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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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Kruczek J, Chiu SW, Varma S, Jakobsson E, Pandit SA. Interactions of Monovalent and Divalent Cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10522-10532. [PMID: 31337218 DOI: 10.1021/acs.langmuir.9b01275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Li+ is a biologically active and medically important cation. Experiments show that Li+ modulates some phospholipid bilayer properties in a manner similar to divalent cations, rather than other monovalent cations. We previously performed a comparative simulation study of the interaction of several monovalent cations with palmitoyl-oleoyl-phosphatidylcholine bilayers and reported that Li+ exhibited the highest association with lipids and formed a unique tetrahedral coordinated structure with lipid head groups. Here we extend these studies to two biologically important divalent cations, Mg2+ and Ca2+, and observe that, just like monovalent cations, Mg2+ and Ca2+ reduce bilayer areas and increase chain order. Bilayer area changes induced by cations are strongly correlated with the amount of charge inside the headgroup region; however, Mg2+ and Li+ are clear outliers. At the same time though, Mg2+ adsorption in the bilayer is the smallest among all cations, which is in contrast to Li+ that binds strongly to lipids. In fact, in contrast to all other cations, Mg2+ remains fully hydrated in the lipid headgroup region. However, Li+ and Mg2+ share high overlap between their inner-shell coordination topologies. This suggests that Li+ can structurally replace Mg2+, which is bound to other biomolecules with up to fourfold coordination, provided such replacement is energetically feasible. We compute structural topologies and compare them quantitatively using a new weighted-graphs-based method. Finally, we find that the specificity of cation interaction with lipid head groups exhibit consistent trend with the solvation shell energetics of ions in lipid headgroup and bulk water regions.
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The Charge Properties of Phospholipid Nanodiscs. Biophys J 2017; 111:989-98. [PMID: 27602726 DOI: 10.1016/j.bpj.2016.06.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/22/2016] [Accepted: 06/15/2016] [Indexed: 11/23/2022] Open
Abstract
Phospholipids (PLs) are a major, diverse constituent of cell membranes. PL diversity arises from the nature of the fatty acid chains, as well as the headgroup structure. The headgroup charge is thought to contribute to both the strength and specificity of protein-membrane interactions. Because it has been difficult to measure membrane charge, ascertaining the role charge plays in these interactions has been challenging. Presented here are charge measurements on lipid Nanodiscs at 20°C in 100 mM NaCl, 50 mM Tris, at pH 7.4. Values are also reported for measurements made in the presence of Ca(2+) and Mg(2+) as a function of NaCl concentration, pH, and temperature, and in solvents containing other types of cations and anions. Measurements were made for neutral (phosphatidylcholine and phosphatidylethanolamine) and anionic (phosphatidylserine, phosphatidic acid, cardiolipin, and phosphatidylinositol 4,5-bisphosphate (PIP2)) PLs containing palmitoyl-oleoyl and dimyristoyl fatty acid chains. In addition, charge measurements were made on Nanodiscs containing an Escherichia coli lipid extract. The data collected reveal that 1) POPE is anionic and not neutral at pH 7.4; 2) high-anionic-content Nanodiscs exhibit polyelectrolyte behavior; 3) 3 mM Ca(2+) neutralizes a constant fraction of the charge, but not a constant amount of charge, for POPS and POPC Nanodiscs; 4) in contrast to some previous work, POPC only interacts weakly with Ca(2+); 5) divalent cations interact with lipids in a lipid- and ion-specific manner for POPA and PIP2 lipids; and 6) the monovalent anion type has little influence on the lipid charge. These results should help eliminate inconsistencies among data obtained using different techniques, membrane systems, and experimental conditions, and they provide foundational data for developing an accurate view of membranes and membrane-protein interactions.
