1
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Zaatouf L, Kumar K, Marcotte I, Warschawski DE. Assessment of membrane labelling mechanisms with exogenous fatty acids and detergents in bacteria. Biochimie 2024:S0300-9084(24)00134-2. [PMID: 38825063 DOI: 10.1016/j.biochi.2024.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Labelling of bacterial membranes using exogenous fatty acids has proven to be a valuable tool to investigate molecular interactions by in-cell solid-state nuclear magnetic resonance (ssNMR) spectroscopy, notably with antimicrobial peptides. However, the mechanism by which this labelling takes place in non-mutated bacteria has not yet been investigated. In this work, we propose a rapid method to assess the fate of the fatty acids during the labelling of bacteria, involving two different methylation schemes and gas chromatography coupled to mass spectrometry. We applied this approach to Gram(+) and Gram(-) bacteria grown with deuterated palmitic acid under different conditions. We assessed the extent of labelling, then the resulting membrane rigidity by 2H ssNMR. Our results reveal that the labelling mechanism depends on the detergent used to micellize the fatty acids. This labelling can be either active or passive, whether the fatty acids are metabolized and used in the phospholipids biosynthesis, or remain unmodified in the membrane. We discuss the best labelling protocol for studying peptide-membrane interactions.
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Affiliation(s)
- Laila Zaatouf
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005, Paris, France
| | - Kiran Kumar
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal, H3C 3P8, Canada
| | - Isabelle Marcotte
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal, H3C 3P8, Canada
| | - Dror E Warschawski
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005, Paris, France.
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2
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Sani MA, Rajput S, Keizer DW, Separovic F. NMR techniques for investigating antimicrobial peptides in model membranes and bacterial cells. Methods 2024; 224:10-20. [PMID: 38295893 DOI: 10.1016/j.ymeth.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
AMPs are short, mainly cationic membrane-active peptides found in all living organism. They perform diverse roles including signaling and acting as a line of defense against bacterial infections. AMPs have been extensively investigated as templates to facilitate the development of novel antimicrobial therapeutics. Understanding the interplay between these membrane-active peptides and the lipid membranes is considered to be a significant step in elucidating the specific mechanism of action of AMPs against prokaryotic and eukaryotic cells to aid the development of new therapeutics. In this review, we have provided a brief overview of various NMR techniques commonly used for studying AMP structure and AMP-membrane interactions in model membranes and whole cells.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - David W Keizer
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia; School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
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3
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Kumar K, Arnold AA, Gauthier R, Mamone M, Paquin JF, Warschawski DE, Marcotte I. 19F solid-state NMR approaches to probe antimicrobial peptide interactions with membranes in whole cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184269. [PMID: 38176532 DOI: 10.1016/j.bbamem.2023.184269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
To address the global problem of bacterial antibiotic resistance, antimicrobial peptides (AMPs) are considered promising therapeutic candidates due to their broad-spectrum and membrane-lytic activity. As preferential interactions with bacteria are crucial, it is equally important to investigate and understand their impact on eukaryotic cells. In this study, we employed 19F solid-state nuclear magnetic resonance (ssNMR) as a novel approach to examine the interaction of AMPs with whole red blood cells (RBCs). We used RBC ghosts (devoid of hemoglobin) and developed a protocol to label their lipid membranes with palmitic acid (PA) monofluorinated at carbon positions 4, 8, or 14 on the acyl chain, allowing us to probe different locations in model and intact RBC ghost membranes. Our work revealed that changes in the 19F chemical shift anisotropy, monitored through a CF bond order parameter (SCF), can provide insights into lipid bilayer dynamics. This information was also obtained using magic-angle spinning 19F ssNMR spectra with and without 1H decoupling, by studying alterations in the second spectral moment (M2) as well as the 19F isotropic chemical shift, linewidth, T1, and T2 relaxation times. The appearance of an additional isotropic peak with a smaller chemical shift anisotropy, a narrower linewidth, and a shorter T1, induced by the AMP caerin 1.1, supports the presence of high-curvature regions in RBCs indicative of pore formation, analogous to its antimicrobial mechanism. In summary, the straightforward incorporation of monofluorinated FAs and rapid signal acquisition offer promising avenues for the study of whole cells using 19F ssNMR.
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Affiliation(s)
- Kiran Kumar
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Alexandre A Arnold
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada
| | - Raphaël Gauthier
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Marius Mamone
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Jean-François Paquin
- PROTEO, CCVC, Département de chimie, Université Laval, 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Dror E Warschawski
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada; Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005 Paris, France.
| | - Isabelle Marcotte
- Departement of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montreal H3C 3P8, Canada.
