1
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Burr DJ, Drauschke J, Kanevche K, Kümmel S, Stryhanyuk H, Heberle J, Perfumo A, Elsaesser A. Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400289. [PMID: 38708804 DOI: 10.1002/smll.202400289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/16/2024] [Indexed: 05/07/2024]
Abstract
This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.
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Affiliation(s)
- David J Burr
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Janina Drauschke
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Katerina Kanevche
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Steffen Kümmel
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Amedea Perfumo
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Telegrafenberg, 14473, Potsdam, Germany
| | - Andreas Elsaesser
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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2
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Quintana JI, Delgado S, Rábano M, Azkargorta M, Florencio-Zabaleta M, Unione L, Vivanco MDM, Elortza F, Jiménez-Barbero J, Ardá A. The impact of glycosylation on the structure, function, and interactions of CD14. Glycobiology 2024; 34:cwae002. [PMID: 38227775 PMCID: PMC10987292 DOI: 10.1093/glycob/cwae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/18/2024] Open
Abstract
CD14 is an innate immune receptor that senses pathogen-associated molecular patterns, such as lipopolysaccharide, to activate the innate immune response. Although CD14 is known to be glycosylated, detailed understanding about the structural and functional significance of this modification is still missing. Herein, an NMR and MS-based study, assisted by MD simulations, has provided a 3D-structural model of glycosylated CD14. Our results reveal the existence of a key N-glycosylation site at Asn282 that exclusively contains unprocessed oligomannnose N-glycans that perfectly fit the concave cavity of the bent-solenoid shaped protein. This site is not accessible to glycosidases and is fundamental for protein folding and secretion. A second N-site at Asn151 displays mostly complex N-glycans, with the typical terminal epitopes of the host cell-line expression system (i.e. βGal, α2,3 and α2,6 sialylated βGal, here), but also particularities, such as the lack of core fucosylation. The glycan at this site points outside the protein surface, resulting in N-glycoforms fully exposed and available for interactions with lectins. In fact, NMR experiments show that galectin-4, proposed as a binder of CD14 on monocytes to induce their differentiation into macrophages-like cells, interacts in vitro with CD14 through the recognition of the terminal glycoepitopes on Asn151. This work provides key information about CD14 glycosylation, which helps to better understand its functional roles and significance. Although protein glycosylation is known to be dynamic and influenced by many factors, some of the features found herein (presence of unprocessed N-glycans and lack of core Fuc) are likely to be protein specific.
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Affiliation(s)
- Jon Imanol Quintana
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Sandra Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Miriam Rábano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Mirane Florencio-Zabaleta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Luca Unione
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
| | - Maria dM Vivanco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Bizkaia 48940, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Carlos III Health Institute, C. de Melchor Fernández Almagro, 3, Fuencarral-El Pardo, Madrid 28029, Spain
| | - Ana Ardá
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park bld 800, Derio, Bizkaia 48160, Spain
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009, Bilbao, Spain
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3
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Davis AR, Roberts ET, Amster IJ, Barb AW. Uniform [ 13C, 15N]-labeled and glycosylated IgG1 Fc expressed in Saccharomyces cerevisiae. JOURNAL OF BIOMOLECULAR NMR 2024; 78:9-18. [PMID: 37989910 PMCID: PMC11025670 DOI: 10.1007/s10858-023-00428-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Despite the prevalence and importance of glycoproteins in human biology, methods for isotope labeling suffer significant limitations. Common prokaryotic platforms do not produce mammalian post-translation modifications that are essential to the function of many human glycoproteins, including immunoglobulin G1 (IgG1). Mammalian expression systems require complex media and thus introduce significant costs to achieve uniform labeling. Expression with Pichia is available, though expertise and equipment requirements surpass E. coli culture. We developed a system utilizing Saccharomyces cerevisiae, [13C]-glucose, and [15N]-ammonium chloride with complexity comparable to E. coli. Here we report two vectors for expressing the crystallizable fragment (Fc) of IgG1 for secretion into the culture medium, utilizing the ADH2 or DDI2 promoters. We also report a strategy to optimize the expression yield using orthogonal Taguchi arrays. Lastly, we developed two different media formulations, a standard medium which provides 86-92% 15N and 30% 13C incorporation into the polypeptide, or a rich medium which provides 98% 15N and 95% 13C incorporation as determined by mass spectrometry. This advance represents an expression and optimization strategy accessible to experimenters with the capability to grow and produce proteins for NMR-based experiments using E. coli.