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Komoroski RA, Lindquist DM, Pearce JM. Lithium compartmentation in brain by 7Li MRS: effect of total lithium concentration. NMR IN BIOMEDICINE 2013; 26:1152-1157. [PMID: 23401319 PMCID: PMC3665720 DOI: 10.1002/nbm.2929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/03/2013] [Accepted: 01/06/2013] [Indexed: 06/01/2023]
Abstract
In previous work at 4.7 T, the individual components of biexponential (7) Li transverse (T2 ) spin relaxation in rat brain in vivo were tentatively identified with intra- and extracellular Li. The goal in this work was to estimate Li's compartmental distribution as a function of total Li concentration in brain from the biexponential decays. Here a localized, biexponential (7) Li T2 MR spin-relaxation study with isotopically enriched (7) LiCl is reported in rat brain in vivo at 7 T. Additionally, a simple linear interpolation using the biexponential T2 values to estimate intracellular Li from individual monoexponential T2 decays was assessed. Intracellular T2 was 14.8 ± 4.3 ms and extracellular T2 was 295 ± 61 ms. The fraction of intracellular brain Li ranged from 37.3 to 64.8% (mean 54.5 ± 6.7%) and did not correlate with total Li concentration. The estimated intracellular Li concentration ranged from 47 to 80% (mean 68.3 ± 8.5%) of the total brain Li concentration and was highly correlated with it. The monoexponential estimates of the intracellular-Li fractions and derived concentrations averaged about 15% higher than the corresponding biexponential estimates. This work supports the previous conclusion that a large fraction of Li in the brain is within the intracellular compartment.
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Affiliation(s)
- Richard A Komoroski
- Center for Imaging Research, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0583, USA.
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Shalbuyeva N, Brustovetsky T, Brustovetsky N. Lithium desensitizes brain mitochondria to calcium, antagonizes permeability transition, and diminishes cytochrome C release. J Biol Chem 2007; 282:18057-18068. [PMID: 17485418 DOI: 10.1074/jbc.m702134200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Among the numerous effects of lithium on intracellular targets, its possible action on mitochondria remains poorly explored. In the experiments with suspension of isolated brain mitochondria, replacement of KCl by LiCl suppressed mitochondrial swelling, depolarization, and a release of cytochrome c induced by a single Ca2+ bolus. Li+ robustly protected individual brain mitochondria loaded with rhodamine 123 against Ca2+-induced depolarization. In the experiments with slow calcium infusion, replacement of KCl by LiCl in the incubation medium increased resilience of synaptic and nonsynaptic brain mitochondria as well as resilience of liver and heart mitochondria to the deleterious effect of Ca2+. In LiCl medium, mitochondria accumulated larger amounts of Ca2+ before they lost the ability to sequester Ca2+. However, lithium appeared to be ineffective if mitochondria were challenged by Sr2+ instead of Ca2+. Cyclosporin A, sanglifehrin A, and Mg2+, inhibitors of the mitochondrial permeability transition (mPT), increased mitochondrial Ca2+ capacity in KCl medium but failed to do so in LiCl medium. This suggests that the mPT might be a common target for Li+ and mPT inhibitors. In addition, lithium protected mitochondria against high Ca2+ in the presence of ATP, where cyclosporin A was reported to be ineffective. SB216763 and SB415286, inhibitors of glycogen synthase kinase-3beta, which is implicated in regulating reactive oxygen species-induced mPT in cardiac mitochondria, did not increase Ca2+ capacity of brain mitochondria. Altogether, these findings suggest that Li+ desensitizes mitochondria to elevated Ca2+ and diminishes cytochrome c release from brain mitochondria by antagonizing the Ca2+-induced mPT.
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Affiliation(s)
- Natalia Shalbuyeva
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Tatiana Brustovetsky
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Nickolay Brustovetsky
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202.
