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Brevetoxins (PbTx) are a well-recognized group of neurotoxins associated with harmful algal blooms, and specifically recurrent “Florida Red Tides,” in marine waters that are linked to impacts on both human and ecosystem health including well-documented “fish kills” and marine mammal mortalities in affected coastal waters. Understanding mechanisms and pathways of PbTx toxicity enables identification of relevant biomarkers to better understand these environmental impacts, and improve monitoring efforts, in relation to this toxin. Toward a systems-level understanding of toxicity, and identification of potential biomarkers, high-resolution magic angle spinning nuclear magnetic resonance (HRMAS NMR) was utilized for metabolic profiling of zebrafish (Danio rerio) embryos, as an established toxicological model, exposed to PbTx-2 (the most common congener in marine waters). Metabolomics studies were, furthermore, complemented by an assessment of the toxicity of PbTx-2 in embryonic stages of zebrafish and mahi-mahi (Coryphaena hippurus), the latter representing an ecologically and geographically relevant marine species of fish, which identified acute embryotoxicity at environmentally relevant (i.e., parts-per-billion) concentrations in both species. HRMAS NMR analysis of intact zebrafish embryos exposed to sub-lethal concentrations of PbTx-2 afforded well-resolved spectra, and in turn, identification of 38 metabolites of which 28 were found to be significantly altered, relative to controls. Metabolites altered by PbTx-2 exposure specifically included those associated with (1) neuronal excitotoxicity, as well as associated neural homeostasis, and (2) interrelated pathways of carbohydrate and energy metabolism. Metabolomics studies, thereby, enabled a systems-level model of PbTx toxicity which integrated multiple metabolic, molecular and cellular pathways, in relation to environmentally relevant concentrations of the toxin, providing insight to not only targets and mechanisms, but potential biomarkers pertinent to environmental risk assessment and monitoring strategies.
Mark Annunziato; Muhamed N.H. Eeza; Narmin Bashirova; Ariel Lawson; Jörg Matysik; Daniel Benetti; Martin Grosell; John D. Stieglitz; A. Alia; John P. Berry. An integrated systems-level model of the toxicity of brevetoxin based on high-resolution magic-angle spinning nuclear magnetic resonance (HRMAS NMR) metabolic profiling of zebrafish embryos. Science of The Total Environment 2021, 149858 .
AMA StyleMark Annunziato, Muhamed N.H. Eeza, Narmin Bashirova, Ariel Lawson, Jörg Matysik, Daniel Benetti, Martin Grosell, John D. Stieglitz, A. Alia, John P. Berry. An integrated systems-level model of the toxicity of brevetoxin based on high-resolution magic-angle spinning nuclear magnetic resonance (HRMAS NMR) metabolic profiling of zebrafish embryos. Science of The Total Environment. 2021; ():149858.
Chicago/Turabian StyleMark Annunziato; Muhamed N.H. Eeza; Narmin Bashirova; Ariel Lawson; Jörg Matysik; Daniel Benetti; Martin Grosell; John D. Stieglitz; A. Alia; John P. Berry. 2021. "An integrated systems-level model of the toxicity of brevetoxin based on high-resolution magic-angle spinning nuclear magnetic resonance (HRMAS NMR) metabolic profiling of zebrafish embryos." Science of The Total Environment , no. : 149858.
Among hyperpolarization techniques, quantum-rotor induced polarization (QRIP), also known as Haupt effect, is a peculiar one. It is on one hand rather simple to apply by cooling and heating of a sample. On the other hand, only the methyl groups of a few substances seem to allow for the effect, which strongly limits the applicability of QRIP. While it is known, that a high tunnel frequency is favorable, the structural requirements for the effect to occur are not exhaustively studied yet. Here we report on our efforts to heuristically recognize structural motifs in molecular crystals able to allow to produce QRIP.
Corinna Dietrich; Julia Wissel; Oliver Lorenz; Arafat Hossain Khan; Marko Bertmer; Somayeh Khazaei; Daniel Sebastiani; Jörg Matysik. The relation between crystal structure and the occurrence of quantum-rotor induced polarization. 2021, 2021, 1 -18.
AMA StyleCorinna Dietrich, Julia Wissel, Oliver Lorenz, Arafat Hossain Khan, Marko Bertmer, Somayeh Khazaei, Daniel Sebastiani, Jörg Matysik. The relation between crystal structure and the occurrence of quantum-rotor induced polarization. . 2021; 2021 ():1-18.
Chicago/Turabian StyleCorinna Dietrich; Julia Wissel; Oliver Lorenz; Arafat Hossain Khan; Marko Bertmer; Somayeh Khazaei; Daniel Sebastiani; Jörg Matysik. 2021. "The relation between crystal structure and the occurrence of quantum-rotor induced polarization." 2021, no. : 1-18.
