstract
A selective mono‐N‐arylation strategy of amidines under Chan‐Lam conditions is described. During the reaction optimization phase, the isolation of a mononuclear Cu(II) complex provided unique mechanistic insight into the operation of Chan‐Lam mono‐N‐arylation. The scope of the process is demonstrated, and then applied to access the first mono‐N‐arylated analogues of pentamidine. Sub‐micromolar activity against kinetoplastid parasites was observed for several analogues with no cross‐resistance in pentamidine and diminazene‐resistant trypanosome strains and against Leishmania mexicana. A fluorescent mono‐N‐arylated pentamidine analogue revealed rapid cellular uptake, accumulating in parasite nuclei and the kinetoplasts. The DNA binding capability of the mono‐N‐arylated pentamidine series was confirmed by UV‐melt measurements using AT‐rich DNA. This work highlights the potential to use Chan‐Lam mono‐N‐arylation to develop therapeutic leads against diamidine‐resistant trypanosomiasis and leishmaniasis.
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Affiliation(s)
- Jack Robertson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Marzuq A Ungogo
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Mustafa M Aldfer
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Leandro Lemgruber
- Glasgow Imaging Facility, Institute of Infection, Immunity, and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Fergus S McWhinnie
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Bela E Bode
- EaStCHEM, School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Katherine L Jones
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Allan J B Watson
- EaStCHEM, School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Harry P de Koning
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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18
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Han C, Bradford AJ, Slawin AMZ, Bode BE, Fusco E, Lee SL, Tang CC, Lightfoot P. Structural Features in Some Layered Hybrid Copper Chloride Perovskites: ACuCl 4 or A 2CuCl 4. Inorg Chem 2021; 60:11014-11024. [PMID: 34242021 DOI: 10.1021/acs.inorgchem.1c00705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present three new hybrid copper(II) chloride layered perovskites of generic composition ACuCl4 or A2CuCl4, which exhibit three distinct structure types. (m-PdH2)CuCl4 (m-PdH22+ = protonated m-phenylenediamine) adopts a Dion-Jacobson (DJ)-like layered perovskite structure type and exhibits a very large axial thermal contraction effect upon heating, as revealed via variable-temperature synchrotron X-ray powder diffraction (SXRD). This can be attributed to the contraction of an interlayer block, via a slight repositioning of the m-PdH22+ moiety. (3-AbaH)2CuCl4 (3-AbaH+ = protonated 3-aminobenzoic acid) and (4-AbaH)2CuCl4 (4-AbaH+ = protonated 4-aminobenzoic acid) possess the same generic formula as Ruddlesden-Popper (RP) layered perovskites, A2BX4, but adopt different structures. (4-AbaH)2CuCl4 adopts a near-staggered structure type, whereas (3-AbaH)2CuCl4 adopts a near-eclipsed structure type, which resembles the DJ rather than the RP family. (3-AbaH)2CuCl4 also displays static disorder of the [CuCl4]∞ layers. The crystal structures of each are discussed in terms of the differing nature of the templating molecular species, and these are compared to related layered perovskites. Preliminary magnetic measurements are reported, suggesting dominant ferromagnetic interactions.
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Affiliation(s)
- Ceng Han
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Alasdair J Bradford
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom.,School of Physics, University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - Alexandra M Z Slawin
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Bela E Bode
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Edoardo Fusco
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Stephen L Lee
- School of Physics, University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - Chiu C Tang
- Diamond Light Source Ltd, Didcot, OX11 0DE, United Kingdom
| | - Philip Lightfoot
- School of Chemistry and EaStChem, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
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19
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Abstract
The study of ever more complex biomolecular assemblies implicated in human health and disease is facilitated by a suite of complementary biophysical methods. Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is a powerful tool that provides highly precise geometric constraints in frozen solutions; however, the drive toward PDS at physiologically relevant sub-μM concentrations is limited by the currently achievable concentration sensitivity. Recently, PDS using a combination of nitroxide- and CuII-based spin labels allowed measuring a 500 nM concentration of a model protein. Using commercial instrumentation and spin labels, we demonstrate CuII-CuII and nitroxide-nitroxide PDS measurements at protein concentrations below previous examples reaching 500 and 100 nM, respectively. These results demonstrate the general feasibility of sub-μM PDS measurements at short to intermediate distances (∼1.5 to 3.5 nm), and are of particular relevance for applications where the achievable concentration is limiting.
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20
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Wort JL, Ackermann K, Norman DG, Bode BE. A general model to optimise Cu II labelling efficiency of double-histidine motifs for pulse dipolar EPR applications. Phys Chem Chem Phys 2021; 23:3810-3819. [PMID: 33533341 DOI: 10.1039/d0cp06196d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the dH motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, depending upon pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.