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Layden BT, Abukhdeir AM, Malarkey C, Oriti LA, Salah W, Stigler C, Geraldes CFGC, Mota de Freitas D. Identification of Li+ binding sites and the effect of Li+ treatment on phospholipid composition in human neuroblastoma cells: a 7Li and 31P NMR study. Biochim Biophys Acta Mol Basis Dis 2005; 1741:339-49. [PMID: 16115751 DOI: 10.1016/j.bbadis.2005.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 07/19/2005] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
Li(+) binding in subcellular fractions of human neuroblastoma SH-SY 5 Y cells was investigated using (7)Li NMR spin-lattice (T(1)) and spin-spin (T(2)) relaxation measurements, as the T(1)/T(2) ratio is a sensitive parameter of Li(+) binding. The majority of Li(+) binding occurred in the plasma membrane, microsomes, and nuclear membrane fractions as demonstrated by the Li(+) binding constants and the values of the T(1)/T(2) ratios, which were drastically larger than those observed in the cytosol, nuclei, and mitochondria. We also investigated by (31)P NMR spectroscopy the effects of chronic Li(+) treatment for 4--6 weeks on the phospholipid composition of the plasma membrane and the cell homogenate and found that the levels of phosphatidylinositol and phosphatidylserine were significantly increased and decreased, respectively, in both fractions. From these observations, we propose that Li(+) binding occurs predominantly to membrane domains, and that chronic Li(+) treatment alters the phospholipid composition at these membrane sites. These findings support those from clinical studies that have indicated that Li(+) treatment of bipolar patients results in irregularities in Li(+) binding and phospholipid metabolism. Implications of our observations on putative mechanisms of Li(+) action, including the cell membrane abnormality, the inositol depletion and the G-protein hypotheses, are discussed.
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Affiliation(s)
- Brian T Layden
- Department of Chemistry, Loyola University Chicago, 6525 North Sheridan Road, Chicago, Illinois 60626, USA
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Abstract
The biomedical applications of 7Li MRS and MRI have been progressing slowly. The interest derives primarily from the clinical use of Li to treat bipolar disorder. One area of concern is the nature of ionic transport and binding, so as to elucidate the mechanism(s) of therapeutic action and toxicity. Another is the development of a non-invasive, in vivo analytical tool to measure brain Li concentration and environment in humans, both as an adjunct to treatment and as a mechanistic probe. Here we review the most recent progress toward these goals.
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Affiliation(s)
- Richard A Komoroski
- Department of Radiology, University of Arkansas for Medical Sciences, South Central Mental Illness Research, Education, and Clinical Center (MIRECC), US Veterans Healthcare System, Little Rock, Arkansas 72114, USA.
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Fonseca CP, Montezinho LP, Nabais C, Tomé AR, Freitas H, Geraldes CFGC, Castro MMCA. Effects of Li+ transport and intracellular binding on Li+/Mg2+ competition in bovine chromaffin cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1691:79-90. [PMID: 15110989 DOI: 10.1016/j.bbamcr.2003.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 12/16/2003] [Accepted: 12/17/2003] [Indexed: 11/18/2022]
Abstract
Li(+) transport, intracellular immobilisation and Li(+)/Mg(2+) competition were studied in Li(+)-loaded bovine chromaffin cells. Li(+) influx rate constants, k(i), obtained by atomic absorption (AA) spectrophotometry, in control (without and with ouabain) and depolarising (without and with nitrendipine) conditions, showed that L-type voltage-sensitive Ca(2+) channels have an important role in Li(+) uptake under depolarising conditions. The Li(+) influx apparent rate constant, k(iapp), determined under control conditions by (7)Li NMR spectroscopy with the cells immobilised and perfused, was much lower than the AA-determined value for the cells in suspension. Loading of cell suspensions with 15 mmol l(-1) LiCl led, within 90 min, to a AA-measured total intracellular Li(+) concentration, [Li(+)](iT)=11.39+/-0.56 mmol (l cells)(-1), very close to the steady state value. The intracellular Li(+) T(1)/T(2) ratio of (7)Li NMR relaxation times of the Li(+)-loaded cells reflected a high degree of Li(+) immobilisation in bovine chromaffin cells, similar to neuroblastoma, but larger than for lymphoblastoma and erythrocyte cells. A 52% increase in the intracellular free Mg(2+) concentration, Delta[Mg(2+)](f)=0.27+/-0.05 mmol (l cells)(-1) was measured for chromaffin cells loaded with the Mg(2+)-specific fluorescent probe furaptra, after 90-min loading with 15 mmol l(-1) LiCl, using fluorescence spectroscopy, indicating significant displacement of Mg(2+) by Li(+) from its intracellular binding sites. Comparison with other cell types showed that the extent of intracellular Li(+)/Mg(2+) competition at the same Li(+) loading level depends on intracellular Li(+) transport and immobilisation in a cell-specific manner, being maximal for neuroblastoma cells.