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4
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Fernando LD, Pérez-Llano Y, Dickwella Widanage MC, Jacob A, Martínez-Ávila L, Lipton AS, Gunde-Cimerman N, Latgé JP, Batista-García RA, Wang T. Structural adaptation of fungal cell wall in hypersaline environment. Nat Commun 2023; 14:7082. [PMID: 37925437 PMCID: PMC10625518 DOI: 10.1038/s41467-023-42693-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
Halophilic fungi thrive in hypersaline habitats and face a range of extreme conditions. These fungal species have gained considerable attention due to their potential applications in harsh industrial processes, such as bioremediation and fermentation under unfavorable conditions of hypersalinity, low water activity, and extreme pH. However, the role of the cell wall in surviving these environmental conditions remains unclear. Here we employ solid-state NMR spectroscopy to compare the cell wall architecture of Aspergillus sydowii across salinity gradients. Analyses of intact cells reveal that A. sydowii cell walls contain a rigid core comprising chitin, β-glucan, and chitosan, shielded by a surface shell composed of galactomannan and galactosaminogalactan. When exposed to hypersaline conditions, A. sydowii enhances chitin biosynthesis and incorporates α-glucan to create thick, stiff, and hydrophobic cell walls. Such structural rearrangements enable the fungus to adapt to both hypersaline and salt-deprived conditions, providing a robust mechanism for withstanding external stress. These molecular principles can aid in the optimization of halophilic strains for biotechnology applications.
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Affiliation(s)
- Liyanage D Fernando
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Malitha C Dickwella Widanage
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anand Jacob
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Andrew S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology, University of Crete, Heraklion, Greece
- Fungal Respiratory Infections Research Unit, University of Angers, Angers, France
| | | | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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5
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Fernando LD, Zhao W, Gautam I, Ankur A, Wang T. Polysaccharide assemblies in fungal and plant cell walls explored by solid-state NMR. Structure 2023; 31:1375-1385. [PMID: 37597511 PMCID: PMC10843855 DOI: 10.1016/j.str.2023.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/26/2023] [Indexed: 08/21/2023]
Abstract
Structural analysis of macromolecular complexes within their natural cellular environment presents a significant challenge. Recent applications of solid-state NMR (ssNMR) techniques on living fungal cells and intact plant tissues have greatly enhanced our understanding of the structure of extracellular matrices. Here, we selectively highlight the most recent progress in this field. Specifically, we discuss how ssNMR can provide detailed insights into the chemical composition and conformational structure of pectin, and the consequential impact on polysaccharide interactions and cell wall organization. We elaborate on the use of ssNMR data to uncover the arrangement of the lignin-polysaccharide interface and the macrofibrillar structure in native plant stems or during degradation processes. We also comprehend the dynamic structure of fungal cell walls under various morphotypes and stress conditions. Finally, we assess how the combination of NMR with other techniques can enhance our capacity to address unresolved structural questions concerning these complex macromolecular assemblies.
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Affiliation(s)
- Liyanage D Fernando
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wancheng Zhao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ankur Ankur
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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6
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Kenyaga JM, Oteino SA, Sun Y, Qiang W. In-cell 31P solid-state NMR measurements of the lipid dynamics and influence of exogeneous β-amyloid peptides on live neuroblastoma neuro-2a cells. Biophys Chem 2023; 297:107008. [PMID: 36989875 DOI: 10.1016/j.bpc.2023.107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/18/2023] [Accepted: 03/19/2023] [Indexed: 03/29/2023]
Abstract
Non-specific disruption of cellular membranes induced by aggregation of exogeneous β-amyloid (Aβ) peptides is considered a viable pathological mechanism in Alzheimer's disease (AD). The solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been widely applied in model liposomes to provide important insights on the molecular interactions between membranes and Aβ aggregates. Yet, the feasibility of in-cell ssNMR spectroscopy to probe Aβ-membrane interactions in native cellular environments has rarely been tested. Here we report the application of in-cell31P ssNMR spectroscopy on live mouse neuroblastoma Neuro-2a (N2a) cells under moderate magic angle spinning (MAS) conditions. Both cell viability and cytoplasmic membrane integrity are retained for up to six hours under 5 kHz MAS frequency at 277 K, which allow applications of direct-polarization 31P spectroscopy and 31P spin-spin (T2) relaxation measurements. The 31P T2 relaxation time constant of N2a cells is significantly increased compared with the model liposome prepared with comparable major phospholipid compositions. With the addition of 5 μM 40-residue Aβ (Aβ1-40) peptides, the 31P T2 relaxation is instantly accelerated. This work demonstrates the feasibility of using in-cell31P ssNMR to investigate the Aβ-membrane interactions in the biologically relevant cellular system.
