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Di Mauro GM, Hardin NZ, Ramamoorthy A. Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition. Biochim Biophys Acta Biomembr 2020; 1862:183332. [PMID: 32360741 PMCID: PMC7340147 DOI: 10.1016/j.bbamem.2020.183332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nathaniel Z Hardin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics and Chemistry Department, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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Russell AE, Sneider A, Witwer KW, Bergese P, Bhattacharyya SN, Cocks A, Cocucci E, Erdbrügger U, Falcon-Perez JM, Freeman DW, Gallagher TM, Hu S, Huang Y, Jay SM, Kano SI, Lavieu G, Leszczynska A, Llorente AM, Lu Q, Mahairaki V, Muth DC, Noren Hooten N, Ostrowski M, Prada I, Sahoo S, Schøyen TH, Sheng L, Tesch D, Van Niel G, Vandenbroucke RE, Verweij FJ, Villar AV, Wauben M, Wehman AM, Yin H, Carter DRF, Vader P. Biological membranes in EV biogenesis, stability, uptake, and cargo transfer: an ISEV position paper arising from the ISEV membranes and EVs workshop. J Extracell Vesicles 2019; 8:1684862. [PMID: 31762963 PMCID: PMC6853251 DOI: 10.1080/20013078.2019.1684862] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Paracrine and endocrine roles have increasingly been ascribed to extracellular vesicles (EVs) generated by multicellular organisms. Central to the biogenesis, content, and function of EVs are their delimiting lipid bilayer membranes. To evaluate research progress on membranes and EVs, the International Society for Extracellular Vesicles (ISEV) conducted a workshop in March 2018 in Baltimore, Maryland, USA, bringing together key opinion leaders and hands-on researchers who were selected on the basis of submitted applications. The workshop was accompanied by two scientific surveys and covered four broad topics: EV biogenesis and release; EV uptake and fusion; technologies and strategies used to study EV membranes; and EV transfer and functional assays. In this ISEV position paper, we synthesize the results of the workshop and the related surveys to outline important outstanding questions about EV membranes and describe areas of consensus. The workshop discussions and survey responses reveal that while much progress has been made in the field, there are still several concepts that divide opinion. Good consensus exists in some areas, including particular aspects of EV biogenesis, uptake and downstream signalling. Areas with little to no consensus include EV storage and stability, as well as whether and how EVs fuse with target cells. Further research is needed in these key areas, as a better understanding of membrane biology will contribute substantially towards advancing the field of extracellular vesicles.
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Affiliation(s)
- Ashley E. Russell
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexandra Sneider
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, Università degli Studi di Brescia, CSGI and INSTM, Brescia, Italy
| | | | | | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | | | - Juan M. Falcon-Perez
- Exosomes laboratory and Metabolomics Platform, CIC bioGUNE, CIBERehd, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bizkaia, Spain
| | - David W. Freeman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Thomas M. Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Chicago, IL, USA
| | - Shuaishuai Hu
- School of Biological and Healthy Sciences, Technological University Dublin, Dublin, Ireland
| | - Yiyao Huang
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Clinical Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Steven M. Jay
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Shin-ichi Kano
- Department of Psychiatry and Behavioral Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Gregory Lavieu
- INSERM U932, Institut Curie, PSL Research University, France
| | | | - Alicia M. Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences Departments of Environmental Health, Genetics & Complex Diseases Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasiliki Mahairaki
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Dillon C. Muth
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Matias Ostrowski
- INBIRS Institute, UBA-CONICET School of Medicine University of Buenos Aires, Buenos Aires, Argentina
| | | | - Susmita Sahoo
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tine Hiorth Schøyen
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- K. G. Jebsen - Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Lifu Sheng
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Deanna Tesch
- Department of Chemistry, Shaw University, Raleigh, NC, USA
| | - Guillaume Van Niel
- Institute for Psychiatry and Neuroscience of Paris, INSERM U1266, Hopital Saint-Anne, Université Descartes, Paris, France
| | - Roosmarijn E. Vandenbroucke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederik J. Verweij
- Institute for Psychiatry and Neuroscience of Paris, INSERM U1266, Hopital Saint-Anne, Université Descartes, Paris, France
| | - Ana V. Villar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria and Departamento de Fisiología y Farmacología, Universidad de Cantabria, Santander, Spain
| | - Marca Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ann M. Wehman
- Rudolf Virchow Center, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | | | - Pieter Vader
