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Journal articles on the topic 'Cellular solid-state NMR'

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Author: Grafiati
Published: 10 March 2023

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1

Baldus, Marc. "Cellular Solid-State NMR Applied to Bacterial and Human cells." Biophysical Journal 114, no. 3 (February 2018): 399a—400a. http://dx.doi.org/10.1016/j.bpj.2017.11.2210.

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2

Opella, S. J., P. L. Stewart, and K. G. Valentine. "Protein structure by solid-state NMR spectroscopy." Quarterly Reviews of Biophysics 19, no. 1-2 (February 1987): 7–49. http://dx.doi.org/10.1017/s0033583500004017.

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The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoff et al, 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfield et al. (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.
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3

Damman, Reinier, Alessandra Lucini Paioni, Katerina T. Xenaki, Irati Beltrán Hernández, Paul M. P. van Bergen en Henegouwen, and Marc Baldus. "Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy." Journal of Biomolecular NMR 74, no. 8-9 (June 19, 2020): 401–12. http://dx.doi.org/10.1007/s10858-020-00328-8.

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Abstract Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins within the complexity of a 3D cellular environment. Here we investigate the use of the hanging drop method to grow spheroids which are homogenous in size and shape as a model system to study solid tumors using solid-state NMR (ssNMR) spectroscopy. We find that these spheroids are stable under magic-angle-spinning conditions and show a clear change in metabolic profile as compared to single cell preparations. Finally, we utilize dynamic nuclear polarization (DNP)-supported ssNMR measurements to show that low concentrations of labelled nanobodies targeting EGFR (7D12) can be detected inside the spheroids. These findings suggest that solid-state NMR can be used to directly examine proteins or other biomolecules in a 3D cellular microenvironment with potential applications in pharmacological research.
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4

Baker, Lindsay A., Mark Daniëls, Elwin A. W. van der Cruijsen, Gert E. Folkers, and Marc Baldus. "Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling." Journal of Biomolecular NMR 62, no. 2 (May 9, 2015): 199–208. http://dx.doi.org/10.1007/s10858-015-9936-5.

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5

Renault, Marie, Shane Pawsey, Martine P. Bos, Eline J. Koers, Deepak Nand, Ria Tommassen-van Boxtel, Melanie Rosay, Jan Tommassen, Werner E. Maas, and Marc Baldus. "Solid-State NMR Spectroscopy on Cellular Preparations Enhanced by Dynamic Nuclear Polarization." Angewandte Chemie International Edition 51, no. 12 (February 1, 2012): 2998–3001. http://dx.doi.org/10.1002/anie.201105984.

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6

Chakraborty, Arnab, Fabien Deligey, Jenny Quach, Frederic Mentink-Vigier, Ping Wang, and Tuo Wang. "Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy." Biochemical Society Transactions 48, no. 3 (May 7, 2020): 1089–99. http://dx.doi.org/10.1042/bst20191084.

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Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. These structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.
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7

Yamamoto, Kazutoshi, Marc A. Caporini, Sang-Choul Im, Lucy Waskell, and Ayyalusamy Ramamoorthy. "Cellular solid-state NMR investigation of a membrane protein using dynamic nuclear polarization." Biochimica et Biophysica Acta (BBA) - Biomembranes 1848, no. 1 (January 2015): 342–49. http://dx.doi.org/10.1016/j.bbamem.2014.07.008.

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8

Li, Jingyu, and Erni Ma. "Characterization of Water in Wood by Time-Domain Nuclear Magnetic Resonance Spectroscopy (TD-NMR): A Review." Forests 12, no. 7 (July 7, 2021): 886. http://dx.doi.org/10.3390/f12070886.

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This review summarizes the development of the experimental technique and analytical method for using TD-NMR to study wood-water interactions in recent years. We briefly introduce the general concept of TD-NMR and magnetic resonance imaging (MRI), and demonstrate their applications for characterizing the following aspects of wood-water interactions: water state, fiber saturation state, water distribution at the cellular scale, and water migration in wood. The aim of this review is to provide an overview of the utilizations and future research opportunities of TD-NMR in wood-water relations. It should be noted that this review does not cover the NMR methods that provide chemical resolution of wood macromolecules, such as solid-state NMR.
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9

Overall, Sarah A., Shiying Zhu, Eric Hanssen, Frances Separovic, and Marc-Antoine Sani. "In Situ Monitoring of Bacteria under Antimicrobial Stress Using 31P Solid-State NMR." International Journal of Molecular Sciences 20, no. 1 (January 6, 2019): 181. http://dx.doi.org/10.3390/ijms20010181.