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Affiliation(s)
- Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St, Davison Life Science Complex, Athens, GA, 30602, USA
| | | | | | - Adam W Barb
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St, Davison Life Science Complex, Athens, GA, 30602, USA.
- Department of Chemistry, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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4
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Borgini M, Wieteska Ł, Hinck CS, Krzysiak T, Hinck AP, Wipf P. Synthesis of 13C-methyl-labeled amino acids and their incorporation into proteins in mammalian cells. Org Biomol Chem 2023; 21:9216-9229. [PMID: 37964666 PMCID: PMC10825848 DOI: 10.1039/d3ob01320k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Isotopic labeling of methyl-substituted proteinogenic amino acids with 13C has transformed applications of solution-based NMR spectroscopy and allowed the study of much larger and more complex proteins than previously possible with 15N labeling. Procedures are well-established for producing methyl-labeled proteins expressed in bacteria, with efficient incorporation of 13C-methyl labeled metabolic precursors to enable the isotopic labeling of Ile, Val, and Leu methyl groups. Recently, similar methodology has been applied to enable 13C-methyl labeling of Ile, Val, and Leu in yeast, extending the approach to proteins that do not readily fold when produced in bacteria. Mammalian or insect cells are nonetheless preferable for production of many human proteins, yet 13C-methyl labeling using similar metabolic precursors is not feasible as these cells lack the requisite biosynthetic machinery. Herein, we report versatile and high-yielding synthetic routes to 13C methyl-labeled amino acids based on palladium-catalyzed C(sp3)-H functionalization. We demonstrate the efficient incorporation of two of the synthesized amino acids, 13C-γ2-Ile and 13C-γ1,γ2-Val, into human receptor extracellular domains with multiple disulfides using suspension-cultured HEK293 cells. Production costs are reasonable, even at moderate expression levels of 2-3 mg purified protein per liter of medium, and the method can be extended to label other methyl groups, such as 13C-δ1-Ile and 13C-δ1,δ2-Leu. In summary, we demonstrate the cost-effective production of methyl-labeled proteins in mammalian cells by incorporation of 13C methyl-labeled amino acids generated de novo by a versatile synthetic route.
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Affiliation(s)
- Matteo Borgini
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Łukasz Wieteska
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Cynthia S Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Andrew P Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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5
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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6
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Hou Z, Zhan L, Cao K, Luan M, Wang X, Zhang B, Ma L, Yin H, Liu Z, Liu Y, Huang G. Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry. Anal Chim Acta 2023; 1241:340795. [PMID: 36657872 DOI: 10.1016/j.aca.2023.340795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/04/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
Direct observation of metabolites in living cells by mass spectrometry offers a bright future for biological studies but also suffers a severe challenge to untargeted peak assignment to tentative metabolite candidates. In this study, we developed a method combining stable isotope tracing and induced electrospray mass spectrometry for living-cells metabolite measurement and identification. By using 13C6-glucose and ammonium chloride-15N as the sole carbon and nitrogen sources for cell culture, Escherichia coli synthesized metabolites with 15N and 13C elements. Tracing the number of carbon and nitrogen atoms could offer a complementary dimension for candidate peak searching. As a result, the identification confidence of metabolites achieved a universal improvement based on carbon/nitrogen labelling and filtration.
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Affiliation(s)
- Zhuanghao Hou
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China.
| | - Liujuan Zhan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Kaiming Cao
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China
| | - Moujun Luan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Xinchen Wang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Buchun Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China
| | - Likun Ma
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China
| | - Hao Yin
- Mass Spectrometry Lab, Instruments Center for Physical Science, University of Science and Technology of China, 230026, Hefei, China
| | - Zhicheng Liu
- Anhui Provincial Laboratory of Inflammatory and Immunity Disease, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, 81 Meishan Road, 230032, Hefei, China
| | - Yangzhong Liu
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China; Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China
| | - Guangming Huang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001, Hefei, China; School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China.