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Affiliation(s)
- C P Fonseca
- Department of Biochemistry and Centre for Neuroscience of Coimbra, University of Coimbra, P.O. Box 3126, 3001-401 Coimbra, Portugal
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Williams N, Layden BT, Suhy J, Metreger T, Foley K, Abukhdeir AM, Borge G, Crayton J, Bryant FB, Mota de Freitas D. Testing competing path models linking the biochemical variables in red blood cells from Li+-treated bipolar patients. Bipolar Disord 2003; 5:320-9. [PMID: 14525552 DOI: 10.1034/j.1399-5618.2003.00054.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Red blood cells (RBCs) from Li+-treated bipolar patients have shown abnormalities in intracellular Li+ concentration ([Li+]i), Na+/Li+ exchange rates, and membrane phospholipid levels. Based on Li+-loaded RBC studies, we hypothesized that Li+-treated bipolar patients also have varied intracellular free Mg2+ concentrations ([Mg2+]f) as compared with normotensive patients. We addressed how these experimentally determined values are intercorrelated. Assuming that Li+ treatment alters these biochemical parameters, we provide hypothetical pathways based upon structural equation modeling statistics. METHODS In RBCs from 30 Li+-treated bipolar patients, we determined [Li+]i, serum [Li+] ([Li+]e), Na+/Li+ exchange parameters, membrane phospholipid levels, [Mg2+]f, and Li+ membrane binding affinities. Comprehensive statistical analyses assessed correlations among the biochemical data. We used path analysis statistics to propose potential pathways in which the data were correlated. RESULTS We found significant correlations within the three Na+/Li+ exchange parameters and percentage composition of the membrane phospholipids. Additional correlations existed between [Mg2+]f and Vstd, Km, or phospholipid composition, between [Li+]i and percentage of phosphatidylcholine, and between percentage of phosphatidylserine and Km. Based on these findings, we hypothesized and statistically determined the most probable pathway through which these parameters were intercorrelated. CONCLUSIONS Significant correlations existed between the biochemical parameters that describe the cell membrane abnormality and the Li+/Mg2+ competition hypotheses. Using path analysis statistics, we identified a biochemical pathway by which Li+ may assert its cellular effects. This study serves as an illustrative example how path analysis is a valuable tool in determining the direction of a certain biochemical pathway.
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Affiliation(s)
- Nicole Williams
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
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Schiller J, Hammerschmidt S, Wirtz H, Arnhold J, Arnold K. Lipid analysis of bronchoalveolar lavage fluid (BAL) by MALDI-TOF mass spectrometry and 31P NMR spectroscopy. Chem Phys Lipids 2001; 112:67-79. [PMID: 11518574 DOI: 10.1016/s0009-3084(01)00163-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite the high clinical relevance, only the cellular moiety of bronchoalveolar lavage (BAL) has been intensively investigated and is used for diagnosis purposes. On the other hand, the cell-free fluid is, by far, less characterized. Although this fluid represents a relatively simple mixture of only a few different phospholipids (mainly phosphatidylcholine, phosphatidylglycerol and cholesterol), methods for the routine analysis of these fluids are still lacking. In the present investigation we have applied, for the first time, MALDI-TOF mass spectrometry, as well as 31P NMR spectroscopy to the analysis of organic extracts of bronchoalveolar lavage fluids. BAL from different mammals (rat, minipig, rabbit and man) were investigated and, for means of comparison, organic extracts of lung tissue were also examined. Both applied methods provide fast and reliable information on the lipid composition of the bronchoalveolar lavage. However, despite of its comparably low sensitivity, 31P NMR spectroscopy detects all phospholipid species in a single experiment and with the same sensitivity, whereas MALDI-TOF fails in the detection of phosphatidylethanolamine in the presence of higher quantities of phosphatidylcholine. In contrast, MALDI-TOF mass spectrometry is more suitable for the detection of cholesterol and the determination of the fatty acid composition of the individual phospholipids, especially lysolipids. It will be shown that all BALs exhibit significant, species-dependent differences that mainly concern the content of phosphatidylglycerol and lyso-phosphatidylcholine. It is concluded that both methods are suitable tools in lipid research due to the (in comparison to alternative methods) simplicity of performance.
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Affiliation(s)
- J Schiller
- Institute of Medical Physics and Biophysics, Medical Department, University of Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany.
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