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In-cell NMR offers great insight into the characterization of the effect of toxins and antimicrobial peptides on intact cells. However, the complexity of intact live cells remains a significant challenge for the analysis of the effect these agents have on different cellular components. Here we show that 31P solid-state NMR can be used to quantitatively characterize the dynamic behaviour of DNA within intact live bacteria. Lipids were also identified and monitored, although 31P dynamic filtering methods indicated a range of dynamic states for phospholipid headgroups. We demonstrate the usefulness of this methodology for monitoring the activity of the antibiotic ampicillin and the antimicrobial peptide (AMP) maculatin 1.1 (Mac1.1) against Gram-negative bacteria. Perturbations in the dynamic behaviour of DNA were observed in treated cells, which indicated additional mechanisms of action for the AMP Mac1.1 not previously reported. This work highlights the value of 31P in-cell solid-state NMR as a tool for assessing the antimicrobial activity of antibiotics and AMPs in bacterial cells.
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10

McDowell, Lynda M., Susan M. Holl, Shijun Qian, Ellen Li, and Jacob Schaefer. "Inter-tryptophan distances in rat cellular retinol binding protein II by solid-state NMR." Biochemistry 32, no. 17 (May 4, 1993): 4560–63. http://dx.doi.org/10.1021/bi00068a011.

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11

Pinto, Cecilia, Deni Mance, Manon Julien, Mark Daniels, Markus Weingarth, and Marc Baldus. "Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy." Journal of Structural Biology 206, no. 1 (April 2019): 1–11. http://dx.doi.org/10.1016/j.jsb.2017.11.015.

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12

Sakol, Nat, Ayako Egawa, and Toshimichi Fujiwara. "Gadolinium Complexes as Contrast Agent for Cellular NMR Spectroscopy." International Journal of Molecular Sciences 21, no. 11 (June 5, 2020): 4042. http://dx.doi.org/10.3390/ijms21114042.

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Aqua Gd3+ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the extracellular space without disturbing biological functions. Cell membrane permeability to Gd complexes was evaluated from the concentrations of gadolinium complexes in the inside and outside of E. coli cells measured by the 1H-NMR relaxation. The site-specific binding of the complexes to E. coli cells was also analyzed by high-resolution solid-state 13C-NMR. The aqua Gd3+ complex did not enhance T1 relaxation in proportion to the amount of added Gd3+. This Gd3+ concentration dependence and the 13C-NMR indicated that its strong cytotoxicity should be due to the binding of the paramagnetic ions to cellular components especially at the lipid membranes. In contrast, Gd-DOTA stayed in the solution states and enhanced relaxation in proportion to the added amount. This agent exhibited strong T1 contrast between the intra- and extracellular spaces by a factor of ten at high concentrations under which the cells were viable over a long experimental time of days. These properties make Gd-DOTA suitable for selectively contrasting the living cellular space in NMR spectroscopy primarily owing to its weak interaction with cellular components.
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13

Vasa, Suresh, Lin Lin, Chaowei Shi, Birgit Habenstein, Dietmar Riedel, Juliane Kühn, Martin Thanbichler, and Adam Lange. "β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR." Proceedings of the National Academy of Sciences 112, no. 2 (December 30, 2014): E127—E136. http://dx.doi.org/10.1073/pnas.1418450112.

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Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments fromCaulobacter crescentusby high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.
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14

Porcelli, Fernando, Bethany Buck, Dong-Kuk Lee, Kevin J. Hallock, Ayyalusamy Ramamoorthy, and Gianluigi Veglia. "Structure and Orientation of Pardaxin Determined by NMR Experiments in Model Membranes." Journal of Biological Chemistry 279, no. 44 (July 29, 2004): 45815–23. http://dx.doi.org/10.1074/jbc.m405454200.

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Pardaxins are a class of ichthyotoxic peptides isolated from fish mucous glands. Pardaxins physically interact with cell membranes by forming pores or voltage-gated ion channels that disrupt cellular functions. Here we report the high-resolution structure of synthetic pardaxin Pa4 in sodium dodecylphosphocholine micelles, as determined by1H solution NMR spectroscopy. The peptide adopts a bend-helix-bend-helix motif with an angle between the two structure helices of 122 ± 9°, making this structure substantially different from the one previously determined in organic solvents. In addition, paramagnetic solution NMR experiments on Pa4 in micelles reveal that except for the C terminus, the peptide is not solvent-exposed. These results are complemented by solid-state NMR experiments on Pa4 in lipid bilayers. In particular,13C-15N rotational echo double-resonance experiments in multilamellar vesicles support the helical conformation of the C-terminal segment, whereas2H NMR experiments show that the peptide induces considerable disorder in both the head-groups and the hydrophobic core of the bilayers. These solid-state NMR studies indicate that the C-terminal helix has a transmembrane orientation in DMPC bilayers, whereas in POPC bilayers, this domain is heterogeneously oriented on the lipid surface and undergoes slow motion on the NMR time scale. These new data help explain how the non-covalent interactions of Pa4 with lipid membranes induce a stable secondary structure and provide an atomic view of the membrane insertion process of Pa4.
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15

Libich, David S., Mumdooh A. M. Ahmed, Ligang Zhong, Vladimir V. Bamm, Vladimir Ladizhansky, and George Harauz. "Fuzzy complexes of myelin basic protein: NMR spectroscopic investigations of a polymorphic organizational linker of the central nervous systemThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 2 (April 2010): 143–55. http://dx.doi.org/10.1139/o09-123.