This publication, in honour of Robert Kaptein's 80th birthday, contains contributions from colleagues, many of whom have worked with him, and others who admire his work and have been stimulated by his research. The contributions show current research in biomolecular NMR, spin hyperpolarisation and spin chemistry, including CIDNP (chemically induced dynamic nuclear polarisation), topics to which he has contributed enormously. His proposal of the radical pair mechanism was the birth of the field of spin chemistry, and the laser CIDNP NMR experiment on a protein was a major breakthrough in hyperpolarisation research. He set milestones for biomolecular NMR by developing computational methods for protein structure determination, including restrained molecular dynamics and 3D NMR methodology. With a lac repressor headpiece, he determined one of the first protein structures determined by NMR. His studies of the lac repressor provided the first examples of detailed studies of protein nucleic acid complexes by NMR. This deepened our understanding of protein DNA recognition and led to a molecular model for protein sliding along the DNA. Furthermore, he played a leading role in establishing the cluster of NMR large-scale facilities in Europe. This editorial gives an introduction to the publication and is followed by a biography describing his contributions to magnetic resonance.
Rolf Boelens; Konstantin Ivanov; Jörg Matysik. Introduction to a special issue of Magnetic Resonance in honour of Robert Kaptein at the occasion of his 80th birthday. Magnetic Resonance 2021, 2, 465 -474.
AMA StyleRolf Boelens, Konstantin Ivanov, Jörg Matysik. Introduction to a special issue of Magnetic Resonance in honour of Robert Kaptein at the occasion of his 80th birthday. Magnetic Resonance. 2021; 2 (1):465-474.
Chicago/Turabian StyleRolf Boelens; Konstantin Ivanov; Jörg Matysik. 2021. "Introduction to a special issue of Magnetic Resonance in honour of Robert Kaptein at the occasion of his 80th birthday." Magnetic Resonance 2, no. 1: 465-474.
Circadian rhythm disturbance is commonly observed in Alzheimer’s disease (AD). In mammals, these rhythms are orchestrated by the superchiasmatic nucleus (SCN). Our previous study in the Tg2576 AD mouse model suggests that inflammatory responses, most likely manifested by low GABA production, may be one of the underlying perpetrators for the changes in circadian rhythmicity and sleep disturbance in AD. However, the mechanistic connections between SCN dysfunction, GABA modulation, and inflammation in AD is not fully understood. To reveal influences of amyloid pathology in Tg2576 mouse brain on metabolism in SCN and to identify key metabolic sensors that couple SCN dysfunction with GABA modulation and inflammation. High resolution magic angle spinning (HR-MAS) NMR in conjunction with multivariate analysis was applied for metabolic profiling in SCN of control and Tg2576 female mice. Immunohistochemical analysis was used to detect neurons, astrocytes, expression of GABA transporter 1 (GAT1) and Bmal1. Metabolic profiling revealed significant metabolic deficits in SCN of Tg2576 mice. Reductions in glucose, glutamate, GABA, and glutamine provide hints toward an impaired GABAergic glucose oxidation and neurotransmitter cycling in SCN of AD mice. In addition, decreased redox co-factor NADPH and glutathione support a redox disbalance. Immunohistochemical examinations showed low expression of the core clock protein, Bmal1, especially in activated astrocytes. Moreover, decreased expression of GAT1 in astrocytes indicates low GABA recycling in this cell type. Our results suggest that redox disbalance and compromised GABA signaling are important denominators and connectors between neuroinflammation and clock dysfunction in AD.
Muhamed N.H. Eeza; Rico Singer; Corinna Höfling; Jörg Matysik; Huub J.M. de Groot; Steffen Roβner; A. Alia. Metabolic Profiling of Suprachiasmatic Nucleus Reveals Multifaceted Effects in an Alzheimer’s Disease Mouse Model. Journal of Alzheimer's Disease 2021, 81, 797 -808.
AMA StyleMuhamed N.H. Eeza, Rico Singer, Corinna Höfling, Jörg Matysik, Huub J.M. de Groot, Steffen Roβner, A. Alia. Metabolic Profiling of Suprachiasmatic Nucleus Reveals Multifaceted Effects in an Alzheimer’s Disease Mouse Model. Journal of Alzheimer's Disease. 2021; 81 (2):797-808.
Chicago/Turabian StyleMuhamed N.H. Eeza; Rico Singer; Corinna Höfling; Jörg Matysik; Huub J.M. de Groot; Steffen Roβner; A. Alia. 2021. "Metabolic Profiling of Suprachiasmatic Nucleus Reveals Multifaceted Effects in an Alzheimer’s Disease Mouse Model." Journal of Alzheimer's Disease 81, no. 2: 797-808.
The capability of 1H and 13C flow magic-angle spinning NMR is demonstrated for monitoring the capture of CO2 on the surface of mesoporous amine-functionalized silica and the progress of heterogeneously catalyzed CO2 hydrogenation over the microporous titanosilicate Pt/ETS-10 under in situ conditions. The custom-built gas-handling system allows to maintain a controllable and stable delivery of reaction gases to the sample compartment containing porous material over a period of hours. Using calibration of NMR signals, we obtained the amounts of reactants and products. The presented approach demonstrates a complementary NMR-based in situ method for quantitative investigation of CO2 capture and conversion over nanoporous solids.
Marianne Wenzel; Muhammad A. Zaheer; Dilara Issayeva; David Poppitz; Jörg Matysik; Roger Gläser; Muslim Dvoyashkin. Flow MAS NMR for In Situ Monitoring of Carbon Dioxide Capture and Hydrogenation Using Nanoporous Solids. The Journal of Physical Chemistry C 2021, 125, 10219 -10225.