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7
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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8
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Yanaka S, Yogo R, Yagi H, Onitsuka M, Wakaizumi N, Yamaguchi Y, Uchiyama S, Kato K. Negative interference with antibody-dependent cellular cytotoxicity mediated by rituximab from its interactions with human serum proteins. Front Immunol 2023; 14:1090898. [PMID: 36761774 PMCID: PMC9905677 DOI: 10.3389/fimmu.2023.1090898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Although interactions of small molecular drugs with serum proteins have been widely studied from pharmacokinetic and pharmacodynamic perspectives, there have been few reports on the effects of serum components on therapeutic antibody functions. This study reports the effect of abundant serum proteins on antibody-dependent cellular cytotoxicity (ADCC) mediated by rituximab and Fcγ receptor III (FcγRIII). Human serum albumin (HSA) and the Fab fragment from the pooled serum polyclonal IgG were found to compromise ADCC as non-competitive inhibitors. Our nuclear magnetic resonance data provided direct evidence for the interactions of HSA with both the Fab and Fc regions of rituximab and also with the extracellular region of FcγRIII (sFcγRIII). The degree of involvement in the interaction decreased in the order of rituximab-Fab > rituximab-Fc > sFcγRIII, suggesting preferential binding of HSA to net positively charged proteins. Although much less pronounced than the effect of HSA, polyclonal IgG-Fab specifically interacted with rituximab-Fc. The NMR data also showed that the serum protein interactions cover the Fc surface extensively, suggesting that they can act as pan-inhibitors against various Fc receptor-mediated functions and pharmacokinetics. Our findings highlight the importance of considering serum-protein interactions in the design and application of antibody-based drugs with increased efficacy and safety.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Hirokazu Yagi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | | | - Yuki Yamaguchi
- Graduate School of Engineering, University of Osaka, Osaka, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, University of Osaka, Osaka, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
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9
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Rowlinson B, Crublet E, Kerfah R, Plevin MJ. Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: using metabolic precursors in sample preparation. Biochem Soc Trans 2022; 50:1555-1567. [PMID: 36382942 DOI: 10.1042/bst20210586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
The study of protein structure, dynamics and function by NMR spectroscopy commonly requires samples that have been enriched ('labelled') with the stable isotopes 13C and/or 15N. The standard approach is to uniformly label a protein with one or both of these nuclei such that all C and/or N sites are in principle 'NMR-visible'. NMR spectra of uniformly labelled proteins can be highly complicated and suffer from signal overlap. Moreover, as molecular size increases the linewidths of NMR signals broaden, which decreases sensitivity and causes further spectral congestion. Both effects can limit the type and quality of information available from NMR data. Problems associated with signal overlap and signal broadening can often be alleviated though the use of alternative, non-uniform isotopic labelling patterns. Specific isotopic labelling 'turns on' signals at selected sites while the rest of the protein is NMR-invisible. Conversely, specific isotopic unlabelling (also called 'reverse' labelling) 'turns off' selected signals while the rest of the protein remains NMR-visible. Both approaches can simplify NMR spectra, improve sensitivity, facilitate resonance assignment and permit a range of different NMR strategies when combined with other labelling tools and NMR experiments. Here, we review methods for producing proteins with enrichment of stable NMR-visible isotopes, with particular focus on residue-specific labelling and reverse labelling using Escherichia coli expression systems. We also explore how these approaches can aid NMR studies of proteins.
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Affiliation(s)
- Benjamin Rowlinson
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
| | - Elodie Crublet
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Rime Kerfah
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Michael J Plevin
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
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10
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Shenoy A, Davis AR, Roberts ET, Amster IJ, Barb AW. Metabolic 15N labeling of the N-glycosylated immunoglobulin G1 Fc with an engineered Saccharomyces cerevisiae strain. JOURNAL OF BIOMOLECULAR NMR 2022; 76:95-105. [PMID: 35802275 DOI: 10.1007/s10858-022-00397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The predominant protein expression host for NMR spectroscopy is Escherichia coli, however, it does not synthesize appropriate post-translation modifications required for mammalian protein function and is not ideal for expressing naturally secreted proteins that occupy an oxidative environment. Mammalian expression platforms can address these limitations; however, these are not amenable to cost-effective uniform 15 N labeling resulting from highly complex growth media requirements. Yeast expression platforms combine the simplicity of bacterial expression with the capabilities of mammalian platforms, however yeasts require optimization prior to isotope labeling. Yeast expression will benefit from methods to boost protein expression levels and developing labeling conditions to facilitate growth and high isotope incorporation within the target protein. In this work, we describe a novel platform based on the yeast Saccharomyces cerevisiae that simultaneously expresses the Kar2p chaperone and protein disulfide isomerase in the ER to facilitate the expression of secreted proteins. Furthermore, we developed a growth medium for uniform 15 N labeling. We recovered 2.2 mg/L of uniformly 15 N-labeled human immunoglobulin (Ig)G1 Fc domain with 90.6% 15 N labeling. NMR spectroscopy revealed a high degree of similarity between the yeast and mammalian-expressed IgG1 Fc domains. Furthermore, we were able to map the binding interaction between IgG1 Fc and the Z domain through chemical shift perturbations. This platform represents a novel cost-effective strategy for 15 N-labeled immunoglobulin fragments.