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The classic 18.5 kDa isoform of myelin basic protein (MBP) is central to maintaining the structural homeostasis of the myelin sheath of the central nervous system. It is an intrinsically disordered, promiscuous, multifunctional, peripheral membrane protein, whose conformation adapts to its particular environment. Its study requires the selective and complementary application of diverse approaches, of which solution and solid-state NMR spectroscopy are the most powerful to elucidate site-specific features. We review here several recent solution and solid-state NMR spectroscopic studies of 18.5 kDa MBP, and the induced partial disorder-to-order transitions that it has been demonstrated to undergo when complexed with calmodulin, actin, and phospholipid membranes.
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16

Kremkow, Jan, Meike Luck, Daniel Huster, Peter Müller, and Holger A. Scheidt. "Membrane Interaction of Ibuprofen with Cholesterol-Containing Lipid Membranes." Biomolecules 10, no. 10 (September 28, 2020): 1384. http://dx.doi.org/10.3390/biom10101384.

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Deciphering the membrane interaction of drug molecules is important for improving drug delivery, cellular uptake, and the understanding of side effects of a given drug molecule. For the anti-inflammatory drug ibuprofen, several studies reported contradictory results regarding the impact of ibuprofen on cholesterol-containing lipid membranes. Here, we investigated membrane localization and orientation as well as the influence of ibuprofen on membrane properties in POPC/cholesterol bilayers using solid-state NMR spectroscopy and other biophysical assays. The presence of ibuprofen disturbs the molecular order of phospholipids as shown by alterations of the 2H and 31P-NMR spectra of the lipids, but does not lead to an increased membrane permeability or changes of the phase state of the bilayer. 1H MAS NOESY NMR results demonstrate that ibuprofen adopts a mean position in the upper chain/glycerol region of the POPC membrane, oriented with its polar carbonyl group towards the aqueous phase. This membrane position is only marginally altered in the presence of cholesterol. A previously reported result that ibuprofen is expelled from the membrane interface in cholesterol-containing DMPC bilayers could not be confirmed.
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17

Sherman, Patrick J., Frances Separovic, and John H. Bowie. "The investigation of membrane binding by amphibian peptide agonists of CCK2R using 31P and 2H solid-state NMR." Peptides 55 (May 2014): 98–102. http://dx.doi.org/10.1016/j.peptides.2014.02.007.

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18

Jacso, Tomas, W. Trent Franks, Honor Rose, Uwe Fink, Jana Broecker, Sandro Keller, Hartmut Oschkinat, and Bernd Reif. "Characterization of Membrane Proteins in Isolated Native Cellular Membranes by Dynamic Nuclear Polarization Solid-State NMR Spectroscopy without Purification and Reconstitution." Angewandte Chemie 124, no. 2 (November 23, 2011): 447–50. http://dx.doi.org/10.1002/ange.201104987.

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19

Jacso, Tomas, W. Trent Franks, Honor Rose, Uwe Fink, Jana Broecker, Sandro Keller, Hartmut Oschkinat, and Bernd Reif. "Characterization of Membrane Proteins in Isolated Native Cellular Membranes by Dynamic Nuclear Polarization Solid-State NMR Spectroscopy without Purification and Reconstitution." Angewandte Chemie International Edition 51, no. 2 (November 23, 2011): 432–35. http://dx.doi.org/10.1002/anie.201104987.

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20

Lim, Ji Youn, Janine M. May, and Lynette Cegelski. "Dimethyl Sulfoxide and Ethanol Elicit Increased Amyloid Biogenesis and Amyloid-Integrated Biofilm Formation in Escherichia coli." Applied and Environmental Microbiology 78, no. 9 (March 2, 2012): 3369–78. http://dx.doi.org/10.1128/aem.07743-11.

