1
|
Chongsaritsinsuk J, Rangel-Angarita V, Mahoney KE, Lucas TM, Enny OM, Katemauswa M, Malaker SA. Quantification and site-specific analysis of co-occupied N- and O-glycopeptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602348. [PMID: 39005468 PMCID: PMC11245114 DOI: 10.1101/2024.07.06.602348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.
Collapse
|
2
|
Scheim DE, Vottero P, Santin AD, Hirsh AG. Sialylated Glycan Bindings from SARS-CoV-2 Spike Protein to Blood and Endothelial Cells Govern the Severe Morbidities of COVID-19. Int J Mol Sci 2023; 24:17039. [PMID: 38069362 PMCID: PMC10871123 DOI: 10.3390/ijms242317039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Consistent with well-established biochemical properties of coronaviruses, sialylated glycan attachments between SARS-CoV-2 spike protein (SP) and host cells are key to the virus's pathology. SARS-CoV-2 SP attaches to and aggregates red blood cells (RBCs), as shown in many pre-clinical and clinical studies, causing pulmonary and extrapulmonary microthrombi and hypoxia in severe COVID-19 patients. SARS-CoV-2 SP attachments to the heavily sialylated surfaces of platelets (which, like RBCs, have no ACE2) and endothelial cells (having minimal ACE2) compound this vascular damage. Notably, experimentally induced RBC aggregation in vivo causes the same key morbidities as for severe COVID-19, including microvascular occlusion, blood clots, hypoxia and myocarditis. Key risk factors for COVID-19 morbidity, including older age, diabetes and obesity, are all characterized by markedly increased propensity to RBC clumping. For mammalian species, the degree of clinical susceptibility to COVID-19 correlates to RBC aggregability with p = 0.033. Notably, of the five human betacoronaviruses, the two common cold strains express an enzyme that releases glycan attachments, while the deadly SARS, SARS-CoV-2 and MERS do not, although viral loads for COVID-19 and the two common cold infections are similar. These biochemical insights also explain the previously puzzling clinical efficacy of certain generics against COVID-19 and may support the development of future therapeutic strategies for COVID-19 and long COVID patients.
Collapse
Affiliation(s)
- David E Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060, USA
| | - Paola Vottero
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Alessandro D Santin
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, P.O. Box 208063, New Haven, CT 06520, USA
| | | |
Collapse
|
3
|
Du Y, Chen Y, Li F, Mao Z, Ding Y, Wang W. Genetically Engineered Cellular Nanovesicle as Targeted DNase I Delivery System for the Clearance of Neutrophil Extracellular Traps in Acute Lung Injury. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303053. [PMID: 37759381 PMCID: PMC10646266 DOI: 10.1002/advs.202303053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/18/2023] [Indexed: 09/29/2023]
Abstract
Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) are prevalent critical illnesses with a high mortality rate among patients in intensive care units. Neutrophil extracellular traps (NETs) are implicated in the pathogenesis of ALI/ARDS and represent a promising therapeutic target. However, the clinical application of deoxyribonuclease I (DNase I), the only drug currently available to clear NETs, is limited due to the lack of precise and efficient delivery strategies. Therefore, targeted delivery of DNase I to the inflamed lung remains a critical issue to be addressed. Herein, a novel biomimetic DNase I delivery system is developed (DCNV) that employs genetically and bioorthogonally engineered cellular nanovesicles for pulmonary NETs clearance. The CXC motif chemokine receptor 2 overexpressed cellular nanovesicles can mimic the inflammatory chemotaxis of neutrophils in ALI/ARDS, leading to enhanced lung accumulation. Furthermore, DNase I immobilized through bioorthogonal chemistry exhibits remarkable enzymatic activity in NETs degradation, thus restraining inflammation and safeguarding lung tissue in the lipopolysaccharide-induced ALI murine model. Collectively, the findings present a groundbreaking proof-of-concept in the utilization of biomimetic cellular nanovesicles to deliver DNase I for treating ALI/ARDS. This innovative strategy may usher in a new era in the development of pharmacological interventions for various inflammation-related diseases.
Collapse
Affiliation(s)
- Yang Du
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouZhejiang310009China
- National Innovation Center for Fundamental Research on Cancer MedicineHangzhouZhejiang310009China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- ZJU‐Pujian Research & Development Center of Medical Artificial Intelligence for Hepatobiliary and Pancreatic DiseaseHangzhouZhejiang310058China
| | - Yining Chen
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouZhejiang310009China
- National Innovation Center for Fundamental Research on Cancer MedicineHangzhouZhejiang310009China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- ZJU‐Pujian Research & Development Center of Medical Artificial Intelligence for Hepatobiliary and Pancreatic DiseaseHangzhouZhejiang310058China
| | - Fangyuan Li
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- Institute of PharmaceuticsHangzhou Institute of Innovative MedicineCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Zhengwei Mao
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- MOE Key Laboratory of Macromolecular Synthesis and FunctionalizationDepartment of Polymer Science and EngineeringZhejiang UniversityHangzhouZhejiang310027China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouZhejiang310009China
- National Innovation Center for Fundamental Research on Cancer MedicineHangzhouZhejiang310009China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- ZJU‐Pujian Research & Development Center of Medical Artificial Intelligence for Hepatobiliary and Pancreatic DiseaseHangzhouZhejiang310058China
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic SurgeryThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouZhejiang310009China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouZhejiang310009China
- National Innovation Center for Fundamental Research on Cancer MedicineHangzhouZhejiang310009China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- ZJU‐Pujian Research & Development Center of Medical Artificial Intelligence for Hepatobiliary and Pancreatic DiseaseHangzhouZhejiang310058China
| |
Collapse
|
4
|
Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
Collapse
Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| |
Collapse
|
5
|
Boyd R, Zhang L, Fromme P. Native Deglycosylation and Size Exclusion Chromatography of Viral Chemokine Binding Proteins for Structural Discovery. Methods Mol Biol 2023; 2597:251-259. [PMID: 36374426 DOI: 10.1007/978-1-0716-2835-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Structural discovery of viral chemokine binding proteins can provide valuable information on the binding domains and protein-protein interfaces (PPI) of these immunologically relevant proteins. Protein expression in mammalian cells produces high-quality protein compared to other expression methods; however, because structural discovery methods such as cryo-EM-based single particle analysis (SPA) and x-ray crystallography use methods which combine data from many individual proteins, these demand a highly monodispersed sample composed of protein with ordered structure. These techniques are often incompatible with flexible glycosyl groups commonly present on proteins produced by mammalian cells and require deglycosylation to enable observation of the conserved tertiary structure beneath these variable, flexible, glycans. Using the Myxoma viral protein M-T7 as a test case, we discuss considerations and preliminary bioinformatic analysis for approaching structural discovery using freely accessible sequence and structure databases to maximize success and guide experiments. We describe a simple deglycosylation optimization protocol utilizing Endo H followed by size exclusion chromatography (SEC) based purification to produce and validate protein suitable for structural discovery. Considerations such as protein concentration and volumes required for crystallography and negative stain electron microscopy are discussed as well as grid blotting techniques for negative stain experiments to validate protein quality.