AMA StyleMarianne Wenzel, Muhammad A. Zaheer, Dilara Issayeva, David Poppitz, Jörg Matysik, Roger Gläser, Muslim Dvoyashkin. Flow MAS NMR for In Situ Monitoring of Carbon Dioxide Capture and Hydrogenation Using Nanoporous Solids. The Journal of Physical Chemistry C. 2021; 125 (19):10219-10225.
Chicago/Turabian StyleMarianne Wenzel; Muhammad A. Zaheer; Dilara Issayeva; David Poppitz; Jörg Matysik; Roger Gläser; Muslim Dvoyashkin. 2021. "Flow MAS NMR for In Situ Monitoring of Carbon Dioxide Capture and Hydrogenation Using Nanoporous Solids." The Journal of Physical Chemistry C 125, no. 19: 10219-10225.
Photo-CIDNP (photo-chemically induced dynamic nuclear polarization) refers to nuclear polarization created by the spin-chemical evolution of spin-correlated radical pairs (SCRPs). This phenomenon occurs in gases, liquids and solids. Based on the solid-state photo-CIDNP effect observed under magic-angle spinning (MAS), photo-CIDNP MAS NMR has been developed as analytical method. Here we report the origin, the theory and the state of the art of this method.
Jörg Matysik; Yonghong Ding; Yunmi Kim; Patrick Kurle; Alexandra Yurkovskaya; Konstantin Ivanov; A. Alia. Photo-CIDNP in Solid State. Applied Magnetic Resonance 2021, 1 -17.
AMA StyleJörg Matysik, Yonghong Ding, Yunmi Kim, Patrick Kurle, Alexandra Yurkovskaya, Konstantin Ivanov, A. Alia. Photo-CIDNP in Solid State. Applied Magnetic Resonance. 2021; ():1-17.
Chicago/Turabian StyleJörg Matysik; Yonghong Ding; Yunmi Kim; Patrick Kurle; Alexandra Yurkovskaya; Konstantin Ivanov; A. Alia. 2021. "Photo-CIDNP in Solid State." Applied Magnetic Resonance , no. : 1-17.
Hinge-type molecular models for electron donors in reaction centers of Photosystems I and II and purple bacteria were investigated using a two-state computational approach based on frozen-density embedding (FDE). This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows a prediction of qualitatively correct spin densities for large biomolecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in the relative orientation of cofactors and amino acid protonation states. This allows a validation of the previously proposed hinge-type models providing hints on possible protonation states of axial histidine molecules.
Denis G. Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as well as of Purple Bacteria. The Journal of Physical Chemistry B 2021, 1 .
AMA StyleDenis G. Artiukhin, Patrick Eschenbach, Jörg Matysik, Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as well as of Purple Bacteria. The Journal of Physical Chemistry B. 2021; ():1.
Chicago/Turabian StyleDenis G. Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. 2021. "Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as well as of Purple Bacteria." The Journal of Physical Chemistry B , no. : 1.
Metabolomics is used to reduce the complexity of plants and to understand the underlying pathways of the plant phenotype. The metabolic profile of plants can be obtained by mass spectrometry or liquid-state NMR. The extraction of metabolites from the sample is necessary for both techniques to obtain the metabolic profile. This extraction step can be eliminated by making use of high-resolution magic angle spinning (HR-MAS) NMR. In this review, an HR-MAS NMR-based workflow is described in more detail, including used pulse sequences in metabolomics. The pre-processing steps of one-dimensional HR-MAS NMR spectra are presented, including spectral alignment, baseline correction, bucketing, normalisation and scaling procedures. We also highlight some of the models which can be used to perform multivariate analysis on the HR-MAS NMR spectra. Finally, applications of HR-MAS NMR in plant metabolomics are described and show that HR-MAS NMR is a powerful tool for plant metabolomics studies.
Dieuwertje Augustijn; Huub de Groot; A. Alia. HR-MAS NMR Applications in Plant Metabolomics. Molecules 2021, 26, 931 .
AMA StyleDieuwertje Augustijn, Huub de Groot, A. Alia. HR-MAS NMR Applications in Plant Metabolomics. Molecules. 2021; 26 (4):931.
Chicago/Turabian StyleDieuwertje Augustijn; Huub de Groot; A. Alia. 2021. "HR-MAS NMR Applications in Plant Metabolomics." Molecules 26, no. 4: 931.
Cyanobacteriochromes (CBCRs) are photoreceptors of the phytochrome superfamily showing remarkable variability in the wavelengths of the first electronic transition—sometimes denoted as Q band—compared to canonical phytochromes. Both classes carry the same cofactor, a bilin, but the molecular basis for the wide variation of their absorption properties is still a matter of debate. The interaction between the cofactor and the surrounding protein moiety has been proposed as a possible tuning factor. Here, we address the impact of hydrogen-bonding interaction between the covalently bound tetrapyrrole cofactor (phycocyanobilin, PCB) and a conserved tyrosine residue (Y302) in the second GAF (cGMP-specific phosphodiesterase, adenylyl cyclases, and FhlA) domain of the red-/green-switching CBCR AnPixJ (AnPixJg2). In the wild type, AnPixJg2 shows absorption maxima of 648 and 543 nm for the dark-adapted (Pr) and photoproduct (Pg) states, respectively. The Y302F mutation leads to the occurrence of an additional absorption band at 687 nm, which is assigned to a new spectroscopically identified sub-state called PIII. Similar spectral changes result upon mutating the Y302F-homologue in another representative red-/green-switching CBCR, Slr1393g3. Molecular dynamics simulations on the dark-adapted state suggest that the removal of the hydrogen bond leads to an additional PCB sub-state differing in its A- and D-ring geometries. The origin of the Q band satellite in the dark-adapted state is discussed.