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7
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Sebastiao M, Babych M, Quittot N, Kumar K, Arnold AA, Marcotte I, Bourgault S. Development of a novel fluorescence assay for studying lipid bilayer perturbation induced by amyloidogenic peptides using cell plasma membrane vesicles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184118. [PMID: 36621762 DOI: 10.1016/j.bbamem.2022.184118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
Numerous pathophysiological conditions are associated with the misfolding and aggregation of proteins into insoluble amyloid fibrils. The mechanisms by which this process leads to cellular dysfunction remain elusive, though several hypotheses point toward the perturbation of the cell plasma membrane by pre-fibrillar intermediates and/or amyloid growth. However, current models to study membrane perturbations are largely limited to synthetic lipid vesicles and most of experimental approaches cannot be transposed to complex cell-derived plasma membrane systems. Herein, vesicles originating from the plasma membrane of erythrocytes and β-pancreatic cells were used to study the perturbations induced by an amyloidogenic peptide, the islet amyloid polypeptide (IAPP). These biologically relevant lipid vesicles displayed a characteristic clustering in the presence of the amyloidogenic peptide, which was able to rupture membranes. By exploiting Förster resonance energy transfer (FRET), a rapid, simple, and potentially high-throughput assay to detect membrane perturbations of intact mammalian cell plasma membrane vesicles was implemented. The FRET kinetics of membrane perturbations closely correlated with the kinetics of thioflavin-T fluorescence associated with amyloid formation. This novel kinetics assay expands the toolbox available to study amyloid-associated membrane damage, bridging the gap between synthetic lipid vesicles and living cells.
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Affiliation(s)
- Mathew Sebastiao
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Margaryta Babych
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Noé Quittot
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Kiran Kumar
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada.
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada.
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8
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Rajan S, Kudryashov DS, Reisler E. Actin Bundles Dynamics and Architecture. Biomolecules 2023; 13:450. [PMID: 36979385 PMCID: PMC10046292 DOI: 10.3390/biom13030450] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Cells use the actin cytoskeleton for many of their functions, including their division, adhesion, mechanosensing, endo- and phagocytosis, migration, and invasion. Actin bundles are the main constituent of actin-rich structures involved in these processes. An ever-increasing number of proteins that crosslink actin into bundles or regulate their morphology is being identified in cells. With recent advances in high-resolution microscopy and imaging techniques, the complex process of bundles formation and the multiple forms of physiological bundles are beginning to be better understood. Here, we review the physiochemical and biological properties of four families of highly conserved and abundant actin-bundling proteins, namely, α-actinin, fimbrin/plastin, fascin, and espin. We describe the similarities and differences between these proteins, their role in the formation of physiological actin bundles, and their properties-both related and unrelated to their bundling abilities. We also review some aspects of the general mechanism of actin bundles formation, which are known from the available information on the activity of the key actin partners involved in this process.
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Affiliation(s)
- Sudeepa Rajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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9
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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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10
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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11
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Booth V. Deuterium Solid State NMR Studies of Intact Bacteria Treated With Antimicrobial Peptides. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 2:621572. [PMID: 35047897 PMCID: PMC8757836 DOI: 10.3389/fmedt.2020.621572] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Solid state NMR has been tremendously useful in characterizing the structure and dynamics of model membranes composed of simple lipid mixtures. Model lipid studies employing solid state NMR have included important work revealing how membrane bilayer structure and dynamics are affected by molecules such as antimicrobial peptides (AMPs). However, solid state NMR need not be applied only to model membranes, but can also be used with living, intact cells. NMR of whole cells holds promise for helping resolve some unsolved mysteries about how bacteria interact with AMPs. This mini-review will focus on recent studies using 2H NMR to study how treatment with AMPs affect membranes in intact bacteria.
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Affiliation(s)
- Valerie Booth
- Department of Biochemistry and Department of Physics and Physical Oceanograpy, Memorial University of Newfoundland, St. John's, NL, Canada
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12
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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13
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Poulhazan A, Dickwella Widanage MC, Muszyński A, Arnold AA, Warschawski DE, Azadi P, Marcotte I, Wang T. Identification and Quantification of Glycans in Whole Cells: Architecture of Microalgal Polysaccharides Described by Solid-State Nuclear Magnetic Resonance. J Am Chem Soc 2021; 143:19374-19388. [PMID: 34735142 PMCID: PMC8630702 DOI: 10.1021/jacs.1c07429] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 12/15/2022]
Abstract
Microalgae are photosynthetic organisms widely distributed in nature and serve as a sustainable source of bioproducts. Their carbohydrate components are also promising candidates for bioenergy production and bioremediation, but the structural characterization of these heterogeneous polymers in cells remains a formidable problem. Here we present a widely applicable protocol for identifying and quantifying the glycan content using magic-angle-spinning (MAS) solid-state NMR (ssNMR) spectroscopy, with validation from glycosyl linkage and composition analysis deduced from mass-spectrometry (MS). Two-dimensional 13C-13C correlation ssNMR spectra of a uniformly 13C-labeled green microalga Parachlorella beijerinckii reveal that starch is the most abundant polysaccharide in a naturally cellulose-deficient strain, and this polymer adopts a well-organized and highly rigid structure in the cell. Some xyloses are present in both the mobile and rigid domains of the cell wall, with their chemical shifts partially aligned with the flat-ribbon 2-fold xylan identified in plants. Surprisingly, most other carbohydrates are largely mobile, regardless of their distribution in glycolipids or cell walls. These structural insights correlate with the high digestibility of this cellulose-deficient strain, and the in-cell ssNMR methods will facilitate the investigations of other economically important algae species.