Collapse
Affiliation(s)
- Ryan Boyd
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Liqiang Zhang
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
6
|
Bourguignon N, Karp P, Attallah C, Chamorro DA, Oggero M, Booth R, Ferrero S, Bhansali S, Pérez MS, Lerner B, Helguera G. Large Area Microfluidic Bioreactor for Production of Recombinant Protein. BIOSENSORS 2022; 12:bios12070526. [PMID: 35884329 PMCID: PMC9313365 DOI: 10.3390/bios12070526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
Abstract
To produce innovative biopharmaceuticals, highly flexible, adaptable, robust, and affordable bioprocess platforms for bioreactors are essential. In this article, we describe the development of a large-area microfluidic bioreactor (LM bioreactor) for mammalian cell culture that works at laminar flow and perfusion conditions. The 184 cm2 32 cisterns LM bioreactor is the largest polydimethylsiloxane (PDMS) microfluidic device fabricated by photopolymer flexographic master mold methodology, reaching a final volume of 2.8 mL. The LM bioreactor was connected to a syringe pump system for culture media perfusion, and the cells’ culture was monitored by photomicrograph imaging. CHO-ahIFN-α2b adherent cell line expressing the anti-hIFN-a2b recombinant scFv-Fc monoclonal antibody (mAb) for the treatment of systemic lupus erythematosus were cultured on the LM bioreactor. Cell culture and mAb production in the LM bioreactor could be sustained for 18 days. Moreover, the anti-hIFN-a2b produced in the LM bioreactor showed higher affinity and neutralizing antiproliferative activity compared to those mAbs produced in the control condition. We demonstrate for the first-time, a large area microfluidic bioreactor for mammalian cell culture that enables a controlled microenvironment suitable for the development of high-quality biologics with potential for therapeutic use.
Collapse
Affiliation(s)
- Natalia Bourguignon
- Centro IREN, Universidad Tecnológica Nacional, Haedo B1706EAH, Provincia de Buenos Aires, Argentina; (N.B.); (D.A.C.); (M.S.P.)
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA;
| | - Paola Karp
- Laboratorio de Biotecnología Farmacéutica, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad de Buenos Aires C1428ADN, Argentina; (P.K.); (S.F.)
| | - Carolina Attallah
- Centro Biotecnológico del Litoral, Laboratorio de Cultivos Celulares, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), CONICET, Santa Fe S3000ZAA, Provincia de Santa Fe, Argentina; (C.A.); (M.O.)
| | - Daniel A. Chamorro
- Centro IREN, Universidad Tecnológica Nacional, Haedo B1706EAH, Provincia de Buenos Aires, Argentina; (N.B.); (D.A.C.); (M.S.P.)
| | - Marcos Oggero
- Centro Biotecnológico del Litoral, Laboratorio de Cultivos Celulares, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), CONICET, Santa Fe S3000ZAA, Provincia de Santa Fe, Argentina; (C.A.); (M.O.)
| | - Ross Booth
- Roche Sequencing Solutions, Inc., Pleasanton, CA 94588, USA;
| | - Sol Ferrero
- Laboratorio de Biotecnología Farmacéutica, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad de Buenos Aires C1428ADN, Argentina; (P.K.); (S.F.)
| | - Shekhar Bhansali
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA;
| | - Maximiliano S. Pérez
- Centro IREN, Universidad Tecnológica Nacional, Haedo B1706EAH, Provincia de Buenos Aires, Argentina; (N.B.); (D.A.C.); (M.S.P.)
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA;
| | - Betiana Lerner
- Centro IREN, Universidad Tecnológica Nacional, Haedo B1706EAH, Provincia de Buenos Aires, Argentina; (N.B.); (D.A.C.); (M.S.P.)
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA;
- Correspondence: (B.L.); (G.H.); Tel.:+5411-4343-1177 (ext. 1209) (B.L.); +54-11-4783-2869 (G.H.)
| | - Gustavo Helguera
- Laboratorio de Biotecnología Farmacéutica, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Ciudad de Buenos Aires C1428ADN, Argentina; (P.K.); (S.F.)
- Correspondence: (B.L.); (G.H.); Tel.:+5411-4343-1177 (ext. 1209) (B.L.); +54-11-4783-2869 (G.H.)
| |
Collapse
|
7
|
Jonsson-Schmunk K, Ghose R, Croyle MA. Immunization and Drug Metabolizing Enzymes: Focus on Hepatic Cytochrome P450 3A. Expert Rev Vaccines 2021; 20:623-634. [PMID: 33666138 DOI: 10.1080/14760584.2021.1899818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVE Infectious disease emergencies like the 2013-2016 Ebola epidemic and the 2009 influenza and current SARS-CoV-2 pandemics illustrate that vaccines are now given to diverse populations with preexisting pathologies requiring pharmacological management. Many natural biomolecules (steroid hormones, fatty acids, vitamins) and ~60% of prescribed medications are processed by hepatic cytochrome P450 (CYP) 3A4. The objective of this work was to determine the impact of infection and vaccines on drug metabolism. METHODS The impact of an adenovirus-based vaccine expressing Ebola glycoprotein (AdEBO) and H1N1 and H3N2 influenza viruses on hepatic CYP 3A4 and associated nuclear receptors was evaluated in human hepatocytes (HC-04 cells) and in mice. RESULTS CYP3A activity was suppressed by 55% in mice 24 h after administration of mouse-adapted H1N1, while ˂10% activity remained in HC-04 cells after infection with H1N1 and H3N2 due to global suppression of cellular translation capacity, indicated by reduction (70%, H1N1, 56%, H3N2) of phosphorylated eukaryotic translation initiation factor 4e (eIF4E). AdEBO suppressed CYP3A activity in vivo (44%) and in vitro (26%) 24 hours after infection. CONCLUSION As the clinical evaluation of vaccines for SARS-CoV-2 and other global pathogens rise, studies to evaluate the impact of new vaccines and emerging pathogens on CYP3A4 and other metabolic enzymes are warranted to avoid therapeutic failures that could further compromise the public health during infectious disease emergencies.