Susanne Altmayer; Sascha Jähnigen; Lisa Köhler; Christian Wiebeler; Chen Song; Daniel Sebastiani; Jörg Matysik. Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes. The Journal of Physical Chemistry B 2021, 125, 1331 -1342.
AMA StyleSusanne Altmayer, Sascha Jähnigen, Lisa Köhler, Christian Wiebeler, Chen Song, Daniel Sebastiani, Jörg Matysik. Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes. The Journal of Physical Chemistry B. 2021; 125 (5):1331-1342.
Chicago/Turabian StyleSusanne Altmayer; Sascha Jähnigen; Lisa Köhler; Christian Wiebeler; Chen Song; Daniel Sebastiani; Jörg Matysik. 2021. "Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes." The Journal of Physical Chemistry B 125, no. 5: 1331-1342.
Hinge-type molecular models for electron donors in reaction centers of Photosystem I, II, and purple bacteria were investigated using a two-state computational approach based on Frozen-Density Embedding. This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows to predict qualitatively correct spin densities for large bio-molecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in relative orientiation of co-factors and amino-acid protonation states. This allows to validate the previously proposed hinge-type models and make predictions on protonation states of axial histidine molecules. Contrary to the reaction centers in Photosystem I and purple bacteria, the axial histidines from Photosystem II were found to be deprotonated. This fact might shed some light on remarkable properties of Photosystem II reaction centers.
Denis Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria. 2020, 1 .
AMA StyleDenis Artiukhin, Patrick Eschenbach, Jörg Matysik, Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria. . 2020; ():1.
Chicago/Turabian StyleDenis Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. 2020. "Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria." , no. : 1.
Hinge-type molecular models for electron donors in reaction centers of Photosystem I, II, and purple bacteria were investigated using a two-state computational approach based on Frozen-Density Embedding. This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows to predict qualitatively correct spin densities for large bio-molecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in relative orientiation of co-factors and amino-acid protonation states. This allows to validate the previously proposed hinge-type models and make predictions on protonation states of axial histidine molecules. Contrary to the reaction centers in Photosystem I and purple bacteria, the axial histidines from Photosystem II were found to be deprotonated. This fact might shed some light on remarkable properties of Photosystem II reaction centers.
Denis Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria. 2020, 1 .
AMA StyleDenis Artiukhin, Patrick Eschenbach, Jörg Matysik, Johannes Neugebauer. Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria. . 2020; ():1.
Chicago/Turabian StyleDenis Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer. 2020. "Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria." , no. : 1.
The electron donor in photosystem I (PSI), the chlorophyll dimer P700, is studied by photochemically induced dynamic nuclear polarization (photo-CIDNP) magic angle spinning (MAS) nuclear magnetic resonance (NMR) on selectively 13C and uniformly 15N labeled PSI core preparations (PSI-100) obtained from the aquatic plant duckweed (Spirodela oligorrhiza). Light-induced signals originate from the isotope-labeled nuclei of the cofactors involved in the spin-correlated radical pair forming upon light excitation. Signals are assigned to the two donor cofactors (Chl a and Chl a') and the two acceptor cofactors (both Chl a). Light-induced signals originating from both donor and acceptor cofactors demonstrate that electron transfer occurs through both branches of cofactors in the pseudo-C2 symmetric reaction center (RC). The experimental results supported by quantum chemical calculations indicate that this functional symmetry occurs in PSI despite similarly sized chemical shift differences between the cofactors of PSI and the functionally asymmetric special pair donor of the bacterial RC of Rhodobacter sphaeroides. This contributes to converging evidence that local differences in time-averaged electronic ground-state properties, over the donor are of little importance for the functional symmetry breaking across photosynthetic RC species.
Geertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. de Groot; Jörg Matysik; Alia Alia. Analysis of the electronic structure of the primary electron donor of photosystem I of Spirodela oligorrhiza by photochemically induced dynamic nuclear polarization (photo-CIDNP) solid-state nuclear magnetic resonance (NMR). Magnetic Resonance 2020, 1, 261 -274.
AMA StyleGeertje J. Janssen, Patrick Eschenbach, Patrick Kurle, Bela E. Bode, Johannes Neugebauer, Huub J. M. de Groot, Jörg Matysik, Alia Alia. Analysis of the electronic structure of the primary electron donor of photosystem I of Spirodela oligorrhiza by photochemically induced dynamic nuclear polarization (photo-CIDNP) solid-state nuclear magnetic resonance (NMR). Magnetic Resonance. 2020; 1 (2):261-274.
Chicago/Turabian StyleGeertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. de Groot; Jörg Matysik; Alia Alia. 2020. "Analysis of the electronic structure of the primary electron donor of photosystem I of Spirodela oligorrhiza by photochemically induced dynamic nuclear polarization (photo-CIDNP) solid-state nuclear magnetic resonance (NMR)." Magnetic Resonance 1, no. 2: 261-274.
The solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-Boltzmann nuclear spin magnetization, referred to as hyperpolarization, allowing for high gain of sensitivity in nuclear magnetic resonance (NMR). Well known to occur in photosynthetic reaction centers, the effect was also observed in a light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin, in which the functional cysteine was removed to prevent photo-chemical reactions with the cofactor, a flavin mononucleotide (FMN). Upon illumination, the FMN abstracts an electron from a tryptophan to form a transient spin-correlated radical pair (SCRP) generating the photo-CIDNP effect. Here, we report on designed molecular spin-machines producing nuclear hyperpolarization upon illumination: a LOV domain of aureochrome1a from Phaeodactylum tricornutum, and a LOV domain named 4511 from Methylobacterium radiotolerans (Mr4511) which lacks an otherwise conserved tryptophan in its wild-type form. Insertion of the tryptophan at canonical and novel positions in Mr4511 yields photo-CIDNP effects observed by 15N and 1H liquid-state high-resolution NMR with a characteristic magnetic-field dependence indicating an involvement of anisotropic magnetic interactions and a slow-motion regime in the transient paramagnetic state. The heuristic biomimetic design opens new categories of experiments to analyze and apply the photo-CIDNP effect.
Yonghong Ding; Alexey S. Kiryutin; Ziyue Zhao; Qian-Zhao Xu; Kai-Hong Zhao; Patrick Kurle; Saskia Bannister; Tilman Kottke; Renad Z. Sagdeev; Konstantin L. Ivanov; Alexandra V. Yurkovskaya; Jörg Matysik. Tailored flavoproteins acting as light-driven spin machines pump nuclear hyperpolarization. Scientific Reports 2020, 10, 1 -13.
AMA StyleYonghong Ding, Alexey S. Kiryutin, Ziyue Zhao, Qian-Zhao Xu, Kai-Hong Zhao, Patrick Kurle, Saskia Bannister, Tilman Kottke, Renad Z. Sagdeev, Konstantin L. Ivanov, Alexandra V. Yurkovskaya, Jörg Matysik. Tailored flavoproteins acting as light-driven spin machines pump nuclear hyperpolarization. Scientific Reports. 2020; 10 (1):1-13.
Chicago/Turabian StyleYonghong Ding; Alexey S. Kiryutin; Ziyue Zhao; Qian-Zhao Xu; Kai-Hong Zhao; Patrick Kurle; Saskia Bannister; Tilman Kottke; Renad Z. Sagdeev; Konstantin L. Ivanov; Alexandra V. Yurkovskaya; Jörg Matysik. 2020. "Tailored flavoproteins acting as light-driven spin machines pump nuclear hyperpolarization." Scientific Reports 10, no. 1: 1-13.
Geertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. De Groot; Jörg Matysik; Alia Alia. Supplementary material to "Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR". 2020, 1 .
AMA StyleGeertje J. Janssen, Patrick Eschenbach, Patrick Kurle, Bela E. Bode, Johannes Neugebauer, Huub J. M. De Groot, Jörg Matysik, Alia Alia. Supplementary material to "Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR". . 2020; ():1.
Chicago/Turabian StyleGeertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. De Groot; Jörg Matysik; Alia Alia. 2020. "Supplementary material to "Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR"." , no. : 1.
The electron donor in photosystem I, the chlorophyll dimer P700, is studied by photo-CIDNP (photochemically induced dynamic nuclear polarization) MAS (magic-angle spinning) NMR on selectively 13C and uniformly 15N labeled PSI core preparations (PSI-100) obtained from the aquatic plant duckweed (Spirodela oligorrhiza). Light-induced signals originate from the isotope labelled nuclei of the cofactors involved in the spin-correlated radical pair forming upon light excitation. Signals are assigned to the two donor cofactors (Chl a and Chl a') and the two acceptor cofactors (both Chl a). Light induced signals originating from both donor and acceptor cofactors demonstrate that electron transfer occurs through both branches of cofactors in the pseudo-C2 symmetric Reaction Center (RC). The experimental results supported by quantum chemical calculations indicate that this functional symmetry occurs in PSI despite similarly sized chemical-shift differences between cofactors of PSI and the functionally asymmetric special-pair donor of the bacterial RC of Rhodobacter sphaeroides. This contributes to converging evidence that local differences in time-averaged electronic ground-state properties, over the donor are of little importance for functional symmetry breaking across photosynthetic RC species.
Geertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. De Groot; Jörg Matysik; Alia Alia. Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR. 2020, 2020, 1 -28.
AMA StyleGeertje J. Janssen, Patrick Eschenbach, Patrick Kurle, Bela E. Bode, Johannes Neugebauer, Huub J. M. De Groot, Jörg Matysik, Alia Alia. Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR. . 2020; 2020 ():1-28.
Chicago/Turabian StyleGeertje J. Janssen; Patrick Eschenbach; Patrick Kurle; Bela E. Bode; Johannes Neugebauer; Huub J. M. De Groot; Jörg Matysik; Alia Alia. 2020. "Analysis of the electronic asymmetry of the primary electron donor of photosystem I of Spirodela oligorrhiza by photo-CIDNP solid-state NMR." 2020, no. : 1-28.