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Affiliation(s)
- Anjali Shenoy
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | | | | | - Adam W Barb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Department of Chemistry, University of Georgia, Athens, GA, USA.
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11
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Yanaka S, Yagi H, Yogo R, Onitsuka M, Kato K. Glutamine-free mammalian expression of recombinant glycoproteins with uniform isotope labeling: an application for NMR analysis of pharmaceutically relevant Fc glycoforms of human immunoglobulin G1. JOURNAL OF BIOMOLECULAR NMR 2022; 76:17-22. [PMID: 34978013 DOI: 10.1007/s10858-021-00387-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Mammalian cells are widely used for producing recombinant glycoproteins of pharmaceutical interest. However, a major drawback of using mammalian cells is the high production costs associated with uniformly isotope-labeled glycoproteins due to the large quantity of labeled L-glutamine required for their growth. To address this problem, we developed a cost-saving method for uniform isotope labeling by cultivating the mammalian cells under glutamine-free conditions, which was achieved by co-expression of glutamine synthase. We demonstrate the utility of this approach using fucosylated and non-fucosylated Fc glycoforms of human immunoglobulin G1.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, 770-8513, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
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12
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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13
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Lokale Deuterierung ermöglicht NMR‐Messung von Methylgruppen in Proteinen aus eukaryotischen und Zell‐freien Expressionssystemen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Thibault Viennet
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Sandeep Chhabra
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Shantha Elter
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Jan Borggräfe
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Aldino Viegas
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Radosław P. Nowak
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Eric S. Fischer
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Manuel Etzkorn
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Haribabu Arthanari
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
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14
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Local Deuteration Enables NMR Observation of Methyl Groups in Proteins from Eukaryotic and Cell-Free Expression Systems. Angew Chem Int Ed Engl 2021; 60:13783-13787. [PMID: 33768661 PMCID: PMC8251921 DOI: 10.1002/anie.202016070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Indexed: 01/13/2023]
Abstract
Therapeutically relevant proteins such as GPCRs, antibodies and kinases face clear limitations in NMR studies due to the challenges in site-specific isotope labeling and deuteration in eukaryotic expression systems. Here we describe an efficient and simple method to observe the methyl groups of leucine residues in proteins expressed in bacterial, eukaryotic or cell-free expression systems without modification of the expression protocol. The method relies on simple stereo-selective 13 C-labeling and deuteration of leucine that alleviates the need for additional deuteration of the protein. The spectroscopic benefits of "local" deuteration are examined in detail through Forbidden Coherence Transfer (FCT) experiments and simulations. The utility of this labeling method is demonstrated in the cell-free synthesis of bacteriorhodopsin and in the insect-cell expression of the RRM2 domain of human RBM39.
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Affiliation(s)
- Abhinav Dubey
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Thibault Viennet
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Sandeep Chhabra
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Shantha Elter
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Jan Borggräfe
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Aldino Viegas
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Radosław P. Nowak
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Eric S. Fischer
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Manuel Etzkorn
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Vladimir Gelev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Haribabu Arthanari
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
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15
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Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
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Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
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16
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Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. J Biol Chem 2021; 296:100556. [PMID: 33744289 PMCID: PMC8058564 DOI: 10.1016/j.jbc.2021.100556] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function.