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Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - David G Norman
- School of Life Sciences, University of Dundee, Medical Sciences Institute, Dundee, DD1 5EH, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
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21
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Bell NL, Xu C, Fyfe JWB, Vantourout JC, Brals J, Chabbra S, Bode BE, Cordes DB, Slawin AMZ, McGuire TM, Watson AJB. Cu(OTf)
2
‐Mediated Cross‐Coupling of Nitriles and N‐Heterocycles with Arylboronic Acids to Generate Nitrilium and Pyridinium Products**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicola L. Bell
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Chao Xu
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - James W. B. Fyfe
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Julien C. Vantourout
- GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Jeremy Brals
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Sonia Chabbra
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - David B. Cordes
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Alexandra M. Z. Slawin
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Thomas M. McGuire
- AstraZeneca Darwin Building, Unit 310, Cambridge Science Park, Milton Road Cambridge CB4 0WG UK
| | - Allan J. B. Watson
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
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22
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Bell NL, Xu C, Fyfe JWB, Vantourout JC, Brals J, Chabbra S, Bode BE, Cordes DB, Slawin AMZ, McGuire TM, Watson AJB. Cu(OTf) 2 -Mediated Cross-Coupling of Nitriles and N-Heterocycles with Arylboronic Acids to Generate Nitrilium and Pyridinium Products*. Angew Chem Int Ed Engl 2021; 60:7935-7940. [PMID: 33449408 PMCID: PMC8048606 DOI: 10.1002/anie.202016811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Indexed: 12/25/2022]
Abstract
Metal-catalyzed C-N cross-coupling generally forms C-N bonds by reductive elimination from metal complexes bearing covalent C- and N-ligands. We have identified a Cu-mediated C-N cross-coupling that uses a dative N-ligand in the bond-forming event, which, in contrast to conventional methods, generates reactive cationic products. Mechanistic studies suggest the process operates via transmetalation of an aryl organoboron to a CuII complex bearing neutral N-ligands, such as nitriles or N-heterocycles. Subsequent generation of a putative CuIII complex enables the oxidative C-N coupling to take place, delivering nitrilium intermediates and pyridinium products. The reaction is general for a range of N(sp) and N(sp2 ) precursors and can be applied to drug synthesis and late-stage N-arylation, and the limitations in the methodology are mechanistically evidenced.
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Affiliation(s)
- Nicola L. Bell
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Chao Xu
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - James W. B. Fyfe
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Julien C. Vantourout
- GlaxoSmithKlineMedicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
| | - Jeremy Brals
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Sonia Chabbra
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Bela E. Bode
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - David B. Cordes
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | | | - Thomas M. McGuire
- AstraZenecaDarwin Building, Unit 310, Cambridge Science Park, Milton RoadCambridgeCB4 0WGUK
| | - Allan J. B. Watson
- EaStCHEMSchool of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
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23
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Abstract
Pulse-dipolar EPR is an appealing strategy for structural characterization of complex systems in solution that complements other biophysical techniques. Significantly, the emergence of genetically encoded self-assembling spin labels exploiting exogenously introduced double-histidine motifs in conjunction with CuII-chelates offers high precision distance determination in systems nonpermissive to thiol-directed spin labeling. However, the noncovalency of this interaction exposes potential vulnerabilities to competition from adventitious divalent metal ions, and pH sensitivity. Herein, a combination of room-temperature isothermal titration calorimetry (ITC) and cryogenic relaxation-induced dipolar modulation enhancement (RIDME) measurements are applied to the model protein Streptococcus sp. group G. protein G, B1 domain (GB1). Results demonstrate double-histidine motif spin labeling using CuII-nitrilotriacetic acid (CuII-NTA) is robust against the competitor ligand ZnII-NTA at >1000-fold molar excess, and high nM binding affinity is surprisingly retained under acidic and basic conditions even though room temperature affinity shows a stronger pH dependence. This indicates the strategy is well-suited for diverse biological applications, with the requirement of other metal ion cofactors or slightly acidic pH not necessarily being prohibitive.
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Affiliation(s)
| | - Swati Arya
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF, U.K
| | | | - Alan J Stewart
- School of Medicine, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF, U.K
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24
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Wort J, Arya S, Ackermann K, Stewart AJ, Bode BE. Pulse Dipolar EPR Reveals Double-Histidine Motif Cu II-NTA Spin-Labeling Robustness against Competitor Ions. J Phys Chem Lett 2021; 12:2815-2819. [PMID: 33715381 PMCID: PMC8006131 DOI: 10.1021/acs.jpclett.1c00211] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pulse-dipolar EPR is an appealing strategy for structural characterization of complex systems in solution that complements other biophysical techniques. Significantly, the emergence of genetically encoded self-assembling spin labels exploiting exogenously introduced double-histidine motifs in conjunction with CuII-chelates offers high precision distance determination in systems nonpermissive to thiol-directed spin labeling. However, the noncovalency of this interaction exposes potential vulnerabilities to competition from adventitious divalent metal ions, and pH sensitivity. Herein, a combination of room-temperature isothermal titration calorimetry (ITC) and cryogenic relaxation-induced dipolar modulation enhancement (RIDME) measurements are applied to the model protein Streptococcus sp. group G. protein G, B1 domain (GB1). Results demonstrate double-histidine motif spin labeling using CuII-nitrilotriacetic acid (CuII-NTA) is robust against the competitor ligand ZnII-NTA at >1000-fold molar excess, and high nM binding affinity is surprisingly retained under acidic and basic conditions even though room temperature affinity shows a stronger pH dependence. This indicates the strategy is well-suited for diverse biological applications, with the requirement of other metal ion cofactors or slightly acidic pH not necessarily being prohibitive.