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ABSTRACTEscherichia colidirects the assembly of functional amyloid fibers termed “curli” that mediate adhesion and biofilm formation. We discovered thatE. coliexhibits a tunable and selective increase in curli protein expression and fiber assembly in response to moderate concentrations of dimethyl sulfoxide (DMSO) and ethanol. Furthermore, the molecular alterations resulted in dramatic functional phenotypes associated with community behavior, including (i) cellular agglutination in broth, (ii) altered colony morphology, and (iii) increased biofilm formation. Solid-state nuclear magnetic resonance (NMR) spectra of intact pellicles formed in the presence of [13C2]DMSO confirmed that DMSO was not being transformed and utilized directly for metabolism. Collectively, the chemically induced phenotypes emphasize the plasticity ofE. coli's response to environmental stimuli to enhance amyloid production and amyloid-integrated biofilm formation. The data also support our developing model of the extracellular matrix as an organized assembly of polymeric components, including amyloid fibers, in which composition relates to bacterial physiology and community function.
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Kim, Yongae, Yuna Kim, Jae Joon Park, Jung Hyun Hwang, and Tae Joon Park. "Production and Amyloid Fibril Formation of Recombinant Yeast Prion(Sup35)-Like Protein Fragment." Key Engineering Materials 277-279 (January 2005): 67–71. http://dx.doi.org/10.4028/www.scientific.net/kem.277-279.67.

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Amyloid fibrils have long been established as the well-known a-helix to b-sheet transition that characterizes the conversion of the cellular form of prion proteins into a scrapie form. A very short sequence of the Yeast prion-like protein GNNQQNY(SupN) is responsible for the aggregation that induces diseases. As such, in the current study, a GST-fused monomer SupN vector is used to express the SupN peptide in Escherichia coli(E. Coli). In addition, a method for the production, purification, and cleavage of the recombinant SupN in E. coli is also described, which yields as much as 2mg per liter of growth of natural abundance fusion proteins in LB media. To gain a better understanding of the aggregation-structure relationship of the 7 residues of the Yeast prion-like protein, the change in the conformational structure is studied by Transmission Electron Microscopy and will be further studied by 13C solid-state NMR. Accordingly, this is the first investigation of the fibril formation of a heptamer peptide expressed in E.coli.
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22

Bonifer, Christian, and Clemens Glaubitz. "MsbA: an ABC transporter paradigm." Biochemical Society Transactions 49, no. 6 (November 25, 2021): 2917–27. http://dx.doi.org/10.1042/bst20211030.

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ATP-binding cassette (ABC) transporters play an important role in various cellular processes. They display a similar architecture and share a mechanism which couples ATP hydrolysis to substrate transport. However, in the light of current data and recent experimental progress, this protein superfamily appears as multifaceted as their broad substrate range. Among the prokaryotic ABC transporters, MsbA can serve as a paradigm for research in this field. It is located in the inner membrane of Gram-negative bacteria and functions as a floppase for the lipopolysaccharide (LPS) precursor core-LPS, which is involved in the biogenesis of the bacterial outer membrane. While MsbA shows high similarity to eukaryotic ABC transporters, its expression in Gram-negative bacteria makes it conveniently accessible for many experimental approaches from spectroscopy to 3D structure determination. As an essential protein for bacterial membrane integrity, MsbA has also become an attractive target for the development of novel antibiotics. Furthermore, it serves as a model for multidrug efflux pumps. Here we provide an overview of recent findings and their relevance to the field, highlight the potential of methods such as solid-state NMR and EPR spectroscopy and provide a perspective for future work.
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23

Liu, Chun-Hao, Shing-Jong Huang, and Tsyr-Yan Yu. "Cholesterol Modulates the Interaction between HIV-1 Viral Protein R and Membrane." Membranes 11, no. 10 (October 13, 2021): 784. http://dx.doi.org/10.3390/membranes11100784.

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Being a major metabolite for maintaining cellular homeostasis, as well as an important structural component in lipid membrane, cholesterol also plays critical roles in the life cycles of some viruses, including human immunodeficiency virus-1 (HIV-1). The involvement of cholesterol in HIV-1 infectivity, assembly and budding has made it an important research target. Viral protein R (Vpr) is an accessory protein of HIV-1, which is involved in many major events in the life cycle of HIV-1. In addition to its multi-functional roles in the HIV-1 life cycle, it is shown to interact with lipid membrane and form a cation-selective channel. In this work, we examined the effect of cholesterol on the interaction of Vpr and lipid membrane. Using calcein release assay, we found that the membrane permeability induced by the membrane binding of Vpr was significantly reduced in the presence of cholesterol in membrane. In addition, using solid-state NMR (ssNMR) spectroscopy, Vpr was shown to experience multiple chemical environments in lipid membrane, as indicated by the broad line shape of carbonyl 13C resonance of Cys-76 residue ranging from 165–178 ppm, which can be attributed to the existence of complex Vpr-membrane environments. We further showed that the presence of cholesterol in membrane will alter the distribution of Vpr in the complex membrane environments, which may explain the change of the Vpr induced membrane permeability in the presence of cholesterol.
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Chrissian, Christine, Emma Camacho, Man Shun Fu, Rafael Prados-Rosales, Subhasish Chatterjee, Radames J. B. Cordero, Jennifer K. Lodge, Arturo Casadevall, and Ruth E. Stark. "Melanin deposition in two Cryptococcus species depends on cell-wall composition and flexibility." Journal of Biological Chemistry 295, no. 7 (January 2, 2020): 1815–28. http://dx.doi.org/10.1074/jbc.ra119.011949.