Cyanobacteria sense and respond to various colors of light employing a large number of bilin-based phytochrome-like photoreceptors. All2699 from Nostoc 7120 has three GAF domains with GAF1 and GAF3 binding a chromophore. GAF1, even when expressed independently, is photoconverted between red-absorbing Pr and far-red-absorbing Pfr states, while the non-photosensory GAF2 domain is structurally and functionally homologous to the PHY/GAF2 domains in canonical and Cph2-like phytochromes. Here, we characterize possible bilin chromophore conformers using solid-state NMR spectroscopy on the two lyophilized All2699 samples (GAF1-alone and GAF1–GAF2 construct). On the basis of complete 1H, 13C, and 15N assignments for the chromophore obtained on the two Pr lyophilizates, multiple static conformations of the chromophore in both cases are identified. Moreover, most atoms of the chromophore in the bidomain sample show only subtle changes of the mean chemical shifts relative to those in frozen solution, indicating an optimized interaction of the GAF2 domain with the GAF1-bound chromophore. Our results confirm the conservation of key chromophore–protein interactions and the photoreversibility in both All2699 lyophilizates, offering the possibility to investigate conformational distributions of the heterogeneous chromophore as well as its functional consequences in other bilin-dependent photoreceptors intractable by solid-state NMR technique as frozen solutions.
Yunmi Kim; Qian-Zhao Xu; Kai-Hong Zhao; Wolfgang Gärtner; Jörg Matysik; Chen Song. Lyophilization Reveals a Multitude of Structural Conformations in the Chromophore of a Cph2-like Phytochrome. The Journal of Physical Chemistry B 2020, 124, 1 .
AMA StyleYunmi Kim, Qian-Zhao Xu, Kai-Hong Zhao, Wolfgang Gärtner, Jörg Matysik, Chen Song. Lyophilization Reveals a Multitude of Structural Conformations in the Chromophore of a Cph2-like Phytochrome. The Journal of Physical Chemistry B. 2020; 124 (33):1.
Chicago/Turabian StyleYunmi Kim; Qian-Zhao Xu; Kai-Hong Zhao; Wolfgang Gärtner; Jörg Matysik; Chen Song. 2020. "Lyophilization Reveals a Multitude of Structural Conformations in the Chromophore of a Cph2-like Phytochrome." The Journal of Physical Chemistry B 124, no. 33: 1.
Tuberculosis is a highly infectious and potentially fatal disease accompanied by wasting symptoms, which cause severe metabolic changes in infected people. In this study we have compared the effect of mycobacteria infection on the level of metabolites in blood of humans and mice and whole zebrafish larvae using one highly standardized mass spectrometry pipeline, ensuring technical comparability of the results. Quantification of a range of circulating small amines showed that the levels of the majority of these compounds were significantly decreased in all three groups of infected organisms. Ten of these metabolites were common between the three different organisms comprising: methionine, asparagine, cysteine, threonine, serine, tryptophan, leucine, citrulline, ethanolamine and phenylalanine. The metabolomic changes of zebrafish larvae after infection were confirmed by nuclear magnetic resonance spectroscopy. Our study identified common biomarkers for tuberculosis disease in humans, mice and zebrafish, showing across species conservation of metabolic reprogramming processes as a result of disease. Apparently, the mechanisms underlying these processes are independent of environmental, developmental and vertebrate evolutionary factors. The zebrafish larval model is highly suited to further investigate the mechanism of metabolic reprogramming and the connection with wasting syndrome due to infection by mycobacteria.
Yi Ding; Robert Jan Raterink; Ruben Marin Juez; Wouter J. Veneman; Koen Egbers; Susan Van Den Eeden; Mariëlle C. Haks; Simone A. Joosten; Tom H.M. Ottenhoff; Amy C. Harms; A. Alia; Thomas Hankemeier; Herman P. Spaink. Tuberculosis causes highly conserved metabolic changes in human patients, mycobacteria-infected mice and zebrafish larvae. 2020, 1 .
AMA StyleYi Ding, Robert Jan Raterink, Ruben Marin Juez, Wouter J. Veneman, Koen Egbers, Susan Van Den Eeden, Mariëlle C. Haks, Simone A. Joosten, Tom H.M. Ottenhoff, Amy C. Harms, A. Alia, Thomas Hankemeier, Herman P. Spaink. Tuberculosis causes highly conserved metabolic changes in human patients, mycobacteria-infected mice and zebrafish larvae. . 2020; ():1.
Chicago/Turabian StyleYi Ding; Robert Jan Raterink; Ruben Marin Juez; Wouter J. Veneman; Koen Egbers; Susan Van Den Eeden; Mariëlle C. Haks; Simone A. Joosten; Tom H.M. Ottenhoff; Amy C. Harms; A. Alia; Thomas Hankemeier; Herman P. Spaink. 2020. "Tuberculosis causes highly conserved metabolic changes in human patients, mycobacteria-infected mice and zebrafish larvae." , no. : 1.
Interactions between plants and the soil’s microbial & fungal flora are crucial for the health of soil ecosystems and food production. Microbe-plant interactions are difficult to investigate in situ due to their intertwined relationship involving morphology and metabolism. Here, we describe an approach to overcome this challenge by elucidating morphology and the metabolic profile of Medicago truncatula root nodules using Magnetic Resonance (MR) Microscopy, at the highest magnetic field strength (22.3 T) currently available for imaging. A home-built solenoid RF coil with an inner diameter of 1.5 mm was used to study individual root nodules. A 3D imaging sequence with an isotropic resolution of (7 μm)3 was able to resolve individual cells, and distinguish between cells infected with rhizobia and uninfected cells. Furthermore, we studied the metabolic profile of cells in different sections of the root nodule using localised MR spectroscopy and showed that several metabolites, including betaine, asparagine/aspartate and choline, have different concentrations across nodule zones. The metabolite spatial distribution was visualised using chemical shift imaging. Finally, we describe the technical challenges and outlook towards future in vivo MR microscopy of nodules and the plant root system.