Collapse
Affiliation(s)
- Kristina Jonsson-Schmunk
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas, Austin, Texas, USA
| | - Romi Ghose
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas, USA
| | - Maria A Croyle
- Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas, Austin, Texas, USA.,LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
8
|
Hasan M, Khakzad H, Happonen L, Sundin A, Unge J, Mueller U, Malmström J, Westergren-Thorsson G, Malmström L, Ellervik U, Malmström A, Tykesson E. The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms. Chem Sci 2021; 12:1869-1885. [PMID: 33815739 PMCID: PMC8006597 DOI: 10.1039/d0sc05971d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/04/2020] [Indexed: 01/21/2023] Open
Abstract
Dermatan sulfate epimerase 1 (DS-epi1, EC 5.1.3.19) catalyzes the conversion of d-glucuronic acid to l-iduronic acid on the polymer level, a key step in the biosynthesis of the glycosaminoglycan dermatan sulfate. Here, we present the first crystal structure of the catalytic domains of DS-epi1, solved at 2.4 Å resolution, as well as a model of the full-length luminal protein obtained by a combination of macromolecular crystallography and targeted cross-linking mass spectrometry. Based on docking studies and molecular dynamics simulations of the protein structure and a chondroitin substrate, we suggest a novel mechanism of DS-epi1, involving a His/double-Tyr motif. Our work uncovers detailed information about the domain architecture, active site, metal-coordinating center and pattern of N-glycosylation of the protein. Additionally, the structure of DS-epi1 reveals a high structural similarity to proteins from several families of bacterial polysaccharide lyases. DS-epi1 is of great importance in a range of diseases, and the structure provides a necessary starting point for design of active site inhibitors.
Collapse
Affiliation(s)
- Mahmudul Hasan
- Department of Biochemistry and Structural Biology , Lund University , Lund , Sweden
| | - Hamed Khakzad
- Equipe Signalisation Calcique et Infections Microbiennes , Ecole Normale Supérieure Paris-Saclay , 91190 Gif-sur-Yvette , France
- Institut National de la Santé et de la Recherche Médicale U1282 , 91190 Gif-sur-Yvette , France
| | - Lotta Happonen
- Department of Clinical Sciences , Lund University , Lund , Sweden
| | - Anders Sundin
- Department of Chemistry , Lund University , Lund , Sweden
| | - Johan Unge
- Department of Biological Chemistry , University of California Los Angeles , Los Angeles , CA 90095 , USA
| | - Uwe Mueller
- Macromolecular Crystallography Group , Helmholtz-Zentrum-Berlin für Materialien und Energie , Albert-Einstein Str. 15 , 12489 Berlin , Germany
| | - Johan Malmström
- Department of Clinical Sciences , Lund University , Lund , Sweden
| | | | - Lars Malmström
- Department of Clinical Sciences , Lund University , Lund , Sweden
| | - Ulf Ellervik
- Department of Chemistry , Lund University , Lund , Sweden
| | - Anders Malmström
- Department of Experimental Medical Science , Lund University , Lund , Sweden .
| | - Emil Tykesson
- Department of Experimental Medical Science , Lund University , Lund , Sweden .
| |
Collapse
|
9
|
Ibrahim AEC, Reljic R, Drake Pascal MW, Ma JKC. Rational design and expression of a recombinant plant rhabdovirus glycoprotein for production of immunoreactive murine anti-sera. Protein Expr Purif 2020; 175:105691. [PMID: 32679171 DOI: 10.1016/j.pep.2020.105691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
Lettuce necrotic yellows virus (LNYV) is a plant rhabdovirus which has a type-1 transmembrane glycoprotein. Here, we describe the generation of murine anti-sera to the glycoprotein. Rational design, expression, and purification of recombinant glycoprotein, termed rLGe, was undertaken using SignalP4.1 and camSol servers to predict signal peptide cleavage and protein solubility. In order to successfully obtain expression in mammalian cells, LNYV glycoprotein native signal peptide was substituted with that of Rabies virus glycoprotein. In addition, rather than expression of the entire molecule, rLGe consisted of the LNYV glycoprotein ectodomain fused to two affinity tags to minimize the risk of protein aggregation, while facilitating detection and purification. rLGe was transiently expressed in mammalian cell culture, purified using affinity column chromatography, and used to immunize mice. Harvested anti-sera were immunoreactive and specific to the naturally occurring glycoprotein as confirmed by western blotting of plant leaf tissue infected with LNYV.
Collapse
Affiliation(s)
- Ahmad E C Ibrahim
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Rajko Reljic
- Institute for Infection and Immunity, St George's University of London, London, UK.
| | - M W Drake Pascal
- Institute for Infection and Immunity, St George's University of London, London, UK.
| | - Julian K-C Ma
- Institute for Infection and Immunity, St George's University of London, London, UK.
| |
Collapse
|
10
|
Trastoy B, Du JJ, Klontz EH, Li C, Cifuente JO, Wang LX, Sundberg EJ, Guerin ME. Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides. Nat Commun 2020; 11:899. [PMID: 32060313 PMCID: PMC7021837 DOI: 10.1038/s41467-020-14754-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/30/2020] [Indexed: 11/24/2022] Open
Abstract
The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-β-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-Man9GlcNAc2Asn substrate complex, and two EndoBT-3987-Man9GlcNAc and EndoBT-3987-Man5GlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.
Collapse
Affiliation(s)
- Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - Jonathan J Du
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Erik H Klontz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Javier O Cifuente
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| |
Collapse
|
11
|
Wang JW, Gao J, Wang HF, Jin QH, Rao B, Deng W, Cao Y, Lei M, Ye S, Fang Q. Miniaturization of the Whole Process of Protein Crystallographic Analysis by a Microfluidic Droplet Robot: From Nanoliter-Scale Purified Proteins to Diffraction-Quality Crystals. Anal Chem 2019; 91:10132-10140. [PMID: 31276402 DOI: 10.1021/acs.analchem.9b02138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To obtain diffraction-quality crystals is one of the largest barriers to analyze the protein structure using X-ray crystallography. Here we describe a microfluidic droplet robot that enables successful miniaturization of the whole process of crystallization experiments including large-scale initial crystallization screening, crystallization optimization, and crystal harvesting. The combination of the state-of-the-art droplet-based microfluidic technique with the microbatch crystallization mode dramatically reduces the volumes of droplet crystallization reactors to tens nanoliter range, allowing large-scale initial screening of 1536 crystallization conditions and multifactor crystallization condition optimization with extremely low protein consumption, and on-chip harvesting of diffraction-quality crystals directly from the droplet reactors. We applied the droplet robot in miniaturized crystallization experiments of seven soluble proteins and two membrane proteins, and on-chip crystal harvesting of six proteins. The X-ray diffraction data sets of these crystals were collected using synchrotron radiation for analyzing the structures with similar diffraction qualities as conventional crystallization methods.