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Affiliation(s)
- Joshua
L. Wort
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St.
Andrews, North Haugh, St. Andrews, KY16 9ST, U.K.
| | - Swati Arya
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St.
Andrews, North Haugh, St. Andrews, KY16 9ST, U.K.
- School
of Medicine, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF, U.K.
| | - Katrin Ackermann
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St.
Andrews, North Haugh, St. Andrews, KY16 9ST, U.K.
| | - Alan J. Stewart
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St.
Andrews, North Haugh, St. Andrews, KY16 9ST, U.K.
- School
of Medicine, University of St. Andrews, North Haugh, St. Andrews, KY16 9TF, U.K.
| | - Bela E. Bode
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St.
Andrews, North Haugh, St. Andrews, KY16 9ST, U.K.
- E-mail:
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25
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Chabbra S, Smith DM, Bell NL, Watson AJB, Bühl M, Cole-Hamilton DJ, Bode BE. First experimental evidence for a bis-ethene chromium(I) complex forming from an activated ethene oligomerization catalyst. Sci Adv 2020; 6:6/51/eabd7057. [PMID: 33355141 DOI: 10.1126/sciadv.abd7057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
A bis-ethene chromium(I) species, which is the postulated key intermediate in the widely accepted metallacyclic mechanism for ethene oligomerization, is experimentally observed. This catalytic transformation is an important commercial route to linear α-olefins (primarily, 1-hexene and 1-octene), which act as comonomers for the production of polyethene. Here, electron paramagnetic resonance studies of a catalytic system based on [Cr(CO)4(PNP)][Al(OC(CF3)3)4] [PNP = Ph2PN(iPr)PPh2] activated with Et6Al2 provide the first unequivocal evidence for a chromium(I) bis-ethene complex. The concentration of this species is enhanced under ethene and isotope labeling studies that confirm its composition as containing [Cr(C2H4)2(CO)2(PNP)]+ These observations open a new route to mechanistic studies of selective ethene oligomerization.
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Affiliation(s)
- S Chabbra
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
| | - D M Smith
- Drochaid Research Services, St Andrews, Fife KY16 9ST, Scotland, UK
| | - N L Bell
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
| | - A J B Watson
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
| | - M Bühl
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
| | - D J Cole-Hamilton
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
| | - B E Bode
- EaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK.
- Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland, UK
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26
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Watts AE, Lozinska MM, Slawin AMZ, Mayoral A, Dawson DM, Ashbrook SE, Bode BE, Dugulan AI, Shannon MD, Cox PA, Turrina A, Wright PA. Site‐Specific Iron Substitution in STA‐28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1,10‐Phenanthrolines as Framework‐Bound Templates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Abigail E. Watts
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - Magdalena M. Lozinska
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - Alexandra M. Z. Slawin
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - Alvaro Mayoral
- Instituto de Ciencia de Materiales de Aragon (ICMA) CSIC Universidad de Zaragoza Mariano Esquillor 50018 Zaragoza Spain
- Center for High-Resolution Electron Microscopy (CħEM) School of Physical Science and Technology ShanghaiTech University 393 Middle Huaxia Road Pudong Shanghai 201210 China
| | - Daniel M. Dawson
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - Sharon E. Ashbrook
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
| | - A. Iulian Dugulan
- Fundamental Aspects of Materials and Energy Group Delft University of Technology 2629 JB Delft The Netherlands
| | - Mervyn D. Shannon
- Johnson Matthey Technology Centre Chilton P.O. Box 1, Belasis Avenue Billingham TS23 1LB UK
| | - Paul A. Cox
- School of Pharmacy and Biomedical Sciences University of Portsmouth St. Michael's Building, White Swan Road Portsmouth PO1 UK
| | - Alessandro Turrina
- Johnson Matthey Technology Centre Chilton P.O. Box 1, Belasis Avenue Billingham TS23 1LB UK
| | - Paul A. Wright
- EaStCHEM School of Chemistry University of St Andrews Purdie Building North Haugh St Andrews, Fife KY16 9ST UK
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27
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Watts AE, Lozinska MM, Slawin AMZ, Mayoral A, Dawson DM, Ashbrook SE, Bode BE, Dugulan AI, Shannon MD, Cox PA, Turrina A, Wright PA. Site-Specific Iron Substitution in STA-28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1,10-Phenanthrolines as Framework-Bound Templates. Angew Chem Int Ed Engl 2020; 59:15186-15190. [PMID: 32432353 PMCID: PMC7496423 DOI: 10.1002/anie.202005558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/03/2022]
Abstract
An AlPO4 zeotype has been prepared using the aromatic diamine 1,10-phenanthroline and some of its methylated analogues as templates. In each case the two template N atoms bind to a specific framework Al site to expand its coordination to the unusual octahedral AlO4 N2 environment. Furthermore, using this framework-bound template, Fe atoms can be included selectively at this site in the framework by direct synthesis, as confirmed by annular dark field scanning transmission electron microscopy and Rietveld refinement. Calcination removes the organic molecules to give large pore framework solids, with BET surface areas up to 540 m2 g-1 and two perpendicular sets of channels that intersect to give pore space connected by 12-ring openings along all crystallographic directions.