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Affiliation(s)
- Alexandre Poulhazan
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | | | - Artur Muszyński
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Alexandre A. Arnold
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | - Dror E. Warschawski
- Laboratoire
des Biomolécules, LBM, CNRS UMR 7203,
Sorbonne Université, École Normale Supérieure,
PSL University, 75005 Paris, France
| | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Isabelle Marcotte
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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14
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Laydevant F, Mahabadi M, Llido P, Bourgouin JP, Caron L, Arnold AA, Marcotte I, Warschawski DE. Growth-phase dependence of bacterial membrane lipid profile and labeling for in-cell solid-state NMR applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1864:183819. [PMID: 34800428 DOI: 10.1016/j.bbamem.2021.183819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
Cell labeling is a preliminary step in multiple biophysical approaches, including the solid-state nuclear magnetic resonance (NMR) study of bacteria in vivo. Deuterium solid-state NMR has been used in the past years to probe bacterial membranes and their interactions with antimicrobial peptides, following a standard labeling protocol. Recent results from our laboratory on a slow-growing bacterium has shown the need to optimize this protocol, especially the bacterial growth time before harvest and the concentration of exogenous labeled fatty acids to be used for both Escherichia coli and Bacillus subtilis. It is also essential for the protocol to remain harmless to cells while providing optimal labeling. We have therefore developed a fast and facile approach to monitor the lipid composition of bacterial membranes under various growth conditions, combining solution 31P NMR and GCMS. Using this approach, the optimized labeling conditions of Escherichia coli and Bacillus subtilis with deuterated palmitic acid were determined. Our results show a modification of B. subtilis phospholipid profile as a function of the growth stage, as opposed to E. coli. Our protocol recommends low concentrations of exogenous palmitic acid in the growth medium, and bacteria harvest after the exponential phase.
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Affiliation(s)
- Florent Laydevant
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Mahsa Mahabadi
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Pierre Llido
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Jean-Philippe Bourgouin
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Laurence Caron
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.
| | - Dror E Warschawski
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada; Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005 Paris, France.
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15
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Abhyankar N, Szalai V. Challenges and Advances in the Application of Dynamic Nuclear Polarization to Liquid-State NMR Spectroscopy. J Phys Chem B 2021; 125:5171-5190. [PMID: 33960784 PMCID: PMC9871957 DOI: 10.1021/acs.jpcb.0c10937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method to study the molecular structure and dynamics of materials. The inherently low sensitivity of NMR spectroscopy is a consequence of low spin polarization. Hyperpolarization of a spin ensemble is defined as a population difference between spin states that far exceeds what is expected from the Boltzmann distribution for a given temperature. Dynamic nuclear polarization (DNP) can overcome the relatively low sensitivity of NMR spectroscopy by using a paramagnetic matrix to hyperpolarize a nuclear spin ensemble. Application of DNP to NMR can result in sensitivity gains of up to four orders of magnitude compared to NMR without DNP. Although DNP NMR is now more routinely utilized for solid-state (ss) NMR spectroscopy, it has not been exploited to the same degree for liquid-state samples. This Review will consider challenges and advances in the application of DNP NMR to liquid-state samples. The Review is organized into four sections: (i) mechanisms of DNP NMR relevant to hyperpolarization of liquid samples; (ii) applications of liquid-state DNP NMR; (iii) available detection schemes for liquid-state samples; and (iv) instrumental challenges and outlook for liquid-state DNP NMR.
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Affiliation(s)
- Nandita Abhyankar
- Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD 20742, USA,National Institute of Standards and Technology, Gaithersburg, MD 20899, USA,Corresponding authors: ,
| | - Veronika Szalai
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA,Corresponding authors: ,
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16
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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17
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Kent JE, Fujimoto LM, Shin K, Singh C, Yao Y, Park SH, Opella SJ, Plano GV, Marassi FM. Correlating the Structure and Activity of Y. pestis Ail in a Bacterial Cell Envelope. Biophys J 2020; 120:453-462. [PMID: 33359463 DOI: 10.1016/j.bpj.2020.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/08/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding microbe-host interactions at the molecular level is a major goal of fundamental biology and therapeutic drug development. Structural biology strives to capture biomolecular structures in action, but the samples are often highly simplified versions of the complex native environment. Here, we present an Escherichia coli model system that allows us to probe the structure and function of Ail, the major surface protein of the deadly pathogen Yersinia pestis. We show that cell surface expression of Ail produces Y. pestis virulence phenotypes in E. coli, including resistance to human serum, cosedimentation of human vitronectin, and pellicle formation. Moreover, isolated bacterial cell envelopes, encompassing inner and outer membranes, yield high-resolution solid-state NMR spectra that reflect the structure of Ail and reveal Ail sites that are sensitive to the bacterial membrane environment and involved in the interactions with human serum components. The data capture the structure and function of Ail in a bacterial outer membrane and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum.