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Cryptococcus neoformans and Cryptococcus gattii are two species complexes in the large fungal genus Cryptococcus and are responsible for potentially lethal disseminated infections. These two complexes share several phenotypic traits, such as production of the protective compound melanin. In C. neoformans, the pigment associates with key cellular constituents that are essential for melanin deposition within the cell wall. Consequently, melanization is modulated by changes in cell-wall composition or ultrastructure. However, whether similar factors influence melanization in C. gattii is unknown. Herein, we used transmission EM, biochemical assays, and solid-state NMR spectroscopy of representative isolates and “leaky melanin” mutant strains from each species complex to examine the compositional and structural factors governing cell-wall pigment deposition in C. neoformans and C. gattii. The principal findings were the following. 1) C. gattii R265 had an exceptionally high chitosan content compared with C. neoformans H99; a rich chitosan composition promoted homogeneous melanin distribution throughout the cell wall but did not increase the propensity of pigment deposition. 2) Strains from both species manifesting the leaky melanin phenotype had reduced chitosan content, which was compensated for by the production of lipids and other nonpolysaccharide constituents that depended on the species or mutation. 3) Changes in the relative rigidity of cell-wall chitin were associated with aberrant pigment retention, implicating cell-wall flexibility as an independent variable in cryptococcal melanin assembly. Overall, our results indicate that cell-wall composition and molecular architecture are critical factors for the anchoring and arrangement of melanin pigments in both C. neoformans and C. gattii species complexes.
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Xie, Yimin, Yanchao Liu, Chen Jiang, Hongfei Wu, and Shuying Bi. "The existence of cellulose and lignin chemical connections in ginkgo traced by 2H-13C dual isotopes." BioResources 15, no. 4 (October 15, 2020): 9028–44. http://dx.doi.org/10.15376/biores.15.4.9028-9044.

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To elucidate the covalent association between the celluloses and lignins found in gymnosperms, they were labeled with stable isotopes (deuterium and carbon-13) at specific positions and traced via mass spectroscopy and nuclear magnetic resonance (NMR). Both the 2H-labeled cellulose precursor (UDP-glucose-[6-2H2]) and the 13C-labeled lignin precursor (coniferin-[α-13C]) were added to a growing ginkgo plant, in combination with a 4-coumarate-CoA ligase inhibitor. The detection of abundance of 13C and 2H revealed that the lignin precursor and cellulose precursor deposited more actively in 300 to 1300 μm and 100 to 900 μm distance from cambium, respectively. The lignin-carbohydrate complexes (LCCs) were isolated from the newly-formed ginkgo shoot xylem and further degraded with cellulase and hemicellulase to obtain enzymatically degraded lignin-carbohydrate complexes (EDLCCs). Analysis of the solid-state cross polarization / magic angle spinning (CP/MAS) 13C-NMR of the newly-formed xylem, liquid-state 13C-NMR, and 1H-NMR of the EDLCCs confirmed that the major connection between celluloses and lignins was a benzyl ether bond (between cellulose C6 and lignin Cα). A minor ester bond was also found between the hydroxyl group (at the 6-position of cellulose) and ferulic acid (at the γ position in lignins).
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Luo, Yanzhang, ShengQi Xiang, Peter Jan Hooikaas, Laura van Bezouwen, A. S. Jijumon, Carsten Janke, Friedrich Förster, Anna Akhmanova, and Marc Baldus. "Direct observation of dynamic protein interactions involving human microtubules using solid-state NMR spectroscopy." Nature Communications 11, no. 1 (January 2, 2020). http://dx.doi.org/10.1038/s41467-019-13876-x.

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AbstractMicrotubules are important components of the eukaryotic cytoskeleton. Their structural organization is regulated by nucleotide binding and many microtubule-associated proteins (MAPs). While cryo-EM and X-ray crystallography have provided detailed views of interactions between MAPs with the microtubule lattice, little is known about how MAPs and their intrinsically disordered regions interact with the dynamic microtubule surface. NMR carries the potential to directly probe such interactions but so far has been precluded by the low tubulin yield. We present a protocol to produce [13C, 15N]-labeled, functional microtubules (MTs) from human cells for solid-state NMR studies. This approach allowed us to demonstrate that MAPs can differently modulate the fast time-scale dynamics of C-terminal tubulin tails, suggesting distinct interaction modes. Our results pave the way for in-depth NMR studies of protein dynamics involved in MT assembly and their interactions with other cellular components.
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Lau, Sophie, and David Middleton. "Analysis of the orientation of cholesterol in high-density lipoprotein nanodiscs using solid-state NMR." Physical Chemistry Chemical Physics, 2022. http://dx.doi.org/10.1039/d2cp02393h.

