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Wang R, Yue X, Zhu J, Hu R, Li Y, Yang Y, Liu M. Mutation of two residues converts the ligand-binding domain of RXRα into a uniform monomer without impairing the binding of retinoic acid and cofactors. Biochem Biophys Res Commun 2023; 642:50-56. [PMID: 36563628 DOI: 10.1016/j.bbrc.2022.12.042] [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: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Retinoid X receptor (RXRα) is a nuclear receptor (NR) for retinoic acid (RA) and regulates various NR signaling pathways. Ligand-binding domain (LBD) of RXRα can bind with its ligand 9-cis-RA and cofactors, and mediate the forming of homodimer and homotetramer of RXRα and its heterodimer with other NRs, conferring RXRα the ability to play complicated roles in development and diseases. Due to the coexistence of monomer, dimer and tetramer, there are difficulties to study the structure and interaction of RXRα-LBD with its ligands and cofactors in solution and to distinguish the roles of different forms of RXRα in cell. Here, through analyzing available structures of RXRα-LBD, we selected two residues, D379 and L420, in the homodimer interface to design three mutants of RXRα-LBD. Recombinant proteins of the three mutants showed decreased proportions of dimer and tetramer but unchanged overall structure and binding affinities to 9-cis-RA, corepressor SMRT, and coactivator SRC2. Especially, the double-site mutant RXRα-LBDD379A-L420G existed as a uniform monomer. Furthermore, L420 was found to play a similar role in forming RXRα-LBD homodimer and its heterodimer with various NRs, while the role of D379 varies a lot, as it shows almost no interaction with RARα/β, LXRα/β, and THRα/β. This study provides a new insight into the mechanism for forming RXRα-LBD homodimer and its heterodimer with other NRs, and will facilitate the studies on the structure and interaction of RXRα-LBD with ligands, cofactors and drugs in solution, and the broad physiological functions of RXRα cooperating with various NRs in cell.
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Affiliation(s)
- Ru Wang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Xiali Yue
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Mellinger AL, Muddiman DC, Gamcsik MP. Highlighting Functional Mass Spectrometry Imaging Methods in Bioanalysis. J Proteome Res 2022; 21:1800-1807. [PMID: 35749637 DOI: 10.1021/acs.jproteome.2c00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most mass spectrometry imaging (MSI) methods provide a molecular map of tissue content but little information on tissue function. Mapping tissue function is possible using several well-known examples of "functional imaging" such as positron emission tomography and functional magnetic resonance imaging that can provide the spatial distribution of time-dependent biological processes. These functional imaging methods represent the net output of molecular networks influenced by local tissue environments that are difficult to predict from molecular/cellular content alone. However, for decades, MSI methods have also been demonstrated to provide functional imaging data on a variety of biological processes. In fact, MSI exceeds some of the classic functional imaging methods, demonstrating the ability to provide functional data from the nanoscale (subcellular) to whole tissue or organ level. This Perspective highlights several examples of how different MSI ionization and detection technologies can provide unprecedented detailed spatial maps of time-dependent biological processes, namely, nucleic acid synthesis, lipid metabolism, bioenergetics, and protein metabolism. By classifying various MSI methods under the umbrella of "functional MSI", we hope to draw attention to both the unique capabilities and accessibility with the aim of expanding this underappreciated field to include new approaches and applications.