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Affiliation(s)
- James E Kent
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Lynn M Fujimoto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Kyungsoo Shin
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Chandan Singh
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Yong Yao
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sang Ho Park
- Department Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Stanley J Opella
- Department Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Gregory V Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida
| | - Francesca M Marassi
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
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18
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Membrane proteins in magnetically aligned phospholipid polymer discs for solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183333. [PMID: 32371072 DOI: 10.1016/j.bbamem.2020.183333] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Well-hydrated phospholipid bilayers provide a near-native environment for membrane proteins. They enable the preparation of chemically-defined samples suitable for NMR and other spectroscopic experiments that reveal the structure, dynamics, and functional interactions of the proteins at atomic resolution. The synthetic polymer styrene maleic acid (SMA) can be used to prepare detergent-free samples that form macrodiscs with diameters greater than 30 nm at room temperature, and spontaneously align in the magnetic field of an NMR spectrometer at temperatures above 35 °C. Here we show that magnetically aligned macrodiscs are particularly well suited for solid-state NMR experiments of membrane proteins because the SMA-lipid assembly both immobilizes the embedded protein and provides uniaxial order for oriented sample (OS) solid-state NMR studies. We show that aligned macrodiscs incorporating four different membrane proteins with a wide range of sizes and topological complexity yield high-resolution OS solid-state NMR spectra. The work is dedicated to Michelle Auger who made key contributions to the field of membrane and membrane protein biophysics.
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19
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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20
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Ding X, Fu R, Tian F. De novo resonance assignment of the transmembrane domain of LR11/SorLA in E. coli membranes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 310:106639. [PMID: 31734618 PMCID: PMC6935515 DOI: 10.1016/j.jmr.2019.106639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 05/17/2023]
Abstract
Membrane proteins perform many important cellular functions. Historically, structural studies of these proteins have been conducted in detergent preparations and synthetic lipid bilayers. More recently, magic-angle-spinning (MAS) solid-state NMR has been employed to analyze membrane proteins in native membrane environments, but resonance assignments with this technique remain challenging due to limited spectral resolution and high resonance degeneracy. To tackle this issue, we combine reverse labeling of amino acids, frequency-selective dipolar dephasing, and NMR difference spectroscopy. These methods have resulted in nearly complete resonance assignments of the transmembrane domain of human LR11 (SorLA) protein in E. coli membranes. To reduce background signals from E. coli lipids and proteins and improve spectral sensitivity, we effectively utilize amylose affinity chromatography to prepare membrane vesicles when MBP is included as a fusion partner in the expression construct.
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Affiliation(s)
- Xiaoyan Ding
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Hershey, PA 17033, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Dr., Tallahassee, FL 32310, USA.
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Hershey, PA 17033, USA.
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21
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Leung SSW, Brewer J, Bagatolli LA, Thewalt JL. Measuring molecular order for lipid membrane phase studies: Linear relationship between Laurdan generalized polarization and deuterium NMR order parameter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183053. [DOI: 10.1016/j.bbamem.2019.183053] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/27/2019] [Accepted: 08/21/2019] [Indexed: 01/03/2023]
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22
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Siegal G, Selenko P. Cells, drugs and NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:202-212. [PMID: 31358370 DOI: 10.1016/j.jmr.2019.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.
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Affiliation(s)
- Gregg Siegal
- ZoBio B.V., BioPartner 2 Building, J.H. Oortweg 19, 2333 Leiden, the Netherlands
| | - Philipp Selenko
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000 Rehovot, Israel.
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23
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A New Method of Assessing Lipid Mixtures by 31P Magic-Angle Spinning NMR. Biophys J 2019; 114:1368-1376. [PMID: 29590594 DOI: 10.1016/j.bpj.2018.01.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 11/20/2022] Open
Abstract
A variety of lipids that differ by their chains and headgroups are found in biomembranes. In addition to studying the overall membrane phase, determination of the structure, dynamics, and headgroup conformation of individual lipids in the mixture would be of great interest. We have thus developed, to our knowledge, a new approach using solid-state 31P NMR, magic-angle spinning, and chemical-shift anisotropy (CSA) recoupling, using an altered version of the recoupling of chemical shift anisotropy (ROCSA) pulse sequence, here penned PROCSA. The resulting two-dimensional spectra allowed the simultaneous measurement of the isotropic chemical shift and CSA of each lipid headgroup, thus providing a valuable measure of its dynamics and structure. PROCSA was applied to mixtures of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) in various relative proportions, to mimic bacterial membranes and assess the respective roles of lipids in shaping these bilayers. The results were interpreted in terms of membrane topology, lipid propensity to adopt various phases or conformations, and lipid-lipid miscibility. Our results showed that PG dictates the lipid behavior when present in a proportion of 20 mol % or more. A small proportion of PG is thus able to impose a bilayer structure to the hexagonal phase forming PE. We discuss the requirement for lipids, such as PE, to be able to adopt non-bilayer phases in a membrane.