Remco Van Schadewijk; Julia R. Krug; Defeng Shen; Karthick B. S. Sankar Gupta; Frank J. Vergeldt; Ton Bisseling; Andrew G. Webb; Henk Van As; Aldrik H. Velders; Huub J. M. De Groot; A. Alia. Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla. Scientific Reports 2020, 10, 971 -11.
AMA StyleRemco Van Schadewijk, Julia R. Krug, Defeng Shen, Karthick B. S. Sankar Gupta, Frank J. Vergeldt, Ton Bisseling, Andrew G. Webb, Henk Van As, Aldrik H. Velders, Huub J. M. De Groot, A. Alia. Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla. Scientific Reports. 2020; 10 (1):971-11.
Chicago/Turabian StyleRemco Van Schadewijk; Julia R. Krug; Defeng Shen; Karthick B. S. Sankar Gupta; Frank J. Vergeldt; Ton Bisseling; Andrew G. Webb; Henk Van As; Aldrik H. Velders; Huub J. M. De Groot; A. Alia. 2020. "Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla." Scientific Reports 10, no. 1: 971-11.
Amorphous PET films (product no. ES301445) were purchased from Goodfellow Cambridge Ltd. (Huntingdon, UK) and ground in a cryomill in the presence of liquid nitrogen. Particles with diameters of less than 0.25 mm were obtained by sieving and then used in the solid-state NMR analysis. All CP/MAS (cross-polarization magic-angle spinning) NMR experiments were performed at 9.4 T with a Bruker AVANCE III NMR spectrometer equipped with a 4-mm double-resonance MAS probe (Rheinstetten, Germany). A MAS rate of 8 kHz was maintained throughout the experiments. The 207Pb NMR resonance of lead nitrate was used as the thermometer to calibrate the temperature over the sample volume of the in-situ MAS probe at 8 kHz12. The MAS data were acquired respectively at 30 and 70 °C by using two individual samples. Each fine-powdered PET sample (~30 mg) was loaded into a 4 mm ZrO2 MAS rotor with Vespel cap and incubated at their individual target temperatures in the magnet for 24 h prior to the data acquisition. Optimized 1H and 13C 90° pulse lengths were 2.5 and 3.0 μs, respectively. The CP/MAS spectra were recorded with 2512 scans and a relaxation delay of 4 s, with optimized spin-lock pulses to satisfy both Hartmann–Hahn (HH) n = ±1 matching conditions, with 66 kHz effective 13C radio frequency (r.f.) lock field and 100–70% ramp on the 1H channel. Decomposition of methylene carbon resonances from the EG units provided direct quantification for the t/g ratio. The contact time was 2 ms. 1H–13C order parameters were measured using the 2D DIPSHIFT experiments5. The experiments were conducted with 256 scans and a recycle delay of 4 s. 1H–1H homonuclear dipolar decoupling was accomplished with phase-modulated Lee–Goldburg (PMLG) approach13. The PMLG block consists of 10 pulses with the following phases: 339.22°, 297.65°, 256.08°, 214.51°, 172.94°, 352.94°, 34.51°, 76.08°, 117.65°, and 159.22° (m5m shape in TopSpin library, Bruker). The PMLG5-optimized pulse was 2.07 μs and the r.f. decoupling field was set to 80 kHz. The PMLG scaling factor of 0.5 was determined based on adamantane J-splitting. For all experiments, swept-frequency two-pulse phase-modulation (SWf-TPPM) heteronuclear decoupling14 with a r.f. field of 100 kHz was used during the acquisition. 13C chemical shifts were externally referenced to the C(=O)O− signal of solid tyrosine·HCl at 172.1 ppm. The DIPSHIFT dephasing curves were simulated using the SIMPSON program15. The rigid-limit values for both CH and CH2 spin systems were obtained by fitting the experimental curves of crystalline BHET in a site-specific manner. Spectral fitting was conducted with the MestReNova 12.0.0 program (Mestrelab Research, Santiago de Compostela, Spain). A codon-optimized synthetic gene encoding IsPETase lacking the N-terminal signal sequence containing 27 residues was ordered from Genscript (Piscataway, USA) and subcloned into the pET-21b vector (Novagen, San Diego, USA). The recombinant IsPETase containing a C-terminal His6-tag was expressed in Escherichia coli Shuffle T7 Express (New England Biolabs GmbH, Frankfurt am Main, Germany). Briefly, E. coli cells were grown at 30 °C to an optical density (OD600) of 1, followed by induction in the presence of 0.1 mM IPTG at 16 °C for more than 12 h, and then purified by immobilized metal ion chromatography (IMAC) using TALON metal affinity resin (Takara Bio Europe, Saint-Germain-en-Laye, France) to homogeneity. LC-cutinase was recombinantly expressed in E. coli BL21(DE3) and purified by IMAC to homogeneity using Ni-NTA (Qiagen, Hilden, Germany) as previously described16. 