Collapse
Affiliation(s)
- Jian-Wei Wang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Jie Gao
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Hui-Feng Wang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| | - Qiu-Heng Jin
- Life Sciences Institute , Zhejiang University , Hangzhou , 310058 , China
| | - Bing Rao
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Wei Deng
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Yu Cao
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Ming Lei
- State Key Laboratory of Molecular Biology , National Center for Protein Science · Shanghai , Shanghai , 201210 , China
| | - Sheng Ye
- Life Sciences Institute , Zhejiang University , Hangzhou , 310058 , China.,School of Life Sciences , Tianjin University , Tianjin , 300072 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry , Zhejiang University , Hangzhou , 310058 , China
| |
Collapse
|
12
|
An illustration of optimal selected glycosidase for N-glycoproteins deglycosylation and crystallization. Int J Biol Macromol 2019; 122:265-271. [DOI: 10.1016/j.ijbiomac.2018.10.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/02/2018] [Accepted: 10/18/2018] [Indexed: 01/11/2023]
|
13
|
Ma J, Sanda M, Wei R, Zhang L, Goldman R. Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics 2018. [PMID: 29427759 DOI: 10.1016/j.jprot.2018.1002.1003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow. We find increased core fucosylation of 5 glycopeptides at the stage of liver fibrosis (i.e., N630 of serotransferrin, N107 of alpha-1-antitrypsin, N253 of plasma protease C1 inhibitor, N397 of ceruloplasmin, and N86 of vitronectin), increase of additional 6 glycopeptides at the stage of cirrhosis (i.e., N138 and N762 of ceruloplasmin, N354 of clusterin, N187 of hemopexin, N71 of immunoglobulin J chain, and N127 of lumican), while the degree of core fucosylation of 10 glycopeptides did not change. Interestingly, although we observe an increase in the core fucosylation at N86 of vitronectin in liver fibrosis, core fucosylation decreases on the N169 glycopeptide of the same protein. Our results demonstrate that the changes in core fucosylation are protein and site specific during the progression of fibrotic liver disease and independent of the changes in the quantity of N-glycoproteins. It is expected that the fully optimized multiplex LC-MS-MRM assay of core fucosylated glycopeptides will be useful for the serologic assessment of the fibrosis of liver. BIOLOGICAL SIGNIFICANCE: We have quantified the difference in core fucosylation among three comparison groups (healthy control, fibrosis and cirrhosis patients) using a sensitive and selective LC-MS-MRM method. Despite an overall increase in core fucosylation of many of the glycoproteins that we examined, core fucosylation changed in a protein- and site-specific manner. Moreover, increased and decreased fucosylation was observed on different N-glycopeptides of the same protein. Altered core fucosylation of N-glycopeptides might be used as an alternative serologic assay for the evaluation of fibrotic liver disease.
Collapse
Affiliation(s)
- Junfeng Ma
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Miloslav Sanda
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Renhuizi Wei
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Lihua Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Radoslav Goldman
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA.
| |
Collapse
|
14
|
Ereño-Orbea J, Sicard T, Cui H, Akula I, Julien JP. Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. J Vis Exp 2018. [PMID: 30035760 PMCID: PMC6124603 DOI: 10.3791/57750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of these glycoproteins possess immunoglobulin (Ig) folds and are central to immune recognition and regulation. Here, we present a platform for the design, expression and biophysical characterization of the extracellular domain of human B cell receptor CD22. We propose that these approaches are broadly applicable to the characterization of mammalian glycoprotein ectodomains containing Ig domains. Two suspension human embryonic kidney (HEK) cell lines, HEK293F and HEK293S, are used to express glycoproteins harbouring complex and high-mannose glycans, respectively. These recombinant glycoproteins with different glycoforms allow investigating the effect of glycan size and composition on ligand binding. We discuss protocols for studying the kinetics and thermodynamics of glycoprotein binding to biologically relevant ligands and therapeutic antibody candidates. Recombinant glycoproteins produced in HEK293S cells are amenable to crystallization due to glycan homogeneity, reduced flexibility and susceptibility to endoglycosidase H treatment. We present methods for soaking glycoprotein crystals with heavy atoms and small molecules for phase determination and analysis of ligand binding, respectively. The experimental protocols discussed here hold promise for the characterization of mammalian glycoproteins to give insight into their function and investigate the mechanism of action of therapeutics.
Collapse
Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Indira Akula
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto; Department of Immunology, University of Toronto;
| |
Collapse
|
15
|
Ma J, Sanda M, Wei R, Zhang L, Goldman R. Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics 2018; 189:67-74. [PMID: 29427759 DOI: 10.1016/j.jprot.2018.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
Abstract
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow. We find increased core fucosylation of 5 glycopeptides at the stage of liver fibrosis (i.e., N630 of serotransferrin, N107 of alpha-1-antitrypsin, N253 of plasma protease C1 inhibitor, N397 of ceruloplasmin, and N86 of vitronectin), increase of additional 6 glycopeptides at the stage of cirrhosis (i.e., N138 and N762 of ceruloplasmin, N354 of clusterin, N187 of hemopexin, N71 of immunoglobulin J chain, and N127 of lumican), while the degree of core fucosylation of 10 glycopeptides did not change. Interestingly, although we observe an increase in the core fucosylation at N86 of vitronectin in liver fibrosis, core fucosylation decreases on the N169 glycopeptide of the same protein. Our results demonstrate that the changes in core fucosylation are protein and site specific during the progression of fibrotic liver disease and independent of the changes in the quantity of N-glycoproteins. It is expected that the fully optimized multiplex LC-MS-MRM assay of core fucosylated glycopeptides will be useful for the serologic assessment of the fibrosis of liver. BIOLOGICAL SIGNIFICANCE: We have quantified the difference in core fucosylation among three comparison groups (healthy control, fibrosis and cirrhosis patients) using a sensitive and selective LC-MS-MRM method. Despite an overall increase in core fucosylation of many of the glycoproteins that we examined, core fucosylation changed in a protein- and site-specific manner. Moreover, increased and decreased fucosylation was observed on different N-glycopeptides of the same protein. Altered core fucosylation of N-glycopeptides might be used as an alternative serologic assay for the evaluation of fibrotic liver disease.
Collapse
Affiliation(s)
- Junfeng Ma
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Miloslav Sanda
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Renhuizi Wei
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Lihua Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Radoslav Goldman
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA.
| |
Collapse
|
16
|
Pérez S, de Sanctis D. Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience. Beilstein J Org Chem 2017; 13:1145-1167. [PMID: 28684994 PMCID: PMC5480326 DOI: 10.3762/bjoc.13.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/17/2017] [Indexed: 11/29/2022] Open
Abstract
Synchrotron radiation is the most versatile way to explore biological materials in different states: monocrystalline, polycrystalline, solution, colloids and multiscale architectures. Steady improvements in instrumentation have made synchrotrons the most flexible intense X-ray source. The wide range of applications of synchrotron radiation is commensurate with the structural diversity and complexity of the molecules and macromolecules that form the collection of substrates investigated by glycoscience. The present review illustrates how synchrotron-based experiments have contributed to our understanding in the field of structural glycobiology. Structural characterization of protein–carbohydrate interactions of the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution.