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Cholesterol is an essential component of eukaryotic cellular membranes that regulates the order and phase behaviour of dynamic lipid bilayers. Although cholesterol performs many vital physiological roles, hypercholesterolaemia and the...
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Damman, Reinier, Stefan Schütz, Yanzhang Luo, Markus Weingarth, Remco Sprangers, and Marc Baldus. "Atomic-level insight into mRNA processing bodies by combining solid and solution-state NMR spectroscopy." Nature Communications 10, no. 1 (October 4, 2019). http://dx.doi.org/10.1038/s41467-019-12402-3.

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Abstract Liquid–liquid phase separation is increasingly recognized as a process involved in cellular organization. Thus far, a detailed structural characterization of this intrinsically heterogeneous process has been challenging. Here we combine solid- and solution-state NMR spectroscopy to obtain atomic-level insights into the assembly and maturation of cytoplasmic processing bodies that contain mRNA as well as enzymes involved in mRNA degradation. In detail, we have studied the enhancer of decapping 3 (Edc3) protein that is a central hub for processing body formation in yeast. Our results reveal that Edc3 domains exhibit diverse levels of structural organization and dynamics after liquid–liquid phase separation. In addition, we find that interactions between the different Edc3 domains and between Edc3 and RNA in solution are largely preserved in the condensed protein state, allowing processing bodies to rapidly form and dissociate upon small alterations in the cellular environment.
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29

Daskalov, Asen, Nadia El Mammeri, Alons Lends, Jayakrishna Shenoy, Gaelle Lamon, Yann Fichou, Ahmad Saad, et al. "Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective." Frontiers in Molecular Neuroscience 14 (July 1, 2021). http://dx.doi.org/10.3389/fnmol.2021.670513.

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Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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30

Phạm, Trần Thanh Tâm, and Jan K. Rainey. "On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions." Biochemistry and Cell Biology, May 4, 2021. http://dx.doi.org/10.1139/bcb-2021-0052.

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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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31

Rivière, Gwladys, Garima Jaipuria, Loren B. Andreas, Andrei Leonov, Karin Giller, Stefan Becker, and Markus Zweckstetter. "Membrane-embedded TSPO: an NMR view." European Biophysics Journal, December 22, 2020. http://dx.doi.org/10.1007/s00249-020-01487-0.

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AbstractTranslocator Protein (18 kDa) (TSPO) is a mitochondrial transmembrane protein commonly used as a biomarker for neuroinflammation and is also a potential therapeutic target in neurodegenerative diseases. Despite intensive research efforts, the function of TSPO is still largely enigmatic. Deciphering TSPO structure in the native lipid environment is essential to gain insight into its cellular activities and to design improved diagnostic and therapeutic ligands. Here, we discuss the influence of lipid composition on the structure of mammalian TSPO embedded into lipid bilayers on the basis of solid-state NMR experiments. We further highlight that cholesterol can influence both the tertiary and quaternary TSPO structure and also influence TSPO localization in mitochondria-associated endoplasmic reticulum membranes.
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32

Fernando, Liyanage D., Malitha C. Dickwella Widanage, Jackson Penfield, Andrew S. Lipton, Nancy Washton, Jean-Paul Latgé, Ping Wang, Liqun Zhang, and Tuo Wang. "Structural Polymorphism of Chitin and Chitosan in Fungal Cell Walls From Solid-State NMR and Principal Component Analysis." Frontiers in Molecular Biosciences 8 (August 25, 2021). http://dx.doi.org/10.3389/fmolb.2021.727053.

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Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity to the model structures of α- and γ-allomorphs; therefore, chitin structure is not significantly affected by interactions with other cell wall components. Addition of antifungal drugs and salts did not significantly perturb the chemical shifts, revealing the structural resistance of chitin to external stress. In addition, the structure of the deacetylated form, chitosan, was found to resemble a relaxed two-fold helix conformation. This study provides high-resolution information on the structure of chitin and chitosan in their cellular contexts. The method is applicable to the analysis of other complex carbohydrates and polymer composites.
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33

Bouyon Yenda, Tracy, Carine Jiguet-Jiglaire, Imene Khichane, Quentin Gobert, Rathinasabapathi Prabhakaran, Alexandre De Nonneville, Thierry Djenizian, Sébastien Salas, and Frédéric Dallemer. "Controlled Synthesis of Small Water-Soluble Hybrid Gold Nanoparticles: An Optimized Strategy for Stable Nano-Dispersion and Towards Cellular Uptake." Frontiers in Mechanical Engineering 8 (March 22, 2022). http://dx.doi.org/10.3389/fmech.2022.824837.