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Affiliation(s)
- Allyson L Mellinger
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael P Gamcsik
- UNC/NCSU Joint Department of Biomedical Engineering, Raleigh, North Carolina 27695, United States
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De Samber B, De Rycke R, De Bruyne M, Kienhuis M, Sandblad L, Bohic S, Cloetens P, Urban C, Polerecky L, Vincze L. Effect of sample preparation techniques upon single cell chemical imaging: A practical comparison between synchrotron radiation based X-ray fluorescence (SR-XRF) and Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS). Anal Chim Acta 2020; 1106:22-32. [PMID: 32145852 DOI: 10.1016/j.aca.2020.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/16/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]
Abstract
Analytical capabilities of Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS) and Synchrotron Radiation based X-ray Fluorescence (SR nano-XRF) techniques were compared for nanochemical imaging of polymorphonuclear human neutrophils (PMNs). PMNs were high pressure frozen (HPF), cryo-substituted, embedded in Spurr's resin and cut in thin sections (500 nm and 2 μm for both techniques resp.) Nano-SIMS enabled nanoscale mapping of isotopes of C, N, O, P and S, while SR based nano-XRF enabled trace level imaging of metals like Ca, Mn, Fe, Ni, Cu and Zn at a resolution of approx. 50 nm. The obtained elemental distributions were compared with those of whole, cryofrozen PMNs measured at the newly developed ID16A nano-imaging beamline at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Similarities were observed for elements more tightly bound to the cell structure such as phosphorus and sulphur, while differences for mobile ions such as chlorine and potassium were more pronounced. Due to the observed elemental redistribution of mobile ions such as potassium and chlorine, elemental analysis of high pressure frozen (HPF), cryo-substituted and imbedded cells should be interpreted critically. Although decreasing analytical sensitivity occurs due to the presence of ice, analysis of cryofrozen cells - close to their native state - remains the golden standard. In general, we found nanoscale secondary ion mass spectrometry (nano-SIMS) and synchrotron radiation based nanoscopic X-ray fluorescence (SR nano-XRF) to be two supplementary alternatives for nanochemical imaging of single cells at the nanoscale.
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Affiliation(s)
- Björn De Samber
- Department of Chemistry, Ghent University, Ghent, Belgium; Imec - Vision Lab, University of Antwerp, Wilrijk, Belgium.
| | - Riet De Rycke
- Department for Biomedical Molecular Biology, Ghent University, Belgium and VIB Center for Inflammation Research, Ghent, Belgium; Ghent University Expertise Centre for Transmission Electron Microscopy and VIB Bio-Imaging Core, Ghent, Belgium
| | - Michiel De Bruyne
- Department for Biomedical Molecular Biology, Ghent University, Belgium and VIB Center for Inflammation Research, Ghent, Belgium; Ghent University Expertise Centre for Transmission Electron Microscopy and VIB Bio-Imaging Core, Ghent, Belgium
| | - Michiel Kienhuis
- Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, the Netherlands
| | - Linda Sandblad
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Sylvain Bohic
- Inserm, UA07, Synchrotron Research for Biomedicine, Grenoble, France; European Synchrotron Radiation Facility, Grenoble, France
| | - Peter Cloetens
- European Synchrotron Radiation Facility, Grenoble, France
| | - Constantin Urban
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Lubos Polerecky
- Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, the Netherlands
| | - Laszlo Vincze
- Department of Chemistry, Ghent University, Ghent, Belgium
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Cabin-Flaman A, Delaune A, Poutrain P, Gangwe Nana YG, Jourdain B, Gibouin D, Paris JP, Trestour S, Seigneuret JM, Léopoldès de Vendômois A, Cosette P, Etienne JJ, Ripoll C. Effect of zein additive on perfume evaporation. Int J Cosmet Sci 2018; 40:575-582. [PMID: 30414278 DOI: 10.1111/ics.12500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/05/2018] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Zein is known to have filmogen properties. We wanted to show if a zein film containing eugenol (eugenol as model) would retain the fragrances, slow their evaporation and therefore produce a long-lasting perception of perfume. METHODS We added corn zein to eugenol in a hydro-alcoholic solution to form a film in vitro and at the surface of the human skin. We have studied the trapping and release of eugenol from zein film by GC/MS. Also we labelled eugenol with deuterium to image specifically its distribution in the zein film using Secondary Ion Mass Spectrometry technique (NanoSIMS 50). Finally, we applied the zein/D-eugenol formulation onto skin to image the eugenol location on and in skin by SIMS (Secondary Ion Mass Spectrometry). RESULTS We showed that eugenol evaporation from zein film can be divided in three periods. The first period (≤2 h) corresponds to the simultaneous solvent and eugenol evaporation occurring during film formation. The second period corresponds to the continuous and slow eugenol evaporation during a few hours (about 10 h) but not to its completion. The third period (at least up to 48 h) results from the trapping of eugenol in zein film. After 24 or 48 h, trapped eugenol can be released and evaporated under mechanical deformations of the film. Moreover we showed that zein addition does not favour the eugenol penetration into viable epidermis which may cause allergenic cutaneous reaction. CONCLUSION The zein additive is safe to use, does not impact the olfactory perception, allows a better perception of the fragrance (long-lasting effect) in a more protective way and can be used in perfume.