Collapse
Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS-University Grenoble Alpes, France
| | | |
Collapse
|
17
|
Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
Collapse
Affiliation(s)
- Sinéad T Loughran
- Department of Applied Sciences, Dundalk Institute of Technology, Dundalk, Ireland
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
| |
Collapse
|
18
|
Imai A, Tadokoro T, Kita S, Horiuchi M, Fukuhara H, Maenaka K. Establishment of the BacMam system using silkworm baculovirus. Biochem Biophys Res Commun 2016; 478:580-5. [PMID: 27480929 DOI: 10.1016/j.bbrc.2016.07.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 12/26/2022]
Abstract
The BacMam system uses modified insect viruses (baculoviruses) as vehicles to efficiently deliver genes for expression in mammalian cells. The technique can be widely applied to large-scale recombinant protein production with appropriate modifications, high-throughput screening platforms for cell-based assays, and the delivery of large genes. The silkworm system is often employed as a rapid and cost-effective approach for recombinant baculovirus generation. Here we have developed the novel BacMam system using silkworm baculovirus, and shown the successful expression of EGFP in mammalian cells. The transduction to mammalian cells via the BacMam system was improved by adding phosphate-buffered saline and sodium butyrate to the culture medium and lowering the temperature after viral infection. This study provides an alternative gene delivery system for mammalian cells, which has various potential applications, including efficient native protein production and gene therapy.
Collapse
Affiliation(s)
- Atsutoshi Imai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Masataka Horiuchi
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido, 061-0293, Japan
| | - Hideo Fukuhara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan; CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan.
| |
Collapse
|
19
|
Sultana A, Lee JE. Measuring Protein‐Protein and Protein‐Nucleic Acid Interactions by Biolayer Interferometry. ACTA ACUST UNITED AC 2015; 79:19.25.1-19.25.26. [DOI: 10.1002/0471140864.ps1925s79] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Azmiri Sultana
- Department of Laboratory Medicine and Pathobiology, University of Toronto Toronto Ontario Canada
| | - Jeffrey E. Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto Toronto Ontario Canada
| |
Collapse
|
20
|
Choi JH, Schafer SC, Freiberg AN, Croyle MA. Bolstering Components of the Immune Response Compromised by Prior Exposure to Adenovirus: Guided Formulation Development for a Nasal Ebola Vaccine. Mol Pharm 2015; 12:2697-711. [PMID: 25549696 PMCID: PMC4525322 DOI: 10.1021/mp5006454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
The
severity and longevity of the current Ebola outbreak highlight
the need for a fast-acting yet long-lasting vaccine for at-risk populations
(medical personnel and rural villagers) where repeated prime-boost
regimens are not feasible. While recombinant adenovirus (rAd)-based
vaccines have conferred full protection against multiple strains of
Ebola after a single immunization, their efficacy is impaired by pre-existing
immunity (PEI) to adenovirus. To address this important issue, a panel
of formulations was evaluated by an in vitro assay
for their ability to protect rAd from neutralization. An amphiphilic
polymer (F16, FW ∼39,000) significantly improved transgene
expression in the presence of anti-Ad neutralizing antibodies (NAB)
at concentrations of 5 times the 50% neutralizing dose (ND50). In vivo performance of rAd in F16 was compared
with unformulated virus, virus modified with poly(ethylene) glycol
(PEG), and virus incorporated into poly(lactic-co-glycolic) acid (PLGA) polymeric beads. Histochemical analysis of
lung tissue revealed that F16 promoted strong levels of transgene
expression in naive mice and those that were exposed to adenovirus
in the nasal cavity 28 days prior to immunization. Multiparameter
flow cytometry revealed that F16 induced significantly more polyfunctional
antigen-specific CD8+ T cells simultaneously producing
IFN-γ, IL-2, and TNF-α than other test formulations. These
effects were not compromised by PEI. Data from formulations that provided
partial protection from challenge consistently identified specific
immunological requirements necessary for protection. This approach
may be useful for development of formulations for other vaccine platforms
that also employ ubiquitous pathogens as carriers like the influenza
virus.
Collapse
Affiliation(s)
- Jin Huk Choi
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Stephen C Schafer
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander N Freiberg
- ‡Department of Pathology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Maria A Croyle
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States.,§Center for Infectious Disease, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
21
|
|
22
|
Choi JH, Jonsson-Schmunk K, Qiu X, Shedlock DJ, Strong J, Xu JX, Michie KL, Audet J, Fernando L, Myers MJ, Weiner D, Bajrovic I, Tran LQ, Wong G, Bello A, Kobinger GP, Schafer SC, Croyle MA. A Single Dose Respiratory Recombinant Adenovirus-Based Vaccine Provides Long-Term Protection for Non-Human Primates from Lethal Ebola Infection. Mol Pharm 2014; 12:2712-31. [PMID: 25363619 PMCID: PMC4525323 DOI: 10.1021/mp500646d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
As
the Ebola outbreak in West Africa continues and cases appear
in the United States and other countries, the need for long-lasting
vaccines to preserve global health is imminent. Here, we evaluate
the long-term efficacy of a respiratory and sublingual (SL) adenovirus-based
vaccine in non-human primates in two phases. In the first, a single
respiratory dose of 1.4 × 109 infectious virus particles
(ivp)/kg of Ad-CAGoptZGP induced strong Ebola glycoprotein (GP) specific
CD8+ and CD4+ T cell responses and Ebola GP-specific
antibodies in systemic and mucosal compartments and was partially
(67%) protective from challenge 62 days after immunization. The same
dose given by the SL route induced Ebola GP-specific CD8+ T cell responses similar to that of intramuscular (IM) injection,
however, the Ebola GP-specific antibody response was low. All primates
succumbed to infection. Three primates were then given the vaccine
in a formulation that improved the immune response to Ebola in rodents.
Three primates were immunized with 2.0 × 1010 ivp/kg
of vaccine by the SL route. Diverse populations of polyfunctional
Ebola GP-specific CD4+ and CD8+ T cells and
significant anti-Ebola GP antibodies were present in samples collected
150 days after respiratory immunization. The formulated vaccine was
fully protective against challenge 21 weeks after immunization. While
diverse populations of Ebola GP-specific CD4+ T cells were
produced after SL immunization, antibodies were not neutralizing and
the vaccine was unprotective. To our knowledge, this is the first
time that durable protection from a single dose respiratory adenovirus-based
Ebola vaccine has been demonstrated in primates.
