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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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2
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Puthenveetil R, Vinogradova O. Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments. J Biol Chem 2019; 294:15914-15931. [PMID: 31551353 DOI: 10.1074/jbc.rev119.009178] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.
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Affiliation(s)
- Robbins Puthenveetil
- Department of Molecular and Cell Biology, college of liberal arts and sciences, University of Connecticut at Storrs, Storrs, Connecticut 06269
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, Connecticut 06269
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3
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Abstract
Isotope labeling of biologically interesting proteins is a prerequisite for structural and dynamics studies by NMR spectroscopy. Many of these proteins require mammalian cofactors, chaperons, or posttranslational modifications such as myristoylation, glypiation, disulfide bond formation, or N- or O-linked glycosylation; and mammalian cells have the necessary machinery to produce them in their functional forms. Here, we describe recent advances in mammalian expression, including an efficient adenoviral vector-based system, for the production of isotopically labeled proteins. This system enables expression of mammalian proteins and their complexes, including proteins that require posttranslational modifications. We describe a roadmap to produce isotopically labeled (15)N and (13)C posttranslationally modified proteins, such as the outer domain of HIV-1 gp120, which has four disulfide bonds and 15 potential sites of N-linked glycosylation. These methods should allow NMR spectroscopic analysis of the structure and function of posttranslationally modified and secreted, cytoplasmic, or membrane-bound proteins.
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Affiliation(s)
- Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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Abstract
Isotope labeling of proteins represents an important and often required tool for the application of nuclear magnetic resonance (NMR) spectroscopy to investigate the structure and dynamics of proteins. Mammalian expression systems have conventionally been considered to be too weak and inefficient for protein expression. However, recent advances have significantly improved the expression levels of these systems. Here, we provide an overview of some of the recent developments in expression strategies for mammalian expression systems in view of NMR investigations.
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Affiliation(s)
- Arpana Dutta
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Center for, Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Frankfurt, Max-von-Laue-Str.7, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Frankfurt, Max-von-Laue-Str.7, Frankfurt am Main, Germany
| | - Judith Klein-Seetharaman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Sastry M, Bewley CA, Kwong PD. Mammalian expression of isotopically labeled proteins for NMR spectroscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:197-211. [PMID: 23076586 DOI: 10.1007/978-94-007-4954-2_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
NMR spectroscopic characterization of biologically interesting proteins generally requires the incorporation of (15)N/(13)C and/or (2)H stable isotopes. While prokaryotic incorporation systems are regularly used, mammalian ones are not: of the nearly 9,000 NMR macromolecular structures currently deposited in the Protein Data Bank, only a handful (<0.5%) were solved with proteins expressed in mammalian systems. This low number of structures is largely a reflection of the difficulty in producing uniformly labeled, mammalian-expressed proteins. This is unfortunate, as many interesting proteins require mammalian cofactors, chaperons, or post-translational modifications such as N-linked glycosylation, and mammalian cells have the necessary machinery to produce them correctly. Here we describe recent advances in mammalian expression, including an efficient adenoviral vector-based system, for the production of isotopically enriched proteins. This system allows for the expression of mammalian proteins and their complexes, including proteins that require post-translational modifications. We describe how this system can produce isotopically labeled (15)N and (13)C post-translationally modified proteins, such as the outer domain of HIV-1 gp120, which has 15 sites of N-linked glycosylation. Selective amino-acid labeling is also described. These developments should reduce barriers to the determination of NMR structures with isotopically labeled proteins from mammalian expression systems.
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Affiliation(s)
- Mallika Sastry
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3027, USA.