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The development of effective drug delivery systems is one of the major challenges in the fight against cancer. Gold nanoparticles could effectively harness cancer therapies by improving their potency while reducing toxic side effects. In this work, we describe a high-yield one-step synthesis of small water-soluble gold nanoparticles (AuNPs). Efficient purification was monitored, and discrete structure was fully characterized by combining molecular analytical technics (UV-visible and NMR spectroscopies) and solid-state analyses (thermal gravimetric analysis and transmission electron microscopy). These AuNPs have good dispersibility in various biocompatible media and can be used without any additives. Preliminary study with in vitro treatment of IB115 human cancer cells showed massive cellular uptake associated to moderate intrinsic cytotoxicity. The high control of the synthesis and the small size of these AuNPs are offering fine surface properties control, crucial for challenging biological nano-dispersion issues. Thus, limitation of the agglomeration of nanoparticles and improvement of interaction with the surface of cell should open new leads for vectorization of drugs or imaging probes for diagnosis.
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34

Peralta, Ma F., S. N. Mendieta, I. R. Scolari, G. E. Granero, and M. E. Crivello. "Synthesis and release behavior of layered double hydroxides–carbamazepine composites." Scientific Reports 11, no. 1 (October 18, 2021). http://dx.doi.org/10.1038/s41598-021-00117-9.

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AbstractCarbamazepine (CBZ) was incorporated into layered double hydroxides (LDH) to be used as a controlled drug system in solid tumors. CBZ has a formal charge of zero, so its incorporation in the anionic clay implies a challenge. Aiming to overcome this problem, CBZ was loaded into LDH with sodium cholate (SC), a surfactant with negative charge and, for comparison, without SC by the reconstruction method. Surprisingly, it was found that both resultant nanocomposites had similar CBZ encapsulation efficiency, around 75%, and the LDH-CBZ system without SC showed a better performance in relation to the release kinetics of CBZ in simulated body fluid (pH 7.4) and acetate buffer simulating the cellular cytoplasm (pH 4.8) than the system with SC. The CBZ dimensions were measured with Chem3D and, according to the basal spacing obtained from X-ray patterns, it can be arranged in the LDH-CBZ system as a monolayer with the long axis parallel to the LDH layers. Fourier transform infrared spectroscopy and solid state NMR measurements confirmed the presence of the drug, and thermogravimetric analyses showed an enhanced thermal stability for CBZ. These results have interesting implications since they increase the spectrum of LDH application as a controlled drug system to a large number of nonionic drugs, without the addition of other components.
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35

Takamuku, Mika, Tomoaki Sugishita, Hajime Tamaki, Lingyingzi Dong, Masatomo So, Toshimichi Fujiwara, and Yoh Matsuki. "Evolution of α-synuclein conformation ensemble toward amyloid fibril via liquid-liquid phase separation (LLPS) as investigated by dynamic nuclear polarization-enhanced solid-state MAS NMR." Neurochemistry International, April 2022, 105345. http://dx.doi.org/10.1016/j.neuint.2022.105345.

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36

Zhao, Xinghong, Xiaoqi Wang, Rhythm Shukla, Raj Kumar, Markus Weingarth, Eefjan Breukink, and Oscar P. Kuipers. "Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes." Frontiers in Microbiology 12 (July 16, 2021). http://dx.doi.org/10.3389/fmicb.2021.694847.

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Lipo-tridecapeptides, a class of bacterial non-ribosomally produced peptides, show strong antimicrobial activity against Gram-positive pathogens, including antibiotic-resistant Staphylococcus aureus and Enterococcus spp. However, many of these lipo-tridecapeptides have shown high hemolytic activity and cytotoxicity, which has limited their potential to be developed into antibiotics. Recently, we reported a novel antimicrobial lipo-tridecapeptide, brevibacillin 2V, which showed no hemolytic activity against human red blood cells at a high concentration of 128 mg/L, opposite to other brevibacillins and lipo-tridecapeptides. In addition, brevibacillin 2V showed much lower cytotoxicity than the other members of the brevibacillin family. In this study, we set out to elucidate the antimicrobial mode of action of brevibacillin 2V. The results show that brevibacillin 2V acts as bactericidal antimicrobial agent against S. aureus (MRSA). Further studies show that brevibacillin 2V exerts its bactericidal activity by binding to the bacterial cell wall synthesis precursor Lipid II and permeabilizing the bacterial membrane. Combined solid-state NMR, circular dichroism, and isothermal titration calorimetry assays indicate that brevibacillin 2V binds to the GlcNAc-MurNAc moiety and/or the pentapeptide of Lipid II. This study provides an insight into the antimicrobial mode of action of brevibacillin 2V. As brevibacillin 2V is a novel and promising antibiotic candidate with low hemolytic activity and cytotoxicity, the here-elucidated mode of action will help further studies to develop it as an alternative antimicrobial agent.
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37

Ulamec, Sabine M., David J. Brockwell, and Sheena E. Radford. "Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins." Frontiers in Neuroscience 14 (December 1, 2020). http://dx.doi.org/10.3389/fnins.2020.611285.

