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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Bilkova E, Pleskot R, Rissanen S, Sun S, Czogalla A, Cwiklik L, Róg T, Vattulainen I, Cremer PS, Jungwirth P, Coskun Ü. Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. J Am Chem Soc 2017; 139:4019-4024. [PMID: 28177616 PMCID: PMC5364432 DOI: 10.1021/jacs.6b11760] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The orchestrated recognition of phosphoinositides and concomitant intracellular release of Ca2+ is pivotal to almost every aspect of cellular processes, including membrane homeostasis, cell division and growth, vesicle trafficking, as well as secretion. Although Ca2+ is known to directly impact phosphoinositide clustering, little is known about the molecular basis for this or its significance in cellular signaling. Here, we study the direct interaction of Ca2+ with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), the main lipid marker of the plasma membrane. Electrokinetic potential measurements of PI(4,5)P2 containing liposomes reveal that Ca2+ as well as Mg2+ reduce the zeta potential of liposomes to nearly background levels of pure phosphatidylcholine membranes. Strikingly, lipid recognition by the default PI(4,5)P2 lipid sensor, phospholipase C delta 1 pleckstrin homology domain (PLC δ1-PH), is completely inhibited in the presence of Ca2+, while Mg2+ has no effect with 100 nm liposomes and modest effect with giant unilamellar vesicles. Consistent with biochemical data, vibrational sum frequency spectroscopy and atomistic molecular dynamics simulations reveal how Ca2+ binding to the PI(4,5)P2 headgroup and carbonyl regions leads to confined lipid headgroup tilting and conformational rearrangements. We rationalize these findings by the ability of calcium to block a highly specific interaction between PLC δ1-PH and PI(4,5)P2, encoded within the conformational properties of the lipid itself. Our studies demonstrate the possibility that switchable phosphoinositide conformational states can serve as lipid recognition and controlled cell signaling mechanisms.
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Affiliation(s)
- Eva Bilkova
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Roman Pleskot
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Institute of Experimental Botany, Academy of Sciences of the Czech Republic , v.v.i., Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | | | - Aleksander Czogalla
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław , Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,Department of Physics, University of Helsinki , P.O. Box 64, FI-00014, Helsinki, Finland.,MEMPHYS- Center for Biomembrane Physics, University of Southern Denmark , DK-5230 Odense, Denmark
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.,Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research (DZD e.V.) , Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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Elucidating the role of the TRPM7 alpha-kinase: TRPM7 kinase inactivation leads to magnesium deprivation resistance phenotype in mice. Sci Rep 2014; 4:7599. [PMID: 25534891 PMCID: PMC4274504 DOI: 10.1038/srep07599] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022] Open
Abstract
TRPM7 is an unusual bi-functional protein containing an ion channel covalently linked to a protein kinase domain. TRPM7 is implicated in regulating cellular and systemic magnesium homeostasis. While the biophysical properties of TRPM7 ion channel and its function are relatively well characterized, the function of the TRPM7 enzymatically active kinase domain is not understood yet. To investigate the physiological role of TRPM7 kinase activity, we constructed mice carrying an inactive TRPM7 kinase. We found that these mice were resistant to dietary magnesium deprivation, surviving three times longer than wild type mice; also they displayed decreased chemically induced allergic reaction. Interestingly, mutant mice have lower magnesium bone content compared to wild type mice when fed regular diet; unlike wild type mice, mutant mice placed on magnesium-depleted diet did not alter their bone magnesium content. Furthermore, mouse embryonic fibroblasts isolated from TRPM7 kinase-dead animals exhibited increased resistance to magnesium deprivation and oxidative stress. Finally, electrophysiological data revealed that the activity of the kinase-dead TRPM7 channel was not significantly altered. Together, our results suggest that TRPM7 kinase is a sensor of magnesium status and provides coordination of cellular and systemic responses to magnesium deprivation.