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Affiliation(s)
- James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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17
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Tokunaga Y, Takeuchi K. Role of NMR in High Ordered Structure Characterization of Monoclonal Antibodies. Int J Mol Sci 2020; 22:E46. [PMID: 33375207 PMCID: PMC7793058 DOI: 10.3390/ijms22010046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
Obtaining high ordered structure (HOS) information is of importance to guarantee the efficacy and safety of monoclonal antibodies (mAbs) in clinical application. Assessment of HOS should ideally be performed in a non-invasive manner under their formulated storage conditions, as any perturbation can introduce unexpected detritions. However, most of the currently available techniques only indirectly report HOS of mAbs and/or require a certain condition to conduct the analyses. Besides, the flexible multidomain architecture of mAbs has hampered atomic-resolution structural analyses using X-ray crystallography and cryo-electron microscopy. In contrast, the ability of nuclear magnetic resonance (NMR) spectroscopy to structurally analyze biomolecules in various conditions in a non-invasive and quantitative manner is suitable to meet the needs. However, the application of NMR to mAbs is not straightforward due to the high molecular weight of the system. In this review, we will discuss how NMR techniques have been applied to HOS analysis of mAbs, along with the recent advances of the novel 15N direct detection NMR strategy that allows for obtaining the structural fingerprint of mAbs at lower temperatures under multiple formulation conditions. The potential application of these NMR strategies will benefit next-generation mAbs, such as antibody-drug conjugates and bispecific antibodies.
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Affiliation(s)
- Yuji Tokunaga
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
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18
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Jagger AM, Waudby CA, Irving JA, Christodoulou J, Lomas DA. High-resolution ex vivo NMR spectroscopy of human Z α 1-antitrypsin. Nat Commun 2020; 11:6371. [PMID: 33311470 PMCID: PMC7732992 DOI: 10.1038/s41467-020-20147-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/15/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic mutations predispose the serine protease inhibitor α1-antitrypsin to misfolding and polymerisation within hepatocytes, causing liver disease and chronic obstructive pulmonary disease. This misfolding occurs via a transiently populated intermediate state, but our structural understanding of this process is limited by the instability of recombinant α1-antitrypsin variants in solution. Here we apply NMR spectroscopy to patient-derived samples of α1-antitrypsin at natural isotopic abundance to investigate the consequences of disease-causing mutations, and observe widespread chemical shift perturbations for methyl groups in Z AAT (E342K). By comparison with perturbations induced by binding of a small-molecule inhibitor of misfolding we conclude that they arise from rapid exchange between the native conformation and a well-populated intermediate state. The observation that this intermediate is stabilised by inhibitor binding suggests a paradoxical approach to the targeted treatment of protein misfolding disorders, wherein the stabilisation of disease-associated states provides selectivity while inhibiting further transitions along misfolding pathways.
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Affiliation(s)
- Alistair M Jagger
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - James A Irving
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - David A Lomas
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
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19
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Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
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20
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Yagi H, Yanaka S, Yogo R, Ikeda A, Onitsuka M, Yamazaki T, Kato T, Park EY, Yokoyama J, Kato K. Silkworm Pupae Function as Efficient Producers of Recombinant Glycoproteins with Stable-Isotope Labeling. Biomolecules 2020; 10:biom10111482. [PMID: 33114581 PMCID: PMC7692867 DOI: 10.3390/biom10111482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Baculovirus-infected silkworms are promising bioreactors for producing recombinant glycoproteins, including antibodies. Previously, we developed a method for isotope labeling of glycoproteins for nuclear magnetic resonance (NMR) studies using silkworm larvae reared on an artificial diet containing 15N-labeled yeast crude protein extract. Here, we further develop this method by introducing a technique for the expression of isotope-labeled glycoproteins by silkworm pupae, which has several potential advantages relative to larvae-based techniques in terms of production yield, ease of handling, and storage. Here, we fed fifth instar larvae an artificial diet with an optimized composition containing [methyl-13C]methionine, leading to pupation. Nine-day-old pupae were then injected with recombinant Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid for expression of recombinant human immunoglobulin G (IgG). From the whole-body homogenates of pupae, 0.35 mg/pupa of IgG was harvested, which is a yield that is five times higher than can be obtained from larvae. Recombinant IgG, thus prepared, exhibited mainly three kinds of pauci-mannose-type oligosaccharides and had a 13C-enrichment ratio of approximately 80%. This enabled selective observation of NMR signals originating from the methionyl methyl group of IgG, confirming its conformational integrity. These data demonstrate the utility of silkworm pupae as factories for producing recombinant glycoproteins with amino-acid-selective isotope labeling.