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24
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Bouhlel Z, Arnold AA, Warschawski DE, Lemarchand K, Tremblay R, Marcotte I. Labelling strategy and membrane characterization of marine bacteria Vibrio splendidus by in vivo 2H NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:871-878. [DOI: 10.1016/j.bbamem.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/03/2019] [Accepted: 01/31/2019] [Indexed: 01/15/2023]
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25
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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26
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Janssen GJ, Bielytskyi P, Artiukhin DG, Neugebauer J, de Groot HJM, Matysik J, Alia A. Photochemically induced dynamic nuclear polarization NMR on photosystem II: donor cofactor observed in entire plant. Sci Rep 2018; 8:17853. [PMID: 30552342 PMCID: PMC6294776 DOI: 10.1038/s41598-018-36074-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
The solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect allows for increase of signal and sensitivity in magic-angle spinning (MAS) NMR experiments. The effect occurs in photosynthetic reaction centers (RC) proteins upon illumination and induction of cyclic electron transfer. Here we show that the strength of the effect allows for observation of the cofactors forming the spin-correlated radical pair (SCRP) in isolated proteins, in natural photosynthetic membranes as well as in entire plants. To this end, we measured entire selectively 13C isotope enriched duckweed plants (Spirodela oligorrhiza) directly in the MAS rotor. Comparison of 13C photo-CIDNP MAS NMR spectra of photosystem II (PS2) obtained from different levels of RC isolation, from entire plant to isolated RC complex, demonstrates the intactness of the photochemical machinery upon isolation. The SCRP in PS2 is structurally and functionally very similar in duckweed and spinach (Spinacia oleracea). The analysis of the photo-CIDNP MAS NMR spectra reveals a monomeric Chl a donor. There is an experimental evidence for matrix involvement, most likely due to the axial donor histidine, in the formation of the SCRP. Data do not suggest a chemical modification of C-131 carbonyl position of the donor cofactor.
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Affiliation(s)
- Geertje J Janssen
- University of Leiden, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Pavlo Bielytskyi
- Universität Leipzig, Institute of Analytical Chemistry, Johannisallee 29, D-04103, Leipzig, Germany
| | - Denis G Artiukhin
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstraße 40, D-48149, Münster, Germany
| | - Johannes Neugebauer
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstraße 40, D-48149, Münster, Germany
| | - Huub J M de Groot
- University of Leiden, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jörg Matysik
- Universität Leipzig, Institute of Analytical Chemistry, Johannisallee 29, D-04103, Leipzig, Germany.
| | - A Alia
- University of Leiden, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
- Universität Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, D-04107, Leipzig, Germany.
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27
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Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre JP. Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin. ACS Chem Biol 2018; 13:2106-2113. [PMID: 29965728 DOI: 10.1021/acschembio.8b00271] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria.
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Affiliation(s)
- Cedric Laguri
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Alba Silipo
- University of Naples Federico II, Department of Chemical Sciences, via cintia 4, Napoli, Italy
| | - Alessandra M. Martorana
- University of Milano, Department of Pharmacological and Biomolecular Sciences, Via Balzaretti 9, Milano, Italy
| | - Paul Schanda
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Roberta Marchetti
- University of Naples Federico II, Department of Chemical Sciences, via cintia 4, Napoli, Italy
| | - Alessandra Polissi
- University of Milano, Department of Pharmacological and Biomolecular Sciences, Via Balzaretti 9, Milano, Italy
| | - Antonio Molinaro
- University of Naples Federico II, Department of Chemical Sciences, via cintia 4, Napoli, Italy
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28
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Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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29
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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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30
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Arnold AA, Bourgouin JP, Genard B, Warschawski DE, Tremblay R, Marcotte I. Whole cell solid-state NMR study of Chlamydomonas reinhardtii microalgae. JOURNAL OF BIOMOLECULAR NMR 2018; 70:123-131. [PMID: 29327221 DOI: 10.1007/s10858-018-0164-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/04/2018] [Indexed: 05/03/2023]
Abstract
In vivo or whole-cell solid-state NMR is an emerging field which faces tremendous challenges. In most cases, cell biochemistry does not allow the labelling of specific molecules and an in vivo study is thus hindered by the inherent difficulty of identifying, among a formidable number of resonances, those arising from a given molecule. In this work we examined the possibility of studying, by solid-state NMR, the model organism Chlamydomonas reinhardtii fully and non-specifically 13C labelled. The extension of NMR-based dynamic filtering from one-dimensional to two-dimensional experiments enabled an enhanced selectivity which facilitated the assignment of cell constituents. The number of resonances detected with these robust and broadly applicable experiments appears to be surprisingly sparse. Various constituents, notably galactolipids abundant in organelle membranes, carbohydrates from the cell wall, and starch from storage grains could be unambiguously assigned. Moreover, the dominant crystal form of starch could be determined in situ. This work illustrates the feasibility and caveats of using solid-state NMR to study intact non-specifically 13C labelled micro-organisms.