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Affiliation(s)
- Abigail E. Watts
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - Magdalena M. Lozinska
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - Alexandra M. Z. Slawin
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - Alvaro Mayoral
- Instituto de Ciencia de Materiales de Aragon (ICMA)CSICUniversidad de ZaragozaMariano Esquillor50018ZaragozaSpain
- Center for High-Resolution Electron Microscopy (CħEM)School of Physical Science and TechnologyShanghaiTech University393 Middle Huaxia RoadPudongShanghai201210China
| | - Daniel M. Dawson
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - Sharon E. Ashbrook
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - Bela E. Bode
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
| | - A. Iulian Dugulan
- Fundamental Aspects of Materials and Energy GroupDelft University of Technology2629 JBDelftThe Netherlands
| | - Mervyn D. Shannon
- Johnson Matthey Technology CentreChilton P.O. Box 1, Belasis AvenueBillinghamTS23 1LBUK
| | - Paul A. Cox
- School of Pharmacy and Biomedical SciencesUniversity of PortsmouthSt. Michael's Building, White Swan RoadPortsmouthPO1UK
| | - Alessandro Turrina
- Johnson Matthey Technology CentreChilton P.O. Box 1, Belasis AvenueBillinghamTS23 1LBUK
| | - Paul A. Wright
- EaStCHEM School of ChemistryUniversity of St AndrewsPurdie BuildingNorth HaughSt Andrews, FifeKY16 9STUK
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28
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Kapsalis C, Ma Y, Bode BE, Pliotas C. In-Lipid Structure of Pressure-Sensitive Domains Hints Mechanosensitive Channel Functional Diversity. Biophys J 2020; 119:448-459. [PMID: 32621864 PMCID: PMC7376121 DOI: 10.1016/j.bpj.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis has been used as a structural model for rationalizing functional observations in multiple MscL orthologs. Although these orthologs adopt similar structural architectures, they reportedly present significant functional differences. Subtle structural discrepancies on mechanosensitive channel nanopockets are known to affect mechanical gating and may be linked to large variability in tension sensitivity among these membrane channels. Here, we modify the nanopocket regions of MscL from Escherichia coli and M. tuberculosis and employ PELDOR/DEER distance and 3pESEEM deuterium accessibility measurements to interrogate channel structure within lipids, in which both channels adopt a closed conformation. Significant in-lipid structural differences between the two constructs suggest a more compact E. coli MscL at the membrane inner-leaflet, as a consequence of a rotated TM2 helix. Observed differences within lipids could explain E. coli MscL’s higher tension sensitivity and should be taken into account in extrapolated models used for MscL gating rationalization.
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Affiliation(s)
- Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Yue Ma
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, St Andrews, United Kingdom.
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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29
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Sood DE, Champion S, Dawson DM, Chabbra S, Bode BE, Sutherland A, Watson AJB. Deoxyfluorination with CuF
2
: Enabled by Using a Lewis Base Activating Group. Angew Chem Int Ed Engl 2020; 59:8460-8463. [PMID: 32109331 DOI: 10.1002/anie.202001015] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/28/2020] [Indexed: 11/06/2022]
Affiliation(s)
- D. Eilidh Sood
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Sue Champion
- West of Scotland PET Centre Greater Glasgow and Clyde NHS Trust Glasgow G12 OYN UK
| | - Daniel M. Dawson
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Sonia Chabbra
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Andrew Sutherland
- WestCHEM School of Chemistry University of Glasgow Glasgow G12 8QQ UK
| | - Allan J. B. Watson
- EaStCHEM School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
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30
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Wort JL, Ackermann K, Giannoulis A, Stewart AJ, Norman DG, Bode BE. Sub‐Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing Cu
II
‐labelling of Double‐Histidine Motifs with Lower Temperature. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904848] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Joshua L. Wort
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Angeliki Giannoulis
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Alan J. Stewart
- School of Medicine Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9TF UK
| | - David G. Norman
- School of Life Sciences University of Dundee, Medical Sciences Institute Dundee DD1 5EH UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
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31
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Wort JL, Ackermann K, Giannoulis A, Stewart AJ, Norman DG, Bode BE. Sub-Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing Cu II -labelling of Double-Histidine Motifs with Lower Temperature. Angew Chem Int Ed Engl 2019; 58:11681-11685. [PMID: 31218813 PMCID: PMC6771633 DOI: 10.1002/anie.201904848] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/03/2019] [Indexed: 12/20/2022]
Abstract
Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to the studies of biomolecules by providing highly accurate geometric constraints. Combining double‐histidine motifs with CuII spin labels can further increase the precision of distance measurements. It is also useful for proteins containing essential cysteines that can interfere with thiol‐specific labelling. However, the non‐covalent CuII coordination approach is vulnerable to low binding‐affinity. Herein, dissociation constants (KD) are investigated directly from the modulation depths of relaxation‐induced dipolar modulation enhancement (RIDME) EPR experiments. This reveals low‐ to sub‐μm CuIIKDs under EPR distance measurement conditions at cryogenic temperatures. We show the feasibility of exploiting the double‐histidine motif for EPR applications even at sub‐μm protein concentrations in orthogonally labelled CuII–nitroxide systems using a commercial Q‐band EPR instrument.