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Affiliation(s)
- Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
| | - Saeko Yanaka
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Rina Yogo
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Akari Ikeda
- Taiyo Nippon Sanso Corporation, SI Innovation Center, 2008-2 Wada, Tama, Tokyo 206-0001, Japan; (A.I.); (J.Y.)
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Minamijosanjima-cho 2-1, Tokushima 770-8513, Japan;
| | - Toshio Yamazaki
- SPring-8 Center RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan;
| | - Tatsuya Kato
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; (T.K.); (E.Y.P.)
| | - Enoch Y. Park
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; (T.K.); (E.Y.P.)
| | - Jun Yokoyama
- Taiyo Nippon Sanso Corporation, SI Innovation Center, 2008-2 Wada, Tama, Tokyo 206-0001, Japan; (A.I.); (J.Y.)
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
- Correspondence: ; Tel.: +81-564-59-5225
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21
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Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
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Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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22
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Yanaka S, Yogo R, Kato K. Biophysical characterization of dynamic structures of immunoglobulin G. Biophys Rev 2020; 12:637-645. [PMID: 32410186 PMCID: PMC7311591 DOI: 10.1007/s12551-020-00698-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 12/25/2022] Open
Abstract
Immunoglobulin G (IgG) is a major antibody and functions as a hub linking specific antigen binding and recruitment of effector molecules typified by Fcγ receptors (FcγRs). These activities are associated primarily with interactions involving its Fab and Fc sites, respectively. An IgG molecule is characterized by a multiple domain modular structure with conserved N-glycosylation in Fc. The molecule displays significant freedom in internal motion on various spatiotemporal scales. The consequent conformational flexibility and plasticity of IgG glycoproteins are functionally significant and potentially important factors for design and engineering of antibodies with enhanced functionality. In this article, experimental and computational approaches are outlined for characterizing the conformational dynamics of IgG molecules in solution. In particular, the importance of integration of these approaches is highlighted, as illustrated by dynamic intramolecular interactions between the pair of N-glycans and their proximal amino acid residues in Fc. These interactions can critically affect effector functions mediated by human IgG1 and FcγRIII. Further improvements in individual biophysical techniques and their integration will advance understanding of dynamic behaviors of antibodies in physiological and pathological conditions. Such understanding will provide opportunities for engineering antibodies through controlling allosteric networks in IgG molecules.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan.
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23
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Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
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Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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24
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Abstract
Intrinsically disordered proteins (IDPs) describe a group of proteins that do not have a regular tertiary structure and typically have very little ordered secondary structure. Despite not following the biochemical dogma of "structure determines function" and "function determines structure," IDPs have been identified as having numerous biological functions. We describe here the steps to express and purify the intrinsically disordered stress response protein, Late embryogenesis abundant protein 3-2 from Arabidopsis thaliana (AtLEA 3-2), with 15N and 13C isotopes in E. coli, although the protocol can be adapted for any IDP with or without isotopic labeling. The atlea 3-2 gene has been cloned into the pET-SUMO vector that in addition to the SUMO portion encodes an N-terminal hexahistidine sequence (His-tag). This vector allows for the SUMO-AtLEA 3-2 fusion protein to be purified using Ni-affinity chromatography and, through the use of ubiquitin-like-specific protease 1 (Ulp1, a SUMO protease), results in an AtLEA 3-2 with a native N-terminus. We also describe the expression and purification of Ulp1 itself.
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Affiliation(s)
- Karamjeet K Singh
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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25
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Gimeno A, Valverde P, Ardá A, Jiménez-Barbero J. Glycan structures and their interactions with proteins. A NMR view. Curr Opin Struct Biol 2019; 62:22-30. [PMID: 31835069 PMCID: PMC7322516 DOI: 10.1016/j.sbi.2019.11.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/28/2022]
Abstract
Carbohydrate molecules are essential actors in key biological events, being involved as recognition points for cell-cell and cell-matrix interactions related to health and disease. Despite outstanding advances in cryoEM, X-ray crystallography and NMR still remain the most employed techniques to unravel their conformational features and to describe the structural details of their interactions with biomolecular receptors. Given the intrinsic flexibility of saccharides, NMR methods are of paramount importance to deduce the extent of motion around their glycosidic linkages and to explore their receptor-bound conformations. We herein present our particular view on the latest advances in NMR methodologies that are permitting to magnify their applications for deducing glycan conformation and dynamics and understanding the recognition events in which there are involved.
