1
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Bork I, Dombrowsky CS, Bitsch S, Happel D, Geyer FK, Avrutina O, Kolmar H. Tailor-Made Bioactive Papers by Site-Specific and Orthogonal Covalent Immobilization of Proteins. Biomacromolecules 2024. [PMID: 39007485 DOI: 10.1021/acs.biomac.4c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
A strategy for the bioorthogonal immobilization of proteins onto commercially available filter paper is presented. Recently, a two-step approach has been described that relies on covalent immobilization of a