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Lauf PK, Zhang J, Delpire E, Fyffe RE, Mount DB, Adragna NC. K-Cl co-transport: immunocytochemical and functional evidence for more than one KCC isoform in high K and low K sheep erythrocytes. Comp Biochem Physiol A Mol Integr Physiol 2001; 130:499-509. [PMID: 11913461 DOI: 10.1016/s1095-6433(01)00421-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
K-Cl co-transport (COT) is significantly higher in low K (LK), L-antigen (L) positive, than in high K (HK), M-antigen (M) positive, sheep red blood cells (SRBCs) and is inhibited by sheep allo-anti-L1 antibody. To answer the question of whether this difference in K-Cl co-transport activity resides at the level of the transporter or its regulation, a combined immunocytochemical and functional approach was taken. At least four isoforms of K-Cl COT encoded by different KCC genes are known, with 12 transmembrane domains and cytoplasmic C- and N-terminal domains (Ctd and Ntd, respectively). Polyclonal anti-rat (rt)KCC1 antibodies against a fusion peptide with 77 amino acids from the Ctd of rtKCC1 and anti-human (h)KCC3 against an 18-aa peptide from the Ntd of hKCC3, were prepared in rabbits (rb). Two distinctly separate protein bands of 180 and 145 kDa molecular mass were detected in hemoglobin-free ghosts from RBCs of two LK (one homozygous LL and one heterozygous LM) and one HK (homozygous MM) sheep by Western blots with rb anti-rtKCC1 and rb anti-hKCC3. Confocal microscopy showed specific immunostaining of KCC1 with rb anti-rtKCC1, and of KCC3 with rb anti-hKCC3, in white ghosts from both LK and HK SRBCs. To test the functional heterogeneity of K-Cl COT, the effect of the anti-L1 antibody was assessed on K-Cl COT activated by the kinase inhibitor staurosporine. Incubation of LK SRBCs with anti-L1 serum inhibited by 30% staurosporine-stimulated K-Cl COT suggesting that approximately two-thirds of the transport activity is independent of the L1 antigen. That staurosporine altered the L1 antigen/antibody reaction is unlikely since the action of another antibody, anti-Lp, stimulating the Na/K pump flux, was not modified. The present results, in conjunction with earlier work, lead to the hypothesis that the partial anti-L1 inhibition of K-Cl COT may be related to the molecular KCC dimorphism, seen in these cells with anti-KCC1 and anti-KCC3 antibodies.
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Affiliation(s)
- P K Lauf
- Department of Physiology & Biophysics, Wright State University, Dayton, OH 45435, USA.
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Chollet D, Franken P, Raffin Y, Malafosse A, Widmer J, Tafti M. Blood and brain magnesium in inbred mice and their correlation with sleep quality. Am J Physiol Regul Integr Comp Physiol 2000; 279:R2173-8. [PMID: 11080083 DOI: 10.1152/ajpregu.2000.279.6.r2173] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A strong genetic component in the regulation of blood magnesium (Mg) levels has been demonstrated. The regulation and distribution of brain Mg levels, however, have never been assessed. Herein we report on the genetic variation of peripheral and central Mg levels in six inbred strains of mice. In addition, the possible involvement of Mg in sleep regulation was assessed by establishing correlations between Mg and sleep parameters obtained before and after a 6-h sleep deprivation. Although genotype strongly determined blood Mg levels, it did not affect brain Mg, suggesting that central and peripheral Mg are regulated differently. Central Mg displayed a highly structure-specific distribution with frontal cortex having the highest and brain stem the lowest values. Whereas for the amount and distribution of baseline sleep only marginal correlations with Mg were found, Mg contents in four of nine brain structures were highly positively correlated with the length of slow-wave sleep episodes during recovery. This relationship suggests that higher levels of Mg in specific brain sites promote sleep quality as part of a recovery process.
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Affiliation(s)
- D Chollet
- Biochemistry and Neurophysiology Unit, Department of Psychiatry, University of Geneva, 1225 Geneva, Switzerland
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Lauf PK, Erdmann A, Adragna NC. K-Cl cotransport, pH, and role of Mg in volume-clamped low-K sheep erythrocytes: three equilibrium states. Am J Physiol Cell Physiol 1994; 266:C95-103. [PMID: 8304434 DOI: 10.1152/ajpcell.1994.266.1.c95] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ouabain-resistant K efflux and Rb influx in Cl and NO3 media were studied in volume-clamped low-K (LK) sheep red blood cells (SRBC) with normal and experimentally reduced cytoplasmic Mg (Mgi) levels as function of pH and at 37 degrees C. Sucrose was added to solutions with constant ionic strength and variable pH to maintain normal cell volume. Cl-dependent ouabain-resistant K(Rb) fluxes (K-Cl cotransport) at unity relative cell volume exhibited a maximum at pH approximately 7 in normal-Mgi LK cells consistent with the apparent acid pH activation reported for human erythrocytes. However, in LK SRBC with Mgi lowered by A-23187 and an external Mg chelator, K(Rb)-Cl cotransport was reversibly activated as the pH was raised from 6.5 to 9. The alkaline pH effect on Cl-dependent Rb influx in low-Mgi LK SRBC was due to a 10-fold rise in the maximum velocity values without a major change in the Km values. The pH dependence of the experimental flux reversal point, i.e., the extracellular Rb concentration at which no net K-Cl cotransport occurs, approximately paralleled that of the flux reversal point predicted from the ratio of the ion products, in both control and low-Mgi LK cells, albeit with a small displacement to higher extracellular Rb concentration at all pH values. The kinetic data can be explained by a general minimum three-state equilibrium in which deprotonation recruits transporters from a resting R state into the active A state modified by Mgi to an inactive I state.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- P K Lauf
- Department of Physiology and Biophysics, Wright State University, Dayton, Ohio 45435
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