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Affiliation(s)
- Joshua L. Wort
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Katrin Ackermann
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Angeliki Giannoulis
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Alan J. Stewart
- School of MedicineBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9TFUK
| | - David G. Norman
- School of Life SciencesUniversity of Dundee, Medical Sciences InstituteDundeeDD1 5EHUK
| | - Bela E. Bode
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
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32
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Vantourout JC, Li L, Bendito-Moll E, Chabbra S, Arrington K, Bode BE, Isidro-Llobet A, Kowalski JA, Nilson MG, Wheelhouse KMP, Woodard JL, Xie S, Leitch DC, Watson AJB. Mechanistic Insight Enables Practical, Scalable, Room Temperature Chan–Lam N-Arylation of N-Aryl Sulfonamides. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03238] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julien C. Vantourout
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, U.K
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ling Li
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - Enrique Bendito-Moll
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, U.K
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sonia Chabbra
- EaStCHEM, School of Chemistry, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, U.K
| | - Kenneth Arrington
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - Bela E. Bode
- EaStCHEM, School of Chemistry, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, U.K
| | - Albert Isidro-Llobet
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - John A. Kowalski
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - Mark G. Nilson
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | | | - John L. Woodard
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - Shiping Xie
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - David C. Leitch
- GlaxoSmithKline, Medicines Research Centre, 709 Swedeland Road #1539, King of Prussia, Pennsylvania 19406, United States
| | - Allan J. B. Watson
- EaStCHEM, School of Chemistry, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, U.K
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33
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Chabbra S, Smith DM, Bode BE. Isolation of EPR spectra and estimation of spin-states in two-component mixtures of paramagnets. Dalton Trans 2018; 47:10473-10479. [PMID: 29697132 DOI: 10.1039/c8dt00977e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of multiple paramagnetic species can lead to overlapping electron paramagnetic resonance (EPR) signals. This complication can be a critical obstacle for the use of EPR to unravel mechanisms and aid the understanding of earth abundant metal catalysis. Furthermore, redox or spin-crossover processes can result in the simultaneous presence of metal centres in different oxidation or spin states. In this contribution, pulse EPR experiments on model systems containing discrete mixtures of Cr(i) and Cr(iii) or Cu(ii) and Mn(ii) complexes demonstrate the feasibility of the separation of the EPR spectra of these species by inversion recovery filters and the identification of the relevant spin states by transient nutation experiments. We demonstrate the isolation of component spectra and identification of spin states in a mixture of catalyst precursors. The usefulness of the approach is emphasised by monitoring the fate of the chromium species upon activation of an industrially used precatalyst system.
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Affiliation(s)
- Sonia Chabbra
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK.
| | - David M Smith
- Sasol UK Ltd, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK.
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34
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Affiliation(s)
- Bela E. Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland
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35
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Affiliation(s)
- Katrin Ackermann
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
| | - Bela E. Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
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36
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Giannoulis A, Motion CL, Oranges M, Bühl M, Smith GM, Bode BE. Orientation selection in high-field RIDME and PELDOR experiments involving low-spin CoII ions. Phys Chem Chem Phys 2018; 20:2151-2154. [DOI: 10.1039/c7cp07248a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orientation selective pulse dipolar electron paramagnetic resonance unravels relative geometries of spin centres from RIDME and PELDOR data.
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Affiliation(s)
- Angeliki Giannoulis
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | | | - Maria Oranges
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | - Michael Bühl
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
| | - Graham M. Smith
- SUPA, School of Physics & Astronomy, University of St Andrews
- UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
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37
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Montgomery JD, Lancefield CS, Miles-Barrett DM, Ackermann K, Bode BE, Westwood NJ, Lebl T. Fractionation and DOSY NMR as Analytical Tools: From Model Polymers to a Technical Lignin. ACS Omega 2017; 2:8466-8474. [PMID: 31457383 PMCID: PMC6645228 DOI: 10.1021/acsomega.7b01287] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/08/2017] [Indexed: 05/31/2023]
Abstract
One key challenge hindering the valorization of lignin is its structural complexity. Artificial lignin-like materials provide a stepping stone between the simplicity of model compounds and the complexity of lignin. Here, we report an optimized synthesis of an all-G β-O-4 polymer 1 designed to model softwood lignin. After acetylation, the polymer Ac-1(V) was fractionated using a protocol that involved only volatile organic solvents, which left no insoluble residue. Using diffusion ordered spectroscopy NMR in combination with gel permeation chromatography, it was revealed that this fractionated material behaved like a flexible linear polymer in solution (average α > 0.5). Acetylated kraft lignin was subsequently processed using the same fractionation protocol. By comparison with the model polymer, we propose that the acetylated kraft lignin is composed of two classes of materials that exhibit contrasting physical properties. One is comparable to the acetylated all-G β-O-4 polymer Ac-1, and the second has a significantly different macromolecular structure.