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6
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Kamiya Y, Yamamoto S, Chiba Y, Jigami Y, Kato K. Overexpression of a homogeneous oligosaccharide with 13C labeling by genetically engineered yeast strain. JOURNAL OF BIOMOLECULAR NMR 2011; 50:397-401. [PMID: 21698488 DOI: 10.1007/s10858-011-9525-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 05/25/2011] [Indexed: 05/31/2023]
Abstract
This report describes a novel method for overexpression of (13)C-labeled oligosaccharides using genetically engineered Saccharomyces cerevisiae cells, in which a homogeneous high-mannose-type oligosaccharide accumulates because of deletions of genes encoding three enzymes involved in the processing pathway of asparagine-linked oligosaccharides in the Golgi complex. Using uniformly (13)C-labeled glucose as the sole carbon source in the culture medium of these engineered yeast cells, high yields of the isotopically labeled Man(8)GlcNAc(2) oligosaccharide could be successfully harvested from glycoprotein extracts of the cells. Furthermore, (13)C labeling at selected positions of the sugar residues in the oligosaccharide could be achieved using a site-specific (13)C-enriched glucose as the metabolic precursor, facilitating NMR spectral assignments. The (13)C-labeling method presented provides the technical basis for NMR analyses of structures, dynamics, and interactions of larger, branched oligosaccharides.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
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7
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Sastry M, Xu L, Georgiev IS, Bewley CA, Nabel GJ, Kwong PD. Mammalian production of an isotopically enriched outer domain of the HIV-1 gp120 glycoprotein for NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 50:197-207. [PMID: 21667299 PMCID: PMC3133704 DOI: 10.1007/s10858-011-9506-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 04/25/2011] [Indexed: 05/12/2023]
Abstract
NMR spectroscopic characterization of the structure or the dynamics of proteins generally requires the production of samples isotopically enriched in (15)N, (13)C, or (2)H. The bacterial expression systems currently in use to obtain isotopic enrichment, however, cannot produce a number of eukaryotic proteins, especially those that require post-translational modifications such as N-linked glycosylation for proper folding or activity. Here, we report the use of an adenovirus vector-based mammalian expression system to produce isotopically enriched (15)N or (15)N/(13)C samples of an outer domain variant of the HIV-1 gp120 envelope glycoprotein with 15 sites of N-linked glycosylation. Yields for the (15)N- and (15)N/(13)C-labeled gp120s after affinity chromatography were 45 and 44 mg/l, respectively, with an average of over 80% isotope incorporation. Recognition of the labeled gp120 by cognate antibodies that recognize complex epitopes showed affinities comparable to the unlabeled protein. NMR spectra, including (1)H-(15)N and (1)H-(13)C HSQCs, (15)N-edited NOESY-HSQC, and 3D HNCO, were of high quality, with signal-to-noise consistent with an efficient level of isotope incorporation, and with chemical shift dispersion indicative of a well-folded protein. The exceptional protein yields, good isotope incorporation, and ability to obtain well-folded post-translationally modified proteins make this mammalian system attractive for the production of isotopically enriched eukaryotic proteins for NMR spectroscopy.
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Affiliation(s)
- Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3027 USA
| | - Ling Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3027 USA
| | - Ivelin S. Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3027 USA
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Gary J. Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3027 USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3027 USA
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8
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Solution- and solid-state NMR studies of GPCRs and their ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1462-75. [DOI: 10.1016/j.bbamem.2010.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 10/02/2010] [Accepted: 10/05/2010] [Indexed: 12/29/2022]
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9
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Skelton D, Goodyear A, Ni D, Walton WJ, Rolle M, Hare JT, Logan TM. Enhanced production and isotope enrichment of recombinant glycoproteins produced in cultured mammalian cells. JOURNAL OF BIOMOLECULAR NMR 2010; 48:93-102. [PMID: 20683638 DOI: 10.1007/s10858-010-9440-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/17/2010] [Indexed: 05/26/2023]
Abstract
NMR studies of post-translationally modified proteins are complicated by the lack of an efficient method to produce isotope enriched recombinant proteins in cultured mammalian cells. We show that reducing the glucose concentration and substituting glutamate for glutamine in serum-free medium increased cell viability while simultaneously increasing recombinant protein yield and the enrichment of non-essential amino acids compared to culture in unmodified, serum-free medium. Adding dichloroacetate, a pyruvate dehydrogenase kinase inhibitor, further improves cell viability, recombinant protein yield, and isotope enrichment. We demonstrate the method by producing partially enriched recombinant Thy1 glycoprotein from Lec1 Chinese hamster ovary (CHO) cells using U-¹³C-glucose and ¹⁵N-glutamate as labeled precursors. This study suggests that uniformly ¹⁵N,¹³C-labeled recombinant proteins may be produced in cultured mammalian cells starting from a mixture of labeled essential amino acids, glucose, and glutamate.