5 μg of IsPETase and 50 µg of LC-cutinase were used to degrade a piece of amorphous PET film (Goodfellow Cambridge Ltd., 3 × 0.5 cm2, ~45 mg) using the optimal degradation conditions for the respective enzymes2,16. Briefly, IsPETase required 50 mM Na2HPO4-HCl at pH = 7 while LC-cutinase required 1 M K2HPO4/KH2PO4 at pH = 8. Degradation was performed by shaking the reaction vials on a thermoshaker TS1 (Biometra, Göttingen, Germany) at 1000 rpm for 24 h at 30 °C for IsPETase and at 70 °C for LC-cutinase. The reaction was stopped by cooling the samples on ice. PET films were washed sequentially with 0.1% aqueous SDS, ethanol and ultrapure water and then dried at 50 °C for 48 h before subjected to gravimetric weight loss determination. Degradation experiments using higher IsPETase concentrations up to 50 µg enzyme and lower LC-cutinase amount down to 5 µg enzyme were also prepared as control samples which led to significantly lower weight losses of the PET films (data not shown) than using the enzyme amounts mentioned above in main text. The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. Joo, S. et al. Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation. Nat. Commun. 9, 382 (2018). ADS Article Google Scholar Yoshida, S. et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351, 1196–1199 (2016). ADS CAS Article Google Scholar Schmidt-Rohr, K., Hu, W. & Zumbulyadis, N. Elucidation of the chain conformation in a glassy polyester, PET, by two-dimensional NMR. Science 280, 714–717 (1998). ADS CAS Article Google Scholar Austin, H. P. et al. Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc. Natl Acad. Sci. USA 115, E4350–E4357 (2018). CAS Article Google Scholar deAzevedo, E. R. et al. Intermediate motions as studied by solid-state separated local field NMR experiments. J. Chem. Phys. 128, 104505 (2008). ADS Article Google Scholar Fecker, T. et al. Active site flexibility as a hallmark for efficient PET degradation by I. sakaiensis PETase. Biophy. J. 114, 1302–1312 (2018). ADS CAS Article Google Scholar...
Ren Wei; Chen Song; Daniel Gräsing; Tobias Schneider; Pavlo Bielytskyi; Dominique Böttcher; Jörg Matysik; Uwe T. Bornscheuer; Wolfgang Zimmermann. Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation. Nature Communications 2019, 10, 1 -4.
AMA StyleRen Wei, Chen Song, Daniel Gräsing, Tobias Schneider, Pavlo Bielytskyi, Dominique Böttcher, Jörg Matysik, Uwe T. Bornscheuer, Wolfgang Zimmermann. Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation. Nature Communications. 2019; 10 (1):1-4.
Chicago/Turabian StyleRen Wei; Chen Song; Daniel Gräsing; Tobias Schneider; Pavlo Bielytskyi; Dominique Böttcher; Jörg Matysik; Uwe T. Bornscheuer; Wolfgang Zimmermann. 2019. "Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation." Nature Communications 10, no. 1: 1-4.
The solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-equilibrium nuclear spin polarization in frozen electron-transfer proteins upon illumination and radical-pair formation. The effect can be observed in various natural photosynthetic reaction center proteins using magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and in a flavin-binding light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin. In the latter system, a functionally instrumental cysteine has been mutated to interrupt the natural cysteine-involving photochemistry allowing for an electron transfer from a more distant tryptophan to the excited flavin mononucleotide chromophore. We explored the solid-state photo-CIDNP effect and its mechanisms in phototropin-LOV1-C57S from the green alga Chlamydomonas reinhardtii by using field-cycling solution NMR. We observed the 13C and, to our knowledge, for the first time, 15N photo-CIDNP signals from phototropin-LOV1-C57S. Additionally, the 1H photo-CIDNP signals of residual water in the deuterated buffer of the protein were detected. The relative strengths of the photo-CIDNP effect from the three types of nuclei, 1H, 13C and 15N were measured in dependence of the magnetic field, showing their maximum polarizations at different magnetic fields. Theoretical level crossing analysis demonstrates that anisotropic mechanisms play the dominant role at high magnetic fields.
Yonghong Ding; Alexey S. Kiryutin; Alexandra V. Yurkovskaya; Denis V. Sosnovsky; Renad Z. Sagdeev; Saskia Bannister; Tilman Kottke; Rajiv K. Kar; Igor Schapiro; Konstantin L. Ivanov; Jörg Matysik. Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis. Scientific Reports 2019, 9, 18436 .
AMA StyleYonghong Ding, Alexey S. Kiryutin, Alexandra V. Yurkovskaya, Denis V. Sosnovsky, Renad Z. Sagdeev, Saskia Bannister, Tilman Kottke, Rajiv K. Kar, Igor Schapiro, Konstantin L. Ivanov, Jörg Matysik. Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis. Scientific Reports. 2019; 9 (1):18436.
Chicago/Turabian StyleYonghong Ding; Alexey S. Kiryutin; Alexandra V. Yurkovskaya; Denis V. Sosnovsky; Renad Z. Sagdeev; Saskia Bannister; Tilman Kottke; Rajiv K. Kar; Igor Schapiro; Konstantin L. Ivanov; Jörg Matysik. 2019. "Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis." Scientific Reports 9, no. 1: 18436.