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38
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Ackermann K, Pliotas C, Valera S, Naismith JH, Bode BE. Sparse Labeling PELDOR Spectroscopy on Multimeric Mechanosensitive Membrane Channels. Biophys J 2017; 113:1968-1978. [PMID: 29117521 PMCID: PMC5685675 DOI: 10.1016/j.bpj.2017.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/17/2022] Open
Abstract
Pulse electron paramagnetic resonance (EPR) is being applied to ever more complex biological systems comprising multiple subunits. Membrane channel proteins are of great interest as pulse EPR reports on functionally significant but distinct conformational states in a native environment without the need for crystallization. Pulse EPR, in the form of pulsed electron-electron double resonance (PELDOR), using site-directed spin labeling, is most commonly employed to accurately determine distances (in the nanometer range) between different regions of the structure. However, PELDOR data analysis is more challenging in systems containing more than two spins (e.g., homomultimers) due to distorting multispin effects. Without suppression of these effects, much of the information contained in PELDOR data cannot be reliably retrieved. Thus, it is of utmost importance for future PELDOR applications in structural biology to develop suitable approaches that can overcome the multispin problem. Here, two different approaches for suppressing multispin effects in PELDOR, sparse labeling of the protein (reducing the labeling efficiency f) and reducing the excitation probability of spins (λ), are compared on two distinct bacterial mechanosensitive channels. For both the pentameric channel of large conductance (MscL) and the heptameric channel of small conductance (MscS) of Escherichia coli, mutants containing a spin label in the cytosolic or the transmembrane region were tested. Data demonstrate that distance distributions can be significantly improved with either approach compared to the standard PELDOR measurement, and confirm that λ < 1/(n−1) is needed to sufficiently suppress multispin effects (with n being the number of spins in the system). A clear advantage of the sparse labeling approach is demonstrated for the cytosolic mutants due to a significantly smaller loss in sensitivity. For the transmembrane mutants, this advantage is less pronounced but still useful for MscS, but performance is inferior for MscL possibly due to structural perturbations by the bulkier diamagnetic spin label analog.
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Affiliation(s)
- Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - James H Naismith
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom.
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39
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Giannoulis A, Oranges M, Bode BE. Monitoring Complex Formation by Relaxation-Induced Pulse Electron Paramagnetic Resonance Distance Measurements. Chemphyschem 2017; 18:2318-2321. [PMID: 28672084 PMCID: PMC5601224 DOI: 10.1002/cphc.201700666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Indexed: 12/14/2022]
Abstract
Biomolecular complexes are often multimers fueling the demand for methods that allow unraveling their composition and geometric arrangement. Pulse electron paramagnetic resonance (EPR) spectroscopy is increasingly applied for retrieving geometric information on the nanometer scale. The emerging RIDME (relaxation‐induced dipolar modulation enhancement) technique offers improved sensitivity in distance experiments involving metal centers (e.g. on metalloproteins or proteins labelled with metal ions). Here, a mixture of a spin labelled ligand with increasing amounts of paramagnetic CuII ions allowed accurate quantification of ligand‐metal binding in the model complex formed. The distance measurement was highly accurate and critical aspects for identifying multimerization could be identified. The potential to quantify binding in addition to the high‐precision distance measurement will further increase the scope of EPR applications.
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Affiliation(s)
- Angeliki Giannoulis
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
| | - Maria Oranges
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
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40
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Kirst C, Bode BE, Cordes DB, Nejman PS, Slawin AMZ, Karaghiosoff K, Woollins JD. Diphosphane 2,2'-binaphtho[1,8-de][1,3,2]dithiaphosphinine and the easy formation of a stable phosphorus radical cation. Dalton Trans 2016; 45:6348-51. [PMID: 26988270 DOI: 10.1039/c6dt00304d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient synthesis route to 2,2'-binaphtho[1,8-de][1,3,2]di-thiaphosphinine () was found. Its stable radical cation 3˙(+) was accessed easily through one-electron oxidation with NOBF4.
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Affiliation(s)
- Christin Kirst
- Department of Chemistry, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13 (D), 81377 Munich, Germany.
| | - Bela E Bode
- EastCHEM School of Chemistry, University of St. Andrews, Fife, KY16 9ST, UK.
| | - David B Cordes
- EastCHEM School of Chemistry, University of St. Andrews, Fife, KY16 9ST, UK.
| | - Phillip S Nejman
- EastCHEM School of Chemistry, University of St. Andrews, Fife, KY16 9ST, UK.
| | | | - Konstantin Karaghiosoff
- Department of Chemistry, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13 (D), 81377 Munich, Germany.
| | - J Derek Woollins
- EastCHEM School of Chemistry, University of St. Andrews, Fife, KY16 9ST, UK.