Collapse
Affiliation(s)
- Jin Huk Choi
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kristina Jonsson-Schmunk
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Xiangguo Qiu
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Devon J Shedlock
- ∥Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jim Strong
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Jason X Xu
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kelly L Michie
- ⊥The University of Texas College of Natural Sciences Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jonathan Audet
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Lisa Fernando
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark J Myers
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David Weiner
- ∥Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Irnela Bajrovic
- #Department of Biochemistry, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lilian Q Tran
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Gary Wong
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Alexander Bello
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Gary P Kobinger
- §Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada.,∥Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Stephen C Schafer
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Maria A Croyle
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States.,⊥The University of Texas College of Natural Sciences Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States.,¶Center for Infectious Disease, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
23
|
Xylose phosphorylation functions as a molecular switch to regulate proteoglycan biosynthesis. Proc Natl Acad Sci U S A 2014; 111:15723-8. [PMID: 25331875 DOI: 10.1073/pnas.1417993111] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Most eukaryotic cells elaborate several proteoglycans critical for transmitting biochemical signals into and between cells. However, the regulation of proteoglycan biosynthesis is not completely understood. We show that the atypical secretory kinase family with sequence similarity 20, member B (Fam20B) phosphorylates the initiating xylose residue in the proteoglycan tetrasaccharide linkage region, and that this event functions as a molecular switch to regulate subsequent glycosaminoglycan assembly. Proteoglycans from FAM20B knockout cells contain a truncated tetrasaccharide linkage region consisting of a disaccharide capped with sialic acid (Siaα2-3Galβ1-4Xylβ1) that cannot be further elongated. We also show that the activity of galactosyl transferase II (GalT-II, B3GalT6), a key enzyme in the biosynthesis of the tetrasaccharide linkage region, is dramatically increased by Fam20B-dependent xylose phosphorylation. Inactivating mutations in the GALT-II gene (B3GALT6) associated with Ehlers-Danlos syndrome cause proteoglycan maturation defects similar to FAM20B deletion. Collectively, our findings suggest that GalT-II function is impaired by loss of Fam20B-dependent xylose phosphorylation and reveal a previously unappreciated mechanism for regulation of proteoglycan biosynthesis.
Collapse
|
24
|
Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat Protoc 2014; 9:2574-85. [PMID: 25299155 DOI: 10.1038/nprot.2014.173] [Citation(s) in RCA: 463] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.
Collapse
|
25
|
Choi JH, Schafer SC, Zhang L, Juelich T, Freiberg AN, Croyle MA. Modeling pre-existing immunity to adenovirus in rodents: immunological requirements for successful development of a recombinant adenovirus serotype 5-based ebola vaccine. Mol Pharm 2013; 10:3342-55. [PMID: 23915419 DOI: 10.1021/mp4001316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pre-existing immunity (PEI) to human adenovirus serotype 5 (Ad5) worldwide is the primary limitation to routine clinical use of Ad5-based vectors in immunization platforms. Using systemic and mucosal PEI induction models in rodents (mice and guinea pigs), we assessed the influence of PEI on the type of adaptive immune response elicited by an Ad5-based vaccine for Ebola with respect to immunization route. Splenocytes isolated from vaccinated animals revealed that immunization by the same route in which PEI was induced significantly compromised Ebola Zaire glycoprotein (ZGP)-specific IFN-γ+ CD8+ T cells and ZGP-specific multifunctional CD8+ T cell populations. ZGP-specific IgG1 antibody levels were also significantly reduced and a sharp increase in serum anti-Ad5 neutralizing antibody (NAB) titers were noted following immunization. These immune parameters correlated with poor survival after lethal challenge with rodent-adapted Ebola Zaire virus (ZEBOV). Although the number of IFN-γ+ CD8+ T cells was reduced in animals given the vaccine by a different route from that used for PEI induction, the multifunctional CD8+ T cell response was not compromised. Survival rates in these groups were higher than when PEI was induced by the same route as immunization. These results suggest that antigen-specific multifunctional CD8(+) T cell and Th2 type antibody responses compromised by PEI to Ad5 are required for protection from Ebola. They also illustrate that methods for induction of PEI used in preclinical studies must be carefully evaluated for successful development of novel Ad5-based vaccines.
Collapse
Affiliation(s)
- Jin Huk Choi
- Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | | | | | | | | | | |
Collapse
|
26
|
Aricescu AR, Owens RJ. Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology. Curr Opin Struct Biol 2013; 23:345-56. [PMID: 23623336 DOI: 10.1016/j.sbi.2013.04.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 01/26/2023]
Abstract
Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context.
Collapse
Affiliation(s)
- A Radu Aricescu
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | | |
Collapse
|
27
|
Aydin H, Azimi FC, Cook JD, Lee JE. A convenient and general expression platform for the production of secreted proteins from human cells. J Vis Exp 2012:4041. [PMID: 22872008 DOI: 10.3791/4041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombinant protein expression in bacteria, typically E. coli, has been the most successful strategy for milligram quantity expression of proteins. However, prokaryotic hosts are often not as appropriate for expression of human, viral or eukaryotic proteins due to toxicity of the foreign macromolecule, differences in the protein folding machinery, or due to the lack of particular co- or post-translational modifications in bacteria. Expression systems based on yeast (P. pastoris or S. cerevisiae) (1,2), baculovirus-infected insect (S. frugiperda or T. ni) cells (3), and cell-free in vitro translation systems (2,4) have been successfully used to produce mammalian proteins. Intuitively, the best match is to use a mammalian host to ensure the production of recombinant proteins that contain the proper post-translational modifications. A number of mammalian cell lines (Human Embryonic Kidney (HEK) 293, CV-1 cells in Origin carrying the SV40 larget T-antigen (COS), Chinese Hamster Ovary (CHO), and others) have been successfully utilized to overexpress milligram quantities of a number of human proteins (5-9). However, the advantages of using mammalian cells are often countered by higher costs, requirement of specialized laboratory equipment, lower protein yields, and lengthy times to develop stable expression cell lines. Increasing yield and producing proteins faster, while keeping costs low, are major factors for many academic and commercial laboratories. Here, we describe a time- and cost-efficient, two-part procedure for the expression of secreted human proteins from adherent HEK 293T cells. This system is capable of producing microgram to milligram quantities of functional protein for structural, biophysical and biochemical studies. The first part, multiple constructs of the gene of interest are produced in parallel and transiently transfected into adherent HEK 293T cells in small scale. The detection and analysis of recombinant protein secreted into the cell culture medium is performed by western blot analysis using commercially available antibodies directed against a vector-encoded protein purification tag. Subsequently, suitable constructs for large-scale protein production are transiently transfected using polyethyleneimine (PEI) in 10-layer cell factories. Proteins secreted into litre-volumes of conditioned medium are concentrated into manageable amounts using tangential flow filtration, followed by purification by anti-HA affinity chromatography. The utility of this platform is proven by its ability to express milligram quantities of cytokines, cytokine receptors, cell surface receptors, intrinsic restriction factors, and viral glycoproteins. This method was also successfully used in the structural determination of the trimeric ebolavirus glycoprotein (5,10). In conclusion, this platform offers ease of use, speed and scalability while maximizing protein quality and functionality. Moreover, no additional equipment, other than a standard humidified CO2 incubator, is required. This procedure may be rapidly expanded to systems of greater complexity, such as co-expression of protein complexes, antigens and antibodies, production of virus-like particles for vaccines, or production of adenoviruses or lentiviruses for transduction of difficult cell lines.