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Affiliation(s)
- Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain; Department of Organic Chemistry II, University of the Basque Country, UPV/EHU, 48940 Leioa, Bizkaia, Spain
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26
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Kumar A, Narayanan V, Sekhar A. Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy. Biochemistry 2019; 59:57-73. [PMID: 31682116 DOI: 10.1021/acs.biochem.9b00827] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Vaishali Narayanan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
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27
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Valverde P, Ardá A, Reichardt NC, Jiménez-Barbero J, Gimeno A. Glycans in drug discovery. MEDCHEMCOMM 2019; 10:1678-1691. [PMID: 31814952 PMCID: PMC6839814 DOI: 10.1039/c9md00292h] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Abstract
Glycans are key players in many biological processes. They are essential for protein folding and stability and act as recognition elements in cell-cell and cell-matrix interactions. Thus, being at the heart of medically relevant biological processes, glycans have come onto the scene and are considered hot spots for biomedical intervention. The progress in biophysical techniques allowing access to an increasing molecular and structural understanding of these processes has led to the development of effective therapeutics. Indeed, strategies aimed at designing glycomimetics able to block specific lectin-carbohydrate interactions, carbohydrate-based vaccines mimicking self- and non-self-antigens as well as the exploitation of the therapeutic potential of glycosylated antibodies are being pursued. In this mini-review the most prominent contributions concerning recurrent diseases are highlighted, including bacterial and viral infections, cancer or immune-related pathologies, which certainly show the great promise of carbohydrates in drug discovery.
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Affiliation(s)
- Pablo Valverde
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | - Ana Ardá
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | | | - Jesús Jiménez-Barbero
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
- Ikerbasque , Basque Foundation for Science , 48013 Bilbao , Bizkaia , Spain
- Department of Organic Chemistry II , University of the Basque Country , UPV/EHU , 48940 Leioa , Bizkaia , Spain
| | - Ana Gimeno
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
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28
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Unione L, Lenza M, Ardá A, Urquiza P, Laín A, Falcón-Pérez JM, Jiménez-Barbero J, Millet O. Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy. ACS CENTRAL SCIENCE 2019; 5:1554-1561. [PMID: 31572782 PMCID: PMC6764210 DOI: 10.1021/acscentsci.9b00540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 05/10/2023]
Abstract
Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.
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Affiliation(s)
- Luca Unione
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
| | - Maria
Pia Lenza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Pedro Urquiza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Laín
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Juan Manuel Falcón-Pérez
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
- Dept.
Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- E-mail:
| | - Oscar Millet
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
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29
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Valverde P, Quintana JI, Santos JI, Ardá A, Jiménez-Barbero J. Novel NMR Avenues to Explore the Conformation and Interactions of Glycans. ACS OMEGA 2019; 4:13618-13630. [PMID: 31497679 PMCID: PMC6714940 DOI: 10.1021/acsomega.9b01901] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/02/2019] [Indexed: 05/12/2023]
Abstract
This perspective article is focused on the presentation of the latest advances in NMR methods and applications that are behind the exciting achievements in the understanding of glycan receptors in molecular recognition events. Different NMR-based methodologies are discussed along with their applications to scrutinize the conformation and dynamics of glycans as well as their interactions with protein receptors.
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Affiliation(s)
- Pablo Valverde
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jon I. Quintana
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jose I. Santos
- SGIker
UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- E-mail: (A.A.)
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
Organic Chemistry II, Faculty Science &
Technology, EHU-UPV, 48940 Leioa, Bizkaia, Spain
- E-mail: (J.J.-B.)