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41
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Abstract
Pulse electron paramagnetic resonance (EPR) is gaining increasing importance in structural biology. The PELDOR (pulsed electron–electron double resonance) method allows extracting distance information on the nanometer scale. Here, we demonstrate the efficient extraction of distances from multimeric systems such as membrane‐embedded ion channels where data analysis is commonly hindered by multi‐spin effects.
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Affiliation(s)
- Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Hexian Huang
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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42
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Ackermann K, Giannoulis A, Cordes DB, Slawin AMZ, Bode BE. Assessing dimerisation degree and cooperativity in a biomimetic small-molecule model by pulsed EPR. Chem Commun (Camb) 2016; 51:5257-60. [PMID: 25587579 DOI: 10.1039/c4cc08656b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pulsed electron paramagnetic resonance (EPR) spectroscopy is gaining increasing importance as a complementary biophysical technique in structural biology. Here, we describe the synthesis, optimisation, and EPR titration studies of a spin-labelled terpyridine Zn(II) complex serving as a small-molecule model system for tuneable dimerisation.
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Affiliation(s)
- K Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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43
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Ishikawa H, Munaò I, Bode BE, Hiroi Z, Lightfoot P. Na2MoO(2-δ)F(4+δ)--a perovskite with a unique combination of atomic orderings and octahedral tilts. Chem Commun (Camb) 2016; 51:15469-71. [PMID: 26351702 DOI: 10.1039/c5cc05446j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Na2MoO2-δF4+δ (δ ∼ 0.08) displays a unique variant of the perovskite structure, with simultaneous (Na,vacancy) ordering on the A-site, (Na,Mo) ordering on the B-site, (O,F) ordering on the anion site and an unusual NaNbO3-like octahedral tilt system.
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Affiliation(s)
- Hajime Ishikawa
- Institute for Solid State Physics, University of Tokyo, Kashiwa 277-8581, Japan
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44
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Morten MJ, Peregrina JR, Figueira-Gonzalez M, Ackermann K, Bode BE, White MF, Penedo JC. Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach. Nucleic Acids Res 2015; 43:10907-24. [PMID: 26578575 PMCID: PMC4678828 DOI: 10.1093/nar/gkv1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/29/2015] [Indexed: 01/28/2023] Open
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif to recognize single-stranded DNA (ssDNA). Despite their critical role in genome maintenance, our knowledge about SSB function is limited to proteins containing multiple OB-domains and little is known about single OB-folds interacting with ssDNA. Sulfolobus solfataricus SSB (SsoSSB) contains a single OB-fold and being the simplest representative of the SSB-family may serve as a model to understand fundamental aspects of SSB:DNA interactions. Here, we introduce a novel approach based on the competition between Förster resonance energy transfer (FRET), protein-induced fluorescence enhancement (PIFE) and quenching to dissect SsoSSB binding dynamics at single-monomer resolution. We demonstrate that SsoSSB follows a monomer-by-monomer binding mechanism that involves a positive-cooperativity component between adjacent monomers. We found that SsoSSB dynamic behaviour is closer to that of Replication Protein A than to Escherichia coli SSB; a feature that might be inherited from the structural analogies of their DNA-binding domains. We hypothesize that SsoSSB has developed a balance between high-density binding and a highly dynamic interaction with ssDNA to ensure efficient protection of the genome but still allow access to ssDNA during vital cellular processes.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Jose R Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Maria Figueira-Gonzalez
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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45
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Paul S, Bode BE, Matysik J, Alia A. Photochemically Induced Dynamic Nuclear Polarization Observed by Solid-State NMR in a Uniformly (13)C-Isotope-Labeled Photosynthetic Reaction Center. J Phys Chem B 2015; 119:13897-903. [PMID: 26110356 DOI: 10.1021/acs.jpcb.5b04542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A sample of solubilized and quinone-depleted reaction centers from the purple bacterium Rhodobacter (R.) sphaeroides wild type has been prepared entirely (13)C and (15)N isotope labeled at all positions of the protein as well as of the cofactors. In this sample, the occurrence of the solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect has been probed by (13)C solid-state magic-angle spinning NMR under illumination. Under continuous illumination, signal intensities are modified by the three-spin mixing (TSM) mechanism. Time-resolved illumination experiments reveal the occurrence of light-induced nuclear polarization on the time scale of hundreds of microseconds, initially dominated by the transient polarization of the singlet branch of the radical-pair mechanism. A first kinetic analysis shows that the lifetime of the polarization from the singlet branch, indicated by the enhanced absorptive intensities of the signals from aliphatic carbons, is significantly extended. Upon arrival of the polarization from the triplet decay branch, emissive polarization caused by the TSM mechanism is observed. Also, this arrival is significantly delayed. The decay of TSM polarization occurs in two steps, assigned to intra- and intermolecular spin diffusion.