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Affiliation(s)
- David Skelton
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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10
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Takahashi H, Shimada I. Production of isotopically labeled heterologous proteins in non-E. coli prokaryotic and eukaryotic cells. JOURNAL OF BIOMOLECULAR NMR 2010; 46:3-10. [PMID: 19787297 DOI: 10.1007/s10858-009-9377-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 09/15/2009] [Indexed: 05/28/2023]
Abstract
The preparation of stable isotope-labeled proteins is necessary for the application of a wide variety of NMR methods, to study the structures and dynamics of proteins and protein complexes. The E. coli expression system is generally used for the production of isotope-labeled proteins, because of the advantages of ease of handling, rapid growth, high-level protein production, and low cost for isotope-labeling. However, many eukaryotic proteins are not functionally expressed in E. coli, due to problems related to disulfide bond formation, post-translational modifications, and folding. In such cases, other expression systems are required for producing proteins for biomolecular NMR analyses. In this paper, we review the recent advances in expression systems for isotopically labeled heterologous proteins, utilizing non-E. coli prokaryotic and eukaryotic cells.
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Affiliation(s)
- Hideo Takahashi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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11
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Barb AW, Borgert AJ, Liu M, Barany G, Live D. Intramolecular glycan-protein interactions in glycoproteins. Methods Enzymol 2010; 478:365-88. [PMID: 20816490 DOI: 10.1016/s0076-6879(10)78018-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycoproteins are a major class of glycoconjugates displaying a variety of mutual interactions between glycan and protein moieties that ultimately affect molecular organization. Modulation of the pendant glycan structures is important in tuning the functions of glycoproteins. Here we discuss structural aspects and some of the challenges to studying intramolecular interactions between carbohydrate and protein elements in several forms of O-linked as well as N-linked glycoproteins. These illustrate the importance of the relationship of context to function in protein glycosylation.
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Affiliation(s)
- Adam W Barb
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
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12
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Skrisovska L, Schubert M, Allain FHT. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. JOURNAL OF BIOMOLECULAR NMR 2010; 46:51-65. [PMID: 19690964 DOI: 10.1007/s10858-009-9362-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 07/17/2009] [Indexed: 05/19/2023]
Abstract
In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope labeling can be used to define inter-domain interactions in NMR structure determination. Labeling of post-translational modified proteins like glycoproteins remains difficult but some promising developments were recently achieved. Key achievements are segmental and site-specific labeling schemes that improve resonance assignment and structure determination of the glycan moiety. We adjusted the focus of this perspective article to concentrate on the NMR applications based on recent developments rather than on labeling methods themselves to illustrate the considerable potential for biomolecular NMR.