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Affiliation(s)
- Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, Montreal, H3C 3P8, Canada
| | - Jean-Philippe Bourgouin
- Department of Chemistry, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, Montreal, H3C 3P8, Canada
| | - Bertrand Genard
- Department of Chemistry, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, Montreal, H3C 3P8, Canada
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, G5L 3A1, Canada
| | - Dror E Warschawski
- Department of Chemistry, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, Montreal, H3C 3P8, Canada
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot and IBPC, 13 rue Pierre et Marie-Curie, 75005, Paris, France
| | - Réjean Tremblay
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, G5L 3A1, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Downtown Station, P.O. Box 8888, Montreal, H3C 3P8, Canada.
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31
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Itin B, Sergeyev IV. Strategies for Efficient Sample Preparation for Dynamic Nuclear Polarization Solid-State NMR of Biological Macromolecules. Methods Mol Biol 2018; 1688:133-154. [PMID: 29151208 DOI: 10.1007/978-1-4939-7386-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Solid-state NMR (SSNMR) is a powerful tool for the elucidation of structure and dynamics in biological macromolecules. Over the years, SSNMR spectroscopists have developed an array of techniques enabling the measurement of internuclear correlations, distances, and torsional angles; these have been applied to the study of a number of biological systems that are difficult to study by X-ray crystallography and solution NMR, including key biological targets such as membrane proteins and amyloid fibrils. Applications of SSNMR to other topic areas, including materials science, pharmaceuticals, and small molecules, have also flourished in recent years. These studies, however, have always been hampered by the low inherent sensitivity of SSNMR, requiring large amounts of both sample and time for data collection. By taking advantage of unpaired electrons doped into a sample as a ready source of additional nuclear polarization, dynamic nuclear polarization (DNP) has brought about large improvements in SSNMR sensitivity. These, in turn, have enabled structural studies of previously inaccessible targets, such as large protein complexes, nucleic acids, viral capsids, and membrane proteins in vivo. Herein, we focus on sample preparation strategies and considerations for scientists interested in applying DNP to challenging systems.
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Affiliation(s)
- Boris Itin
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA.
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
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32
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Sani MA, Separovic F. Antimicrobial Peptide Structures: From Model Membranes to Live Cells. Chemistry 2017; 24:286-291. [PMID: 29068097 DOI: 10.1002/chem.201704362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Indexed: 01/12/2023]
Abstract
The rise in antibiotic resistance has led to a renewed interest in antimicrobial peptides (AMPs) that target membranes. The mode of action of AMPs involves the disruption of the lipid bilayer and leads to growth inhibition and death of the bacteria. However, details at the molecular level of how these peptides kill bacteria and the reasons for the observed differences in selectivity remain unclear. Structural information is crucial for defining the molecular mechanism by which these peptides recognize, self-assemble and interact with a particular lipid membrane. Solid-state NMR is a non-invasive technique that allows the study of the structural details of lipid-peptide and peptide-peptide interactions. Following on from studies of antibiotic and lytic peptides, gramicidin A and melittin, respectively, we investigated maculatin 1.1, an AMP from the skin of Australian tree frogs that acts against Gram-positive bacteria. By using perdeuterated phospholipids and specifically labelled peptides, 2 H, 31 P and {31 P}15 N REDOR solid-state NMR experiments have been used to localize, maculatin 1.1 in neutral and anionic model membranes. However, the structure, location and activity depend on the composition of the model membrane and current advances in solid-state NMR spectroscopy now allow structure determination of AMPs in live bacteria.
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Affiliation(s)
- Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3010, Australia
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33
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Booth V, Warschawski DE, Santisteban NP, Laadhari M, Marcotte I. Recent progress on the application of 2H solid-state NMR to probe the interaction of antimicrobial peptides with intact bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1500-1511. [PMID: 28844739 DOI: 10.1016/j.bbapap.2017.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
Discoveries relating to innate immunity and antimicrobial peptides (AMPs) granted Bruce Beutler and Jules Hoffmann a Nobel prize in medicine in 2011, and opened up new avenues for the development of therapies against infections, and even cancers. The mechanisms by which AMPs interact with, and ultimately disrupt, bacterial cell membranes is still, to a large extent, incompletely understood. Up until recently, this mechanism was studied using model lipid membranes that failed to reproduce the complexity of molecular interactions present in real cells comprising lipids but also membrane proteins, a cell wall containing peptidoglycan or lipopolysaccharides, and other molecules. In this review, we focus on recent attempts to study, at the molecular level, the interaction between cationic AMPs and intact bacteria, by 2H solid-state NMR. Specifically-labeled lipids allow us to focus on the interaction of AMPs with the heart of the bacterial membrane, and measure the lipid order and its variation upon interaction with various peptides. We will review the important parameters to consider in such a study, and summarize the results obtained in the past 5years on various peptides, in particular aurein 1.2, caerin 1.1, MSI-78 and CA(1-8)M(1-10). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Valerie Booth
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Dror E Warschawski
- UMR 7099, CNRS - Université Paris Diderot, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France; Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada
| | - Nury P Santisteban
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada
| | - Marwa Laadhari
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Downtown Station, Montréal H3C 3P8, Canada.