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Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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38

Cukkemane, Abhishek, Nina Becker, Mara Zielinski, Benedikt Frieg, Nils-Alexander Lakomek, Henrike Heise, Gunnar F. Schröder, Dieter Willbold, and Oliver H. Weiergräber. "Conformational heterogeneity coupled with β-fibril formation of a scaffold protein involved in chronic mental illnesses." Translational Psychiatry 11, no. 1 (December 2021). http://dx.doi.org/10.1038/s41398-021-01765-1.

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AbstractChronic mental illnesses (CMIs) pose a significant challenge to global health due to their complex and poorly understood etiologies and hence, absence of causal therapies. Research of the past two decades has revealed dysfunction of the disrupted in schizophrenia 1 (DISC1) protein as a predisposing factor involved in several psychiatric disorders. DISC1 is a multifaceted protein that serves myriads of functions in mammalian cells, for instance, influencing neuronal development and synapse maintenance. It serves as a scaffold hub forming complexes with a variety (~300) of partners that constitute its interactome. Herein, using combinations of structural and biophysical tools, we demonstrate that the C-region of the DISC1 protein is highly polymorphic, with important consequences for its physiological role. Results from solid-state NMR spectroscopy and electron microscopy indicate that the protein not only forms symmetric oligomers but also gives rise to fibrils closely resembling those found in certain established amyloid proteinopathies. Furthermore, its aggregation as studied by isothermal titration calorimetry (ITC) is an exergonic process, involving a negative enthalpy change that drives the formation of oligomeric (presumably tetrameric) species as well as β-fibrils. We have been able to narrow down the β-core region participating in fibrillization to residues 716–761 of full-length human DISC1. This region is absent in the DISC1Δ22aa splice variant, resulting in reduced association with proteins from the dynein motor complex, viz., NDE-like 1 (NDEL1) and lissencephaly 1 (LIS1), which are crucial during mitosis. By employing surface plasmon resonance, we show that the oligomeric DISC1 C-region has an increased affinity and shows cooperativity in binding to LIS1 and NDEL1, in contrast to the noncooperative binding mode exhibited by the monomeric version. Based on the derived structural models, we propose that the association between the binding partners involves two neighboring subunits of DISC1 C-region oligomers. Altogether, our findings highlight the significance of the DISC1 C-region as a crucial factor governing the balance between its physiological role as a multifunctional scaffold protein and aggregation-related aberrations with potential significance for disease.
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39

Pedro, Rudimar, Lauren da Cunha Duarte, Tauhana Eineck, Fernanda Vilasbôas, and Pietra Barasuci Hammes. "Production of Cellular Concrete Blocks Espumígeno Using Coconut Fatty Acids and Wastes of Foundry-Review of the Literature." Journal of Nanosciences Research & Reports, September 30, 2020, 1–5. http://dx.doi.org/10.47363/jnsrr/2020(2)110.

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The northern region of the state of Rio Grande do Sul, Brazil, is an important polo industrial metal / mechanical, with an extensive and varied portfolio of equipment, principally the manufacture of agricultural implements. In the foundry parts used in the manufacture of agricultural machinery, a large amount of sand is used, generating waste according to the NBR 10004/2004 standard, which deals with the classification of solid waste as its potential risks to the environment and health class II THE. This class includes non-hazardous waste and non-inert. Except in cases of waste containing large amounts of “molds machos’’, in this case framed as ‘’dangerous’’ class I. Its environmentally correct disposal in controlled or sanitary landfills represents an important expense in the cost table and requires careful management for the industries that are directly responsible for incidents and accidents and co-responsible for possible environmental liabilities futures, even with referral to paid landfills. Specifically, this paper seeks search a method of using foundry waste and its blanketing, more precisely, the Sands used in the manner of manufacture of cast piece, Replacing the natural sand, water, foam produced With the espumigeno coconut fatty acids, cement as a binder in the manufacture of blocks of cellular concrete espumígeno (bcce), and consequent use in civil construction. In this context it seeks the state of the art in the construction of theoretical and practical knowledge about the topic, and also based on the models studied in research and publications by this author, using similar residues
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