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Affiliation(s)
- Lenka Skrisovska
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zurich, Switzerland
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13
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Foldynová-Trantirková S, Matulová J, Dötsch V, Löhr F, Cirstea I, Alexandov K, Breitling R, Lukes J, Trantírek L. A cost-effective amino-acid-type selective isotope labeling of proteins expressed in Leishmania tarentolae. J Biomol Struct Dyn 2009; 26:755-61. [PMID: 19385703 DOI: 10.1080/07391102.2009.10507287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We report a cost efficient approach for amino-acid-type selective isotope labeling of proteins expressed in Leishmania tarentolae. The method provides an economically advantageous alternative to recently established protocol for isotopic labeling using expensive synthetic media. The method is based on cultivation of the L. tarentolae expression strain in a cheap complex medium supplemented with labeled amino acid(s). In this protocol, a labeled amino acid is deliberately diluted in the medium of undefined composition, which leads to a low-level isotope enrichment upon protein over-expression. The economic advantage of the protocol is achieved by avoiding large volumes of expensive synthetic medium. Decreased sensitivity of a NMR experiment due to low-level isotope enrichment is compensated by a five- to seven-fold increase of the yield of the recombinant protein in complex medium as compared to that in the synthetic medium. In addition, the decreased sensitivity can be compensated by using a higher magnetic field, cryo-detection system or higher number of transients during the NMR data acquisition. We show that enrichment as low as 5% does not compromise a NMR experiment and makes preparation of the recombinant proteins over-expressed in L. tarentolae economically viable. The method is demonstrated by selective labeling of the approximately 27 kDa enhanced green fluorescent protein (EGFP) with 15N-labeled valine.
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Blanchard V, Gadkari RA, George AVE, Roy S, Gerwig GJ, Leeflang BR, Dighe RR, Boelens R, Kamerling JP. High-level expression of biologically active glycoprotein hormones in Pichia pastoris strains--selection of strain GS115, and not X-33, for the production of biologically active N-glycosylated 15N-labeled phCG. Glycoconj J 2008; 25:245-57. [PMID: 18274893 PMCID: PMC2668595 DOI: 10.1007/s10719-007-9082-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 08/30/2007] [Accepted: 10/19/2007] [Indexed: 11/29/2022]
Abstract
The methylotrophic yeast Pichia pastoris is widely used for the production of recombinant glycoproteins. With the aim to generate biologically active 15N-labeled glycohormones for conformational studies focused on the unravelling of the NMR structures in solution, the P. pastoris strains GS115 and X-33 were explored for the expression of human chorionic gonadotropin (phCG) and human follicle-stimulating hormone (phFSH). In agreement with recent investigations on the N-glycosylation of phCG, produced in P. pastoris GS115, using ammonia/glycerol-methanol as nitrogen/carbon sources, the N-glycosylation pattern of phCG, synthesized using NH4Cl/glucose–glycerol–methanol, comprised neutral and charged, phosphorylated high-mannose-type N-glycans (Man8–15GlcNAc2). However, the changed culturing protocol led to much higher amounts of glycoprotein material, which is of importance for an economical realistic approach of the aimed NMR research. In the context of these studies, attention was also paid to the site specific N-glycosylation in phCG produced in P. pastoris GS115. In contrast to the rather simple N-glycosylation pattern of phCG expressed in the GS115 strain, phCG and phFSH expressed in the X-33 strain revealed, besides neutral high-mannose-type N-glycans, also high concentrations of neutral hypermannose-type N-glycans (Manup-to-30GlcNAc2). The latter finding made the X-33 strain not very suitable for generating 15N-labeled material. Therefore, 15N-phCG was expressed in the GS115 strain using the new optimized protocol. The 15N-enrichment was evaluated by 15N-HSQC NMR spectroscopy and GLC-EI/MS. Circular dichroism studies indicated that 15N-phCG/GS115 had the same folding as urinary hCG. Furthermore, 15N-phCG/GS115 was found to be similar to the unlabeled protein in every respect as judged by radioimmunoassay, radioreceptor assays, and in vitro bioassays.