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Affiliation(s)
- Shubhajit Paul
- Universität Leipzig , Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews , St Andrews KY16 9ST, Scotland
| | - Jörg Matysik
- Universität Leipzig , Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany
| | - A Alia
- Universität Leipzig , Institut für Medizinische Physik und Biophysik, Härtelstr. 16, D-04107 Leipzig, Germany.,Gorlaeus Laboratoria, Leiden Institute of Chemistry , Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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46
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Ackermann K, Giannoulis A, Cordes DB, Slawin AMZ, Bode BE. Correction: Assessing dimerisation degree and cooperativity in a biomimetic small-molecule model by pulsed EPR. Chem Commun (Camb) 2015; 51:15472. [PMID: 26416772 DOI: 10.1039/c5cc90439k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Assessing dimerisation degree and cooperativity in a biomimetic small-molecule model by pulsed EPR' by K. Ackermann et al., Chem. Commun., 2015, 51, 5257-5260.
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Affiliation(s)
- K Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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47
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Pushkarevsky NA, Semenov NA, Dmitriev AA, Kuratieva NV, Bogomyakov AS, Irtegova IG, Vasilieva NV, Bode BE, Gritsan NP, Konstantinova LS, Woollins JD, Rakitin OA, Konchenko SN, Ovcharenko VI, Zibarev AV. Synthesis and Properties of the Heterospin (S1 = S2 = 1/2) Radical-Ion Salt Bis(mesitylene)molybdenum(I) [1,2,5]Thiadiazolo[3,4-c][1,2,5]thiadiazolidyl. Inorg Chem 2015; 54:7007-13. [DOI: 10.1021/acs.inorgchem.5b01033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Bela E. Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | | | | | - J. Derek Woollins
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Oleg A. Rakitin
- Institute
of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | | | - Andrey V. Zibarev
- Department of Chemistry, Tomsk State University, 634050 Tomsk, Russia
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48
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Valera S, Bode BE. Strategies for the synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR. Molecules 2014; 19:20227-56. [PMID: 25479188 PMCID: PMC6271543 DOI: 10.3390/molecules191220227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 01/18/2023] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) techniques have been found to be efficient tools for the elucidation of structure in complex biological systems as they give access to distances in the nanometre range. These measurements can provide additional structural information such as relative orientations, structural flexibility or aggregation states. A wide variety of model systems for calibration and optimisation of pulsed experiments has been synthesised. Their design is based on mimicking biological systems or materials in specific properties such as the distances themselves and the distance distributions. Here, we review selected approaches to the synthesis of chemical systems bearing two or more spin centres, such as nitroxide or trityl radicals, metal ions or combinations thereof and outline their application in pulsed EPR distance measurements.
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Affiliation(s)
- Silvia Valera
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK.
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49
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Kerry PS, Turkington HL, Ackermann K, Jameison SA, Bode BE. Analysis of influenza A virus NS1 dimer interfaces in solution by pulse EPR distance measurements. J Phys Chem B 2014; 118:10882-8. [PMID: 25148246 PMCID: PMC4191058 DOI: 10.1021/jp508386r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Pulsed electron–electron double
resonance (PELDOR) is an
electron paramagnetic resonance (EPR) spectroscopy technique for nanometer
distance measurements between paramagnetic centers such as radicals.
PELDOR has been recognized as a valuable tool to approach structural
questions in biological systems. In this manuscript, we demonstrate
the value of distance measurements for differentiating competing structural
models on the dimerization of the effector domain (ED) of the non-structural
protein 1 (NS1) of the influenza A virus. Our results show NS1 to
be well amenable to nanometer distance measurements by EPR, yielding
high quality data. In combination with mutants perturbing protein
dimerization and in silico prediction based on crystal
structures, we can exclude one of two potential dimerization interfaces.
Furthermore, our results lead to a viable hypothesis of a NS1 ED:ED
interface which is flexible through rotation around the vector interconnecting
the two native cysteines. These results prove the high value of pulse
EPR as a complementary method for structural biology.
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Affiliation(s)
- Philip S Kerry
- Biomedical Sciences Research Complex, University of St Andrews , St Andrews, Fife, KY16 9ST, U.K
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50
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Valera S, Taylor JE, Daniels DSB, Dawson DM, Athukorala Arachchige KS, Ashbrook SE, Slawin AMZ, Bode BE. A modular approach for the synthesis of nanometer-sized polynitroxide multi-spin systems. J Org Chem 2014; 79:8313-23. [PMID: 25102422 DOI: 10.1021/jo5015678] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The synthesis of rigid symmetric polyradical model systems with inter-spin distances between 1.4 and 4 nm and their room temperature continuous wave (CW) EPR spectra are reported. Conditions for attachment of the spin-label via esterification have been optimized on the direct synthesis of polyradicals from commercially available polyphenols and the carboxylic acid functionalized nitroxide TPC. A common synthetic protocol utilizing 4-hydroxy-4'-iodobiphenyl as a key building block has been used to synthesize an equilateral biradical and a triradical in only two steps from commercially available starting materials. The first synthesis of a tetraradical based upon an adamantane core bearing six equivalent nitroxide-nitroxide distances is also reported. These systems are very promising candidates for studying multi-spin effects in pulsed EPR distance measurements.
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Affiliation(s)
- Silvia Valera
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews , North Haugh, St Andrews KY16 9ST, United Kingdom
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