- Laboratory of Clinical Chemistry and Haematology & Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Kocman V, Di Mauro GM, Veglia G, Ramamoorthy A. Use of paramagnetic systems to speed-up NMR data acquisition and for structural and dynamic studies. Solid State Nucl Magn Reson 2019; 102:36-46. [PMID: 31325686 PMCID: PMC6698407 DOI: 10.1016/j.ssnmr.2019.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy is a powerful experimental technique to study biological systems at the atomic resolution. However, its intrinsic low sensitivity results in long acquisition times that in extreme cases lasts for days (or even weeks) often exceeding the lifetime of the sample under investigation. Different paramagnetic agents have been used in an effort to decrease the spin-lattice (T1) relaxation times of the studied nuclei, which are the main cause for long acquisition times necessary for signal averaging to enhance the signal-to-noise ratio of NMR spectra. Consequently, most of the experimental time is "wasted" in waiting for the magnetization to recover between successive scans. In this review, we discuss how to set up an optimal paramagnetic relaxation enhancement (PRE) system to effectively reduce the T1 relaxation times avoiding significant broadening of NMR signals. Additionally, we describe how PRE-agents can be used to provide structural and dynamic information and can even be used to follow the intermediates of chemical reactions and to speed-up data acquisition. We also describe the unique challenges and benefits associated with the application of PRE to solid-state NMR spectroscopy, explaining how the use of PREs is more complex for membrane mimetic systems as PREs can also be exploited to change the alignment of oriented membrane systems. Functionalization of membrane mimetics, such as bicelles, can provide a controlled region of paramagnetic effect that has the potential, together with the desired alignment, to provide crucial biologically relevant structural information. And finally, we discuss how paramagnetic metals can be utilized to further increase the dynamic nuclear polarization (DNP) effects and how to preserve the enhancements when dissolution DNP is implemented.
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Affiliation(s)
- Vojč Kocman
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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Wang S, Gopinath T, Veglia G. Application of paramagnetic relaxation enhancements to accelerate the acquisition of 2D and 3D solid-state NMR spectra of oriented membrane proteins. Methods 2017; 138-139:54-61. [PMID: 29274874 DOI: 10.1016/j.ymeth.2017.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is uniquely suited to determine membrane protein topology at the atomic resolution in liquid crystalline bilayers under physiological temperature. However, the inherent low sensitivity of this technique has hindered the throughput of multidimensional experiments necessary for resonance assignments and structure determination. In this work, we show that doping membrane protein bicelle preparations with paramagnetic ion chelated lipids and exploiting paramagnetic relaxation effects it is possible to accelerate the acquisition of both 2D and 3D multidimensional experiments with significant saving in time. We demonstrate the efficacy of this method for a small membrane protein, sarcolipin, reconstituted in DMPC/POPC/DHPC oriented bicelles. In particular, using Cu2+-DMPE-DTPA as a dopant, we observed a decrease of 1H T1 of sarcolipin by 2/3, allowing us to reduce the recycle delay up to 3 times. We anticipate that these new developments will enable the routine acquisition of multidimensional OS-ssNMR experiments.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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Koroloff SN, Tesch DM, Awosanya EO, Nevzorov AA. Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals. J Biomol NMR 2017; 67:135-144. [PMID: 28205016 DOI: 10.1007/s10858-017-0090-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2.4-3.0 in the case of Pf1 coat protein reconstituted in magnetically aligned bicelles with their normals being either parallel or perpendicular to the main magnetic field. Notably, spectral resolution is not affected at the 2:1 radical-to-protein ratio. Spectroscopic assignment of Pf1 coat protein in the parallel bicelles has been established as an illustration of the method. The proposed methodology will advance applications of oriented-sample NMR technique when applied to samples containing smaller quantities of proteins and three-dimensional experiments.
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Affiliation(s)
- Sophie N Koroloff
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Deanna M Tesch
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
- Shaw University, 118 E. South Street, Raleigh, NC, 27601, USA
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA.
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Mroue KH, Zhang R, Zhu P, McNerny E, Kohn DH, Morris MD, Ramamoorthy A. Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA. J Magn Reson 2014; 244:90-7. [PMID: 24881032 PMCID: PMC4094129 DOI: 10.1016/j.jmr.2014.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/27/2014] [Accepted: 04/27/2014] [Indexed: 05/05/2023]
Abstract
Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.
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Affiliation(s)
- Kamal H Mroue
- Biophysics, The University of Michigan, Ann Arbor, MI 48109-1055, United States; Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Rongchun Zhang
- Biophysics, The University of Michigan, Ann Arbor, MI 48109-1055, United States; Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States; School of Physics, Nankai University, Tianjin 300071, PR China
| | - Peizhi Zhu
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Erin McNerny
- School of Dentistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - David H Kohn
- School of Dentistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Michael D Morris
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, The University of Michigan, Ann Arbor, MI 48109-1055, United States; Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States.
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