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Affiliation(s)
- Véronique Blanchard
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands
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15
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Blanchard V, Gadkari RA, Gerwig GJ, Leeflang BR, Dighe RR, Kamerling JP. Characterization of the N-linked oligosaccharides from human chorionic gonadotropin expressed in the methylotrophic yeast Pichia pastoris. Glycoconj J 2007; 24:33-47. [PMID: 17146714 DOI: 10.1007/s10719-006-9010-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Human chorionic gonadotropin (hCG) is a heterodimeric, placental glycoprotein hormone involved in the maintenance of the corpus luteum during the first trimester of pregnancy. Biologically active hCG has been successfully expressed in the yeast Pichia pastoris (phCG). In the context of structural studies and therapeutic applications of phCG, detailed information about its glycosylation pattern is a prerequisite. To this end N-glycans were released with peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase F and fractionated via anion-exchange chromatography (Resource Q) yielding both neutral (80%) and charged, phosphate-containing (20%) high-mannose-type structures. Subfractionations were carried out via normal phase (Lichrosorb-NH(2)) and high-pH anion-exchange (CarboPac PA-1) chromatography. Structural analyses of the released N-glycans were carried out by using HPLC profiling of fluorescent 2-aminobenzamide derivatives, MALDI-TOF mass spectrometry, and 500-MHz(1)H-NMR spectroscopy. Detailed neutral oligosaccharide structures, in the range of Man(8)GlcNAc(2) to Man(11)GlcNAc(2) including molecular isomers, could be established, and structures up to Man(15)GlcNAc(2) were indicated. Phosphate-containing oligosaccharides ranged from Man(9)PGlcNAc(2) to Man(13)PGlcNAc(2). Mannosyl O-glycans were not detected. Profiling studies carried out on different production batches showed that the oligosaccharide structures are similar, but their relative amounts varied with the culturing media.
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Affiliation(s)
- Véronique Blanchard
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
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16
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Selenko P, Wagner G. Looking into live cells with in-cell NMR spectroscopy. J Struct Biol 2007; 158:244-53. [PMID: 17502240 DOI: 10.1016/j.jsb.2007.04.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 11/23/2022]
Abstract
In-cell NMR spectroscopy has gained recent popularity since it provides means to analyze the conformational and functional properties of proteins inside living cells and at atomic resolution. High-resolution in-cell NMR spectroscopy was originally established in bacterial cells and based on a rationale that relies on protein over-expression and sample analysis within the same cellular environment. Here, we review in-cell NMR approaches in Xenopus laevis oocytes and evaluate potential future applications in other eukaryotic cell types.
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Affiliation(s)
- Philipp Selenko
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (BCMP), Boston, MA 02115, USA.
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17
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Liu S, Venot A, Meng L, Tian F, Moremen KW, Boons GJ, Prestegard JH. Spin-labeled analogs of CMP-NeuAc as NMR probes of the alpha-2,6-sialyltransferase ST6Gal I. CHEMISTRY & BIOLOGY 2007; 14:409-18. [PMID: 17462576 PMCID: PMC3968682 DOI: 10.1016/j.chembiol.2007.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 02/14/2007] [Accepted: 02/27/2007] [Indexed: 12/15/2022]
Abstract
Structural data on mammalian proteins are often difficult to obtain by conventional NMR approaches because of an inability to produce samples with uniform isotope labeling in bacterial expression hosts. Proteins with sparse isotope labels can be produced in eukaryotic hosts by using isotope-labeled forms of specific amino acids, but structural analysis then requires information from experiments other than nuclear Overhauser effects. One source of alternate structural information is distance-dependent perturbation of spin relaxation times by nitroxide spin-labeled analogs of natural protein ligands. Here, we introduce spin-labeled analogs of sugar nucleotide donors for sialyltransferases, specifically, CMP-TEMPO (CMP-4-O-[2,2,6,6-tetramethylpiperidine-1-oxyl]) and CMP-4carboxyTEMPO (CMP-4-O-[4-carboxy-2,2,6,6-tetramethylpiperidinine-1-oxyl]). An ability to identify resonances from active site residues and produce distance constraints is illustrated on a (15)N phenylalanine-labeled version of the structurally uncharacterized, alpha-2,6-linked sialyltransferase, ST6Gal I.