Collapse
Affiliation(s)
- Halil Aydin
- Department of Laboratory Medicine and Pathobiology, University of Toronto
| | | | | | | |
Collapse
|
28
|
Batra J, Robinson J, Soares AS, Fields AP, Radisky DC, Radisky ES. Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure. J Biol Chem 2012; 287:15935-46. [PMID: 22427646 DOI: 10.1074/jbc.m112.341156] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinase 10 (MMP-10, stromelysin-2) is a secreted metalloproteinase with functions in skeletal development, wound healing, and vascular remodeling; its overexpression is also implicated in lung tumorigenesis and tumor progression. To understand the regulation of MMP-10 by tissue inhibitors of metalloproteinases (TIMPs), we have assessed equilibrium inhibition constants (K(i)) of putative physiological inhibitors TIMP-1 and TIMP-2 for the active catalytic domain of human MMP-10 (MMP-10cd) using multiple kinetic approaches. We find that TIMP-1 inhibits the MMP-10cd with a K(i) of 1.1 × 10(-9) M; this interaction is 10-fold weaker than the inhibition of the similar MMP-3 (stromelysin-1) catalytic domain (MMP-3cd) by TIMP-1. TIMP-2 inhibits the MMP-10cd with a K(i) of 5.8 × 10(-9) M, which is again 10-fold weaker than the inhibition of MMP-3cd by this inhibitor (K(i) = 5.5 × 10(-10) M). We solved the x-ray crystal structure of TIMP-1 bound to the MMP-10cd at 1.9 Å resolution; the structure was solved by molecular replacement and refined with an R-factor of 0.215 (R(free) = 0.266). Comparing our structure of MMP-10cd·TIMP-1 with the previously solved structure of MMP-3cd·TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at the binding interface that provide insight into the differential binding of stromelysin family members to TIMP-1. This structural information may ultimately assist in the design of more selective TIMP-based inhibitors tailored for specificity toward individual members of the stromelysin family, with potential therapeutic applications.
Collapse
Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, USA
| | | | | | | | | | | |
Collapse
|
29
|
Overexpressing human membrane proteins in stably transfected and clonal human embryonic kidney 293S cells. Nat Protoc 2012; 7:453-66. [PMID: 22322218 DOI: 10.1038/nprot.2011.453] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
X-ray crystal structures of human membrane proteins, although potentially of extremely great impact, are highly underrepresented relative to those of prokaryotic membrane proteins. One key reason for this is that human membrane proteins can be difficult to express at a level, and at a quality, suitable for structural studies. This protocol describes the methods that we use to overexpress human membrane proteins from clonal human embryonic kidney 293 (HEK293S) cells lacking N-acetylglucosaminyltransferase I (GnTI(-)), and was recently used in our 2.1-Å X-ray crystal structure determination of human RhCG. Upon identification of highly expressing cell lines, suspension cell cultures are scaled up in a facile manner either using spinner flasks or cellbag bioreactors, resulting in a final purified yield of ∼0.5 mg of membrane protein per liter of medium. The protocol described here is reliable and cost effective, can be used to express proteins that would otherwise be toxic to mammalian cells and can be completed in 8-10 weeks.
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Choi JH, Schafer SC, Zhang L, Kobinger GP, Juelich T, Freiberg AN, Croyle MA. A single sublingual dose of an adenovirus-based vaccine protects against lethal Ebola challenge in mice and guinea pigs. Mol Pharm 2011; 9:156-67. [PMID: 22149096 DOI: 10.1021/mp200392g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Sublingual (SL) delivery, a noninvasive immunization method that bypasses the intestinal tract for direct entry into the circulation, was evaluated with an adenovirus (Ad5)-based vaccine for Ebola. Mice and guinea pigs were immunized via the intramuscular (IM), nasal (IN), oral (PO) and SL routes. SL immunization elicited strong transgene expression in and attracted CD11c(+) antigen presenting cells to the mucosa. A SL dose of 1 × 10⁸ infectious particles induced Ebola Zaire glycoprotein (ZGP)-specific IFN-γ⁺ T cells in spleen, bronchoalveolar lavage, mesenteric lymph nodes and submandibular lymph nodes (SMLN) of naive mice in a manner similar to the same dose given IN. Ex vivo CFSE and in vivo cytotoxic T lymphocyte (CTL) assays confirmed that SL immunization elicits a notable population of effector memory CD8+ T cells and strong CTL responses in spleen and SMLN. SL immunization induced significant ZGP-specific Th1 and Th2 type responses unaffected by pre-existing immunity (PEI) that protected mice and guinea pigs from lethal challenge. SL delivery protected more mice with PEI to Ad5 than IM injection. SL immunization also reduced systemic anti-Ad5 T and B cell responses in naive mice and those with PEI, suggesting that secondary immunizations could be highly effective for both populations.
Collapse
Affiliation(s)
- Jin Huk Choi
- Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | | | | | | | | | | |
Collapse
|
32
|
|
33
|
Ebola virus glycoprotein needs an additional trigger, beyond proteolytic priming for membrane fusion. PLoS Negl Trop Dis 2011; 5:e1395. [PMID: 22102923 PMCID: PMC3216919 DOI: 10.1371/journal.pntd.0001395] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/29/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ebolavirus belongs to the family filoviridae and causes severe hemorrhagic fever in humans with 50-90% lethality. Detailed understanding of how the viruses attach to and enter new host cells is critical to development of medical interventions. The virus displays a trimeric glycoprotein (GP(1,2)) on its surface that is solely responsible for membrane attachment, virus internalization and fusion. GP(1,2) is expressed as a single peptide and is cleaved by furin in the host cells to yield two disulphide-linked fragments termed GP1 and GP2 that remain associated in a GP(1,2) trimeric, viral surface spike. After entry into host endosomes, GP(1,2) is enzymatically cleaved by endosomal cathepsins B and L, a necessary step in infection. However, the functional effects of the cleavage on the glycoprotein are unknown. PRINCIPAL FINDINGS We demonstrate by antibody binding and Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS) of glycoproteins from two different ebolaviruses that although enzymatic priming of GP(1,2) is required for fusion, the priming itself does not initiate the required conformational changes in the ectodomain of GP(1,2). Further, ELISA binding data of primed GP(1,2) to conformational antibody KZ52 suggests that the low pH inside the endosomes also does not trigger dissociation of GP1 from GP2 to effect membrane fusion. SIGNIFICANCE The results reveal that the ebolavirus GP(1,2) ectodomain remains in the prefusion conformation upon enzymatic cleavage in low pH and removal of the glycan cap. The results also suggest that an additional endosomal trigger is necessary to induce the conformational changes in GP(1,2) and effect fusion. Identification of this trigger will provide further mechanistic insights into ebolavirus infection.