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30
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Yanaka S, Yogo R, Inoue R, Sugiyama M, Itoh SG, Okumura H, Miyanoiri Y, Yagi H, Satoh T, Yamaguchi T, Kato K. Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations. Antibodies (Basel) 2019; 8:antib8030039. [PMID: 31544845 PMCID: PMC6784063 DOI: 10.3390/antib8030039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
The Fc portion of immunoglobulin G (IgG) is a horseshoe-shaped homodimer, which interacts with various effector proteins, including Fcγ receptors (FcγRs). These interactions are critically dependent on the pair of N-glycans packed between the two CH2 domains. Fucosylation of these N-glycans negatively affects human IgG1-FcγRIIIa interaction. The IgG1-Fc crystal structures mostly exhibit asymmetric quaternary conformations with divergent orientations of CH2 with respect to CH3. We aimed to provide dynamic views of IgG1-Fc by performing long-timescale molecular dynamics (MD) simulations, which were experimentally validated by small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our simulation results indicated that the dynamic conformational ensembles of Fc encompass most of the previously reported crystal structures determined in both free and complex forms, although the major Fc conformers in solution exhibited almost symmetric, stouter quaternary structures, unlike the crystal structures. Furthermore, the MD simulations suggested that the N-glycans restrict the motional freedom of CH2 and endow quaternary-structure plasticity through multiple intramolecular interaction networks. Moreover, the fucosylation of these N-glycans restricts the conformational freedom of the proximal tyrosine residue of functional importance, thereby precluding its interaction with FcγRIIIa. The dynamic views of Fc will provide opportunities to control the IgG interactions for developing therapeutic antibodies.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Satoru G Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan.
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31
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Graether SP. Troubleshooting Guide to Expressing Intrinsically Disordered Proteins for Use in NMR Experiments. Front Mol Biosci 2019; 5:118. [PMID: 30713842 PMCID: PMC6345686 DOI: 10.3389/fmolb.2018.00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/23/2018] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) represent a structural class of proteins that do not have a well-defined, 3D fold in solution, and often have little secondary structure. To characterize their function and molecular mechanism, it is helpful to examine their structure using nuclear magnetic resonance (NMR), which can report on properties, such as residual structure (at both the secondary and tertiary levels), ligand binding affinity, and the effect of ligand binding on IDP structure, all on a per residue basis. This brief review reports on the common problems and decisions that are involved when preparing a disordered protein for NMR studies. The paper covers gene design, expression host choice, protein purification, and the initial NMR experiments that are performed. While many of these steps are essentially identical to those for ordered proteins, a few key differences are highlighted, including the extreme sensitivity of IDPs to proteolytic cleavage, the ability to use denaturing conditions without having to refold the protein, the optimal chromatographic system choice, and the challenges of quantifying an IDP. After successful purification, characterization by NMR can be done using the standard 15N-heteronuclear single quantum coherence (15N-HSQC) experiment, or the newer CON series of experiments that are superior for disordered proteins.
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Affiliation(s)
- Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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32
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Accessing Structure, Dynamics and Function of Biological Macromolecules by NMR Through Advances in Isotope Labeling. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0085-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Boisbouvier J, Kay LE. Advanced isotopic labeling for the NMR investigation of challenging proteins and nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2018; 71:115-117. [PMID: 30043256 DOI: 10.1007/s10858-018-0199-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Medicine, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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34
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Yagi H, Yanaka S, Kato K. Structure and Dynamics of Immunoglobulin G Glycoproteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:219-235. [PMID: 30484251 DOI: 10.1007/978-981-13-2158-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Immunoglobulin G (IgG) is a major serum glycoprotein that exerts the role of antibody in the immune system. This multifunctional glycoprotein couples antigen recognition with a variety of effector functions promoted via interactions with various IgG-binding proteins. Given its versatile functionality, IgG has recently been used for therapeutic interventions. Evidence indicates that the carbohydrate moieties of IgG glycoproteins critically affect their antibody functions, particularly the effector functions mediated by the interactions with Fcγ receptors (FcγRs). N-glycans at specific positions of FcγR also contribute both positively and negatively to the interactions with IgG. The integration of multilateral biophysical approaches, including X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, has provided structural insights into the mechanisms underlying the glycofunctions of this interacting system. The N-glycans of IgG and FcγR mediate their interactions by either strengthening or weakening the affinity on the basis of their glycoforms. Moreover, the N-glycosylation of IgG-Fc is a prerequisite to maintain the integrity of the quaternary structure of the sites interacting with the effector molecules and can also control functionally relevant local conformations. The biopharmaceutical significance of these glycan functions is discussed from a structural point of view.
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Affiliation(s)
- Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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