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Affiliation(s)
- Shan Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Andre Venot
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Lu Meng
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Fang Tian
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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18
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19
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Chen CY, Cheng CH, Chen YC, Lee JC, Chou SH, Huang W, Chuang WJ. Preparation of amino-acid-type selective isotope labeling of protein expressed in Pichia pastoris. Proteins 2005; 62:279-87. [PMID: 16283643 DOI: 10.1002/prot.20742] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the culture conditions for successful amino-acid-type selective (AATS) isotope labeling of protein expressed in Pichia pastoris (P. pastoris). Rhodostomin (Rho), a six disulfide-bonded protein expressed in P. pastoris with the correct fold, was used to optimize the culture conditions. The concentrations of [alpha-15N] selective amino acid, nonlabeled amino acids, and ammonium chloride, as well as induction time, were optimized to avoid scrambling and to increase the incorporation rate and protein yield. The optimized protocol was successfully applied to produce AATS isotope-labeled Rho. The labeling of [alpha-15N]Cys has a 50% incorporation rate, and all 12 cysteine resonances were observed in HSQC spectrum. The labeling of [alpha-15N]Leu, -Lys, and -Met amino acids has an incorporation rate greater than 65%, and the expected number of resonances in the HSQC spectra were observed. In contrast, the labeling of [alpha-15N]Asp and -Gly amino acids has a low incorporation rate and the scrambling problem. In addition, the culture condition was successfully applied to label dendroaspin (Den), a four disulfide-bonded protein expressed in P. pastoris. Therefore, the described condition should be generally applicable to other proteins produced in the P. pastoris expression system. This is the first report to present a protocol for AATS isotope labeling of protein expressed in P. pastoris for NMR study.
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Affiliation(s)
- Chiu-Yueh Chen
- Department of Biochemistry and Institute of Basic Medical Science, National Cheng Kung University College of Medicine, Tainan 701, Taiwan
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Cole LA, Sutton-Riley JM, Khanlian SA, Borkovskaya M, Rayburn BB, Rayburn WF. Sensitivity of Over-the-Counter Pregnancy Tests: Comparison of Utility and Marketing Messages. J Am Pharm Assoc (2003) 2005; 45:608-15. [PMID: 16295647 DOI: 10.1331/1544345055001391] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To determine the sensitivity of seven over-the-counter pregnancy tests (OTC-PTs) using urine containing a mixture of human chorionic gonadotropin (hCG)-related molecules as found on the first day of missed menstrual period. DESIGN Blinded in vitro sensitivity analysis. SETTING Medical school laboratory. PARTICIPANTS None. INTERVENTIONS Urine was tested with OTC-PT devices at titers of 100, 50, 25, 12.5, 6.3, and 0 mIU/mL hCG immunoreactivity, and laboratory workers rated their confidence in the test result based on whether the test result was a clear, sharp, and unquestionable band in the test window. MAIN OUTCOME MEASURES Analytical sensitivity, defined as the urine concentration at which all OTC-PTs tested gave a positive result regardless of operator confidence score; clinical sensitivity of OTC-PTs, defined as the proportion of pregnancies likely to be detected on the first day of a missed period and calculated from the analytical sensitivity and a recently published regression curve for total urine hCG immunoreactivity in 25 urine samples from this period of gestation; percentage of tested devices showing a band in the test window at a specific hCG concentration measured devices positive; percentage faulty devices, defined as the proportion of tested devices failing to yield a band in the control window; and confidence score, determined from operator ratings for each device at each concentration of hCG. RESULTS First Response Early Result had an analytical sensitivity of 6.3 mIU/mL, which was estimated to detect greater than 95% of pregnancies on the day of missed period. The sensitivity of Clearblue Easy Earliest Results was 25 mIU/mL, which indicated detection of 80% of pregnancies. The sensitivity of the five other products was 100 mIU/mL or greater, indicating detection of 16% or less of pregnancies. Three of these last products included faulty devices. CONCLUSION Universal claims for OTC-PTs of more than 99% laboratory accuracy and use as early as the first day of missed period, while cleared for use by the U.S. Food and Drug Administration, are ambiguous and inappropriate for many products, according to these data. The majority of products tested were found to detect only a small percentage of pregnancies on the first day of a missed menstrual period. Until more data become available on the actual clinical sensitivity of these products, pharmacists should advise consumers to be cautious in interpreting test results.