Collapse
|
34
|
Affiliation(s)
- Ryan M Schmaltz
- The Department of Chemistry and Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | |
Collapse
|
35
|
Raymond C, Tom R, Perret S, Moussouami P, L’Abbé D, St-Laurent G, Durocher Y. A simplified polyethylenimine-mediated transfection process for large-scale and high-throughput applications. Methods 2011; 55:44-51. [DOI: 10.1016/j.ymeth.2011.04.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/12/2011] [Accepted: 04/15/2011] [Indexed: 12/13/2022] Open
|
36
|
Walls D, Loughran ST. Tagging recombinant proteins to enhance solubility and aid purification. Methods Mol Biol 2011; 681:151-175. [PMID: 20978965 DOI: 10.1007/978-1-60761-913-0_9] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Protein fusion technology has enormously facilitated the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags are outlined.
Collapse
Affiliation(s)
- Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
| | | |
Collapse
|
37
|
Tabata S, Nampo M, Mihara E, Tamura-Kawakami K, Fujii I, Takagi J. A rapid screening method for cell lines producing singly-tagged recombinant proteins using the "TARGET tag" system. J Proteomics 2010; 73:1777-85. [PMID: 20566373 DOI: 10.1016/j.jprot.2010.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/14/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Recombinant production of extracellular glycoproteins in stable mammalian cell lines is an ideal technique for obtaining a large quantity of high-quality proteins. In most cases, however, current methodologies do not allow for sufficiently rapid cell line development and protein purification. Here, we describe a 21-residue peptide tag (designated as TARGET tag) and its use for rapid stable cell line development and purification. The ability of the anti-tag antibody P20.1 to withstand repetitive regeneration cycles has enabled the development of a sensitive surface plasmon resonance-based screening format that requires only 20 microl of cell culture supernatants. Direct and semi-quantitative screening at the 96-well culture scale eliminated the need for a second screening, re-cloning, or sorting, thereby minimizing culture pre-production time. Using this system, "high producer" cell lines were established in less than a month, and milligram quantities of target proteins could be purified with a standardized protocol.
Collapse
Affiliation(s)
- Sanae Tabata
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | |
Collapse
|
38
|
Recent advances in the production of proteins in insect and mammalian cells for structural biology. J Struct Biol 2010; 172:55-65. [PMID: 20153433 DOI: 10.1016/j.jsb.2010.02.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/04/2010] [Accepted: 02/07/2010] [Indexed: 11/22/2022]
Abstract
The production of proteins in sufficient quantity and of appropriate quality is an essential pre-requisite for structural studies. Escherichia coli remains the dominant expression system in structural biology with nearly 90% of the structures in the Protein Data Bank (PDB) derived from proteins produced in this bacterial host. However, many mammalian and eukaryotic viral proteins require post-translation modification for proper folding and/or are part of large multimeric complexes. Therefore expression in higher eukaryotic cell lines from both invertebrate and vertebrate is required to produce these proteins. Although these systems are generally more time-consuming and expensive to use than bacteria, there have been improvements in technology that have streamlined the processes involved. For example, the use of multi-host vectors, i.e., containing promoters for not only E. coli but also mammalian and baculovirus expression in insect cells, enables target genes to be evaluated in both bacterial and higher eukaryotic hosts from a single vector. Culturing cells in micro-plate format allows screening of large numbers of vectors in parallel and is amenable to automation. The development of large-scale transient expression in mammalian cells offers a way of rapidly producing proteins with relatively high throughput. Strategies for selenomethionine-labelling (important for obtaining phase information in crystallography) and controlling glycosylation (important for reducing the chemical heterogeneity of glycoproteins) have also been reported for higher eukaryotic cell expression systems.
Collapse
|
39
|
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.
Collapse
Affiliation(s)
- Adam W Barb
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | | | | | | |
Collapse
|
40
|
Mark D, Haeberle S, Roth G, Von Stetten F, Zengerle R. Microfluidic Lab-on-a-Chip Platforms: Requirements, Characteristics and Applications. MICROFLUIDICS BASED MICROSYSTEMS 2010. [DOI: 10.1007/978-90-481-9029-4_17] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
41
|
Mark D, Haeberle S, Roth G, von Stetten F, Zengerle R. Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications. Chem Soc Rev 2010; 39:1153-82. [PMID: 20179830 DOI: 10.1039/b820557b] [Citation(s) in RCA: 765] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel Mark
- HSG-IMIT-Institut für Mikro- und Informationstechnik, Wilhelm-Schickard-Strasse 10, 78052 Villingen-Schwenningen, Germany
| | | | | | | | | |
Collapse
|
42
|
Lee JE, Fusco ML, Abelson DM, Hessell AJ, Burton DR, Saphire EO. Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1162-80. [PMID: 19923712 PMCID: PMC2777170 DOI: 10.1107/s0907444909032314] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/14/2009] [Indexed: 11/10/2022]
Abstract
The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008), Nature (London), 454, 177-182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glycoprotein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the proper sequence register was confirmed by building alternate sequences using N-linked glycan sites as anchors and secondary-structural predictions.
Collapse
Affiliation(s)
- Jeffrey E. Lee
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marnie L. Fusco
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dafna M. Abelson
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ann J. Hessell
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| |
Collapse
|
43
|
Lee JE, Saphire EO. Neutralizing ebolavirus: structural insights into the envelope glycoprotein and antibodies targeted against it. Curr Opin Struct Biol 2009; 19:408-17. [PMID: 19559599 DOI: 10.1016/j.sbi.2009.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 04/30/2009] [Accepted: 05/15/2009] [Indexed: 11/30/2022]
Abstract
The ebolavirus (EBOV) envelope glycoprotein (GP) is solely responsible for viral attachment to, fusion with, and entry of new host cells, and consequently is a major target of vaccine design efforts. Recently determined crystal structures of key antibodies in complex with their EBOV epitopes have provided insights into the molecular architecture of GP and defined likely hotspots for viral neutralization. In this review, we discuss the structural basis for antibody-mediated neutralization of ebolavirus and its implications for novel therapeutic or vaccine strategies.
Collapse
Affiliation(s)
- Jeffrey E Lee
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | |
Collapse
|