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Affiliation(s)
- A Cabin-Flaman
- Groupe de Physique des Matériaux, UMR 6634 CNRS, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France.,Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | - A Delaune
- Groupe de Physique des Matériaux, UMR 6634 CNRS, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France.,Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | - P Poutrain
- Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | - Y G Gangwe Nana
- Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | - B Jourdain
- Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | - D Gibouin
- Groupe de Physique des Matériaux, UMR 6634 CNRS, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France.,Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | | | | | | | | | - P Cosette
- Département de Chimie, Plateforme Protéomique PISSARO, UMR 6270 CNRS, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
| | | | - C Ripoll
- Département de Biologie, Faculté des Sciences et Techniques, Université de Rouen Normandie, Mont-Saint-Aignan, France
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Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
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Cole LM, Clench MR. Mass spectrometry imaging for the proteomic study of clinical tissue. Proteomics Clin Appl 2015; 9:335-41. [PMID: 25620724 DOI: 10.1002/prca.201400103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/12/2014] [Accepted: 01/21/2015] [Indexed: 11/08/2022]
Abstract
Over the last decade, MALDI-MS imaging has been used by researchers to explore areas of proteomics, lipidomics and metabolomics in samples of clinical origin for both targeted and global biomarker analysis. Numerous technological advancements in MS and clinical tissue MS imaging have been accomplished; hence, in this article we aim to critically discuss whether MS imaging has now in fact become a true champion of the 'Omics Era'. In order to assess the potential for it to be routinely used in the clinical setting, it is pertinent to discuss some of its limitations, and to examine how these have been addressed by researchers. The key limitations of the technique we will discuss in this viewpoint article are as follows: sample throughput; relevance to patients, the availability of validated/standardised techniques; and integration with conventional pathology and other medical imaging techniques. Good progress has been made over the last 5 years in overcoming these limitations that had previously restricted the use of this technology in the clinical setting.
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Affiliation(s)
- Laura M Cole
- Biomedical Research Centre, Sheffield Hallam University, Sheffield, UK
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7
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Affiliation(s)
- Bernhard Spengler
- Justus Liebig University Giessen, Institute of Inorganic and Analytical
Chemistry, Schubertstrasse
60, Building 16, 35392 Giessen, Germany
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8
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Passarelli MK, Ewing AG. Single-cell imaging mass spectrometry. Curr Opin Chem Biol 2013; 17:854-9. [PMID: 23948695 DOI: 10.1016/j.cbpa.2013.07.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
Abstract
Single-cell imaging mass spectrometry (IMS) is a powerful technique used to map the distributions of endogenous biomolecules with subcellular resolution. Currently, secondary ion mass spectrometry is the predominant technique for single-cell IMS, thanks to its submicron lateral resolution and surface sensitivity. However, recent methodological and technological developments aimed at improving the spatial resolution of matrix assisted laser desorption ionization (MALDI) have made this technique a potential platform of single-cell IMS. MALDI opens the field of single-cell IMS to new possibilities, including single cell proteomic imaging and atmospheric pressure analyses; however, sensitivity is a challenge. In this report, we estimate the availability of proteins and lipids in a single cell and discuss strategies employed to improve sensitivity at the single-cell level.
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