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Affiliation(s)
- Laurence A Cole
- Department of Obstetrics and Gynecology, MSC10 5580, University of New Mexico Health Sciences Center, Albuquerque 87131-0001, USA.
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Cole LA, Khanlian SA, Sutton JM, Davies S, Stephens ND. Hyperglycosylated hCG (invasive trophoblast antigen, ITA) a key antigen for early pregnancy detection. Clin Biochem 2004; 36:647-55. [PMID: 14636881 DOI: 10.1016/s0009-9120(03)00108-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Hyperglycosylated human chorionic gonadotrophin (hCG) is an hCG variant with extra-large O-linked oligosaccharides, produced by phenotypically invasive cytotrophoblast cells in choriocarcinoma and pregnancy. It is the principal form of hCG produced in the first weeks of gestation. We investigated the importance of hyperglycosylated hCG in pregnancy testing and its detection by current hCG tests. DESIGN AND METHODS We measured the concentration of hyperglycosylated hCG and total hCG in 512 pregnancies throughout gestation. We assessed and compared the abilities of 14 commonly used commercial laboratory hCG tests and 18 home pregnancy tests to detect regular and hyperglycosylated hCG. RESULTS Hyperglycosylated hCG is the principal source of hCG-related immunoreactivity in early pregnancy. In the week following missing menses, hyperglycosylated hCG measurements may be more sensitive than regular hCG measurements in detecting pregnancy. Of 14 commercial laboratory hCG tests, 3 appropriately detected hyperglycosylated hCG standard. Of 18 different home pregnancy products 11 poorly or very poorly detected this key antigen. CONCLUSIONS Hyperglycosylated hCG may be the key molecule in the detection of early pregnancy. However, the majority of tests poorly detected or failed to detect this key antigen. New pregnancy tests are needed that either solely detect hyperglycosylated hCG or equally detect regular hCG and hyperglycosylated hCG.
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Affiliation(s)
- Laurence A Cole
- USA hCG Reference Service, Department of Obstetrics and Gynecology, University of New Mexico, Albuquerque, NM 87131, USA.
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Live D, Silks LA, Schmidt J. 13C isotopic enrichment for nuclear magnetic resonance studies of carbohydrates and glycoconjugates. Methods Enzymol 2002; 338:305-19. [PMID: 11460555 DOI: 10.1016/s0076-6879(02)38226-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D Live
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School and College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Goto NK, Kay LE. New developments in isotope labeling strategies for protein solution NMR spectroscopy. Curr Opin Struct Biol 2000; 10:585-92. [PMID: 11042458 DOI: 10.1016/s0959-440x(00)00135-4] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of novel isotope labeling strategies for proteins has facilitated the study of the structure and dynamics of these molecules. In addition, the recent emergence of alternative methods of bacterial expression for obtaining isotopically labeled proteins permits the study of new classes of important proteins by solution NMR methods.
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Affiliation(s)
- N K Goto
- Department of Biochemistry, University of Toronto, M5S 1A8, Toronto, Ontario, Canada
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Birken S, Maydelman Y, Gawinowicz MA. Preparation and analysis of the common urinary forms of human chorionic gonadotropin. Methods 2000; 21:3-14. [PMID: 10764603 DOI: 10.1006/meth.2000.0971] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human chorionic gonadotropin (hCG) is the hormone of pregnancy and forms the basis of all pregnancy tests as well as diagnostic assays for a variety of pathological states including certain types of cancers and some diseases of pregnancy and genetic abnormalities. In recent years, the discovery of the diagnostic utility of measurement of the free subunits and fragments of the hormone, especially in urine, has proven of special use for diagnosis of very early pregnancy loss, an important phenomenon related to infertility, as well as part of screening programs for Down Syndrome and gynecological cancers. This article summarizes existing and new methods for the preparation of hCG, its subunits, and the beta core fragment from urinary sources. The methods for proper analyses of these materials are also described to enable investigators to prepare and analyze these materials in various quantities in their own laboratories.