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34
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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Plitzko JM, Schuler B, Selenko P. Structural Biology outside the box-inside the cell. Curr Opin Struct Biol 2017; 46:110-121. [PMID: 28735108 DOI: 10.1016/j.sbi.2017.06.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/17/2017] [Accepted: 06/23/2017] [Indexed: 01/11/2023]
Abstract
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
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Affiliation(s)
- Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Laboratory, Robert-Roessle Strasse 10, D-13125 Berlin, Germany.
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36
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Auger M. Membrane solid-state NMR in Canada: A historical perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1483-1489. [PMID: 28652206 DOI: 10.1016/j.bbapap.2017.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/17/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Michèle Auger
- Département de chimie, PROTEO, CERMA, CQMF, Université Laval, Québec, Québec G1V 0A6, Canada.
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37
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Li C, Zhao J, Cheng K, Ge Y, Wu Q, Ye Y, Xu G, Zhang Z, Zheng W, Zhang X, Zhou X, Pielak G, Liu M. Magnetic Resonance Spectroscopy as a Tool for Assessing Macromolecular Structure and Function in Living Cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:157-182. [PMID: 28301750 DOI: 10.1146/annurev-anchem-061516-045237] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Investigating the structure, modification, interaction, and function of biomolecules in their native cellular environment leads to physiologically relevant knowledge about their mechanisms, which will benefit drug discovery and design. In recent years, nuclear and electron magnetic resonance (NMR) spectroscopy has emerged as a useful tool for elucidating the structure and function of biomacromolecules, including proteins, nucleic acids, and carbohydrates in living cells at atomic resolution. In this review, we summarize the progress and future of in-cell NMR as it is applied to proteins, nucleic acids, and carbohydrates.
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Affiliation(s)
- Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Yuwei Ge
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Yansheng Ye
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Zeting Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Wenwen Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
| | - Gary Pielak
- Department of Chemistry, Department of Biochemistry and Biophysics, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; ,
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38
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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39
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Daube D, Aladin V, Heiliger J, Wittmann JJ, Barthelmes D, Bengs C, Schwalbe H, Corzilius B. Heteronuclear Cross-Relaxation under Solid-State Dynamic Nuclear Polarization. J Am Chem Soc 2016; 138:16572-16575. [DOI: 10.1021/jacs.6b08683] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diane Daube
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Victoria Aladin
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Jörg Heiliger
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Johannes J. Wittmann
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Dominic Barthelmes
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Institute
of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Christian Bengs
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Institute
of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Björn Corzilius
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
- Center
for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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40
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Affiliation(s)
- Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Hoa Q. Do
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Collin G. Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Emily P. Hardy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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41
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Nonappa, Kolehmainen E. Solid state NMR studies of gels derived from low molecular mass gelators. SOFT MATTER 2016; 12:6015-26. [PMID: 27374054 PMCID: PMC5322468 DOI: 10.1039/c6sm00969g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/16/2016] [Indexed: 06/06/2023]
Abstract
Since its invention more than six decades ago, nuclear magnetic resonance (NMR) spectroscopy has evolved as an inevitable part of chemical as well as structural analysis of small molecules, polymers, biomaterials and hybrid materials. In the solution state, due to the increased viscosity of complex viscoelastic fluids such as gels, liquid crystals and other soft materials, the rate of molecular tumbling is reduced, which in turn affects the chemical shift anisotropy, dipolar and quadrupolar interactions. As a consequence the solution state NMR spectra show broad lines, and therefore, extracting detailed structural information is a challenging task. In this context, solid state (SS) NMR has the ability to distinguish between a minute amount of polymorphic forms, conformational changes, and the number of non-equivalent molecules in an asymmetric unit of a crystal lattice, and to provide both qualitative as well as quantitative analytical data with a short-range order. Therefore, SS NMR has continued to evolve as an indispensable tool for structural analysis and gave birth to a new field called NMR crystallography. Solid state cross polarization (CP) and high resolution (HR) magic angle spinning (MAS) NMR spectroscopy has been used to study weak interactions in polymer gels. However, the application of SS NMR spectroscopy to study gels derived from low molecular weight gelators has been limited until recently. In this review, we will focus on the importance of solid state NMR spectroscopy in understanding and elucidating the structure of supramolecular gels derived from low molecular weight gelators with selected examples.
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Affiliation(s)
- Nonappa
- Department of Applied Physics, Aalto University School of Science, Puumiehenkuja 2, Espoo, FI-02150, Finland.
| | - E Kolehmainen
- Department of Chemistry, University of Jyväskylä, Jyväskylä, FI-41004, Finland.
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