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Affiliation(s)
- S Birken
- Department of Medicine, Columbia University College of Physicians and Surgeons, 630 West 168 Street, New York, New York 10032, USA.
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Coughlin PE, Anderson FE, Oliver EJ, Brown JM, Homans SW, Pollak S, Lustbader JW. Improved Resolution and Sensitivity of Triple-Resonance NMR Methods for the Structural Analysis of Proteins by Use of a Backbone-Labeling Strategy. J Am Chem Soc 1999. [DOI: 10.1021/ja993083w] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philip E. Coughlin
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Frank E. Anderson
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Ed J. Oliver
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Jonathan M. Brown
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Steve W. Homans
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Susan Pollak
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Joyce W. Lustbader
- Contribution from Martek Biosciences, 6480 Dobbin Road, Columbia, Maryland 21045, School of Biochemistry and Molecular Biology, University of Leeds, LS2 9JT UK, and Department of Obstetrics and Gynecology, Columbia University, 630 West 168th Street, New York, New York 10032
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Erbel PJ, Karimi-Nejad Y, De Beer T, Boelens R, Kamerling JP, Vliegenthart JF. Solution structure of the alpha-subunit of human chorionic gonadotropin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 260:490-8. [PMID: 10095786 DOI: 10.1046/j.1432-1327.1999.00188.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The three-dimensional solution structure of the alpha-subunit in the alpha, beta heterodimeric human chorionic gonadotropin (hCG), deglycosylated with endo-beta-N-acetylglucosaminidase-B (dg-alpha hCG), was determined using 2D homonuclear and 2D heteronuclear 1H, 13C NMR spectroscopy at natural abundance in conjunction with the program package XPLOR. The distance geometry/simulated annealing protocol was modified to allow for the efficient modelling of the cystine knot motif present in alpha hCG. The protein structure was modelled with 620 interproton distance restraints and the GlcNAc residue linked to Asn78 was modelled with 30 protein-carbohydrate and 3 intraresidual NOEs. The solution structure of dg-alpha hCG is represented by an ensemble of 27 structures. In comparison to the crystal structure of the dimer, the solution structure of free dg-alpha hCG exhibits: (a) an increased structural disorder (residues 33-57); (b) a different backbone conformation near Val76 and Glu77; and (c) a larger flexibility. These differences are caused by the absence of the interactions with the beta-subunit. Consequently, in free dg-alpha hCG, compared to the intact dimer, the two hairpin loops 20-23 and 70-74 are arranged differently with respect to each other. The beta-GlcNAc(78) is tightly associated with the hydrophobic protein-core in between the beta-hairpins. This conclusion is based on the NOEs from the axial H1, H3, H5 atoms and the N-acetyl protons of beta-GlcNAc(78) to the protein-core. The hydrophobic protein-core between the beta-hairpins is thereby shielded from the solvent.
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Affiliation(s)
- P J Erbel
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, The Netherlands
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27
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Richard F, Robert P, Remy JJ, Martinat N, Bidart JM, Salesse R, Combarnous Y. High-level secretion of biologically active recombinant porcine follicle-stimulating hormone by the methylotrophic yeast Pichia pastoris. Biochem Biophys Res Commun 1998; 245:847-52. [PMID: 9588203 DOI: 10.1006/bbrc.1998.8532] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An active recombinant glycoprotein hormone, porcine follicle-stimulating hormone (recFSH), has been produced for the first time in the methylotrophic yeast, Pichia pastoris. The yield of secreted recFSH (10 mg/l) was the highest ever reached. RecFSH displayed an apparent molecular mass of 41 kDa by SDS-PAGE and was found to bear only N-linked carbohydrates of the high-mannose type. Its in vitro binding and cell-stimulating activities were identical to those of pituitary porcine FSH. The large availability and the noncharged N-glycans of FSHrec should render it highly valuable for structural studies.
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Affiliation(s)
- F Richard
- Unité Récepteurs et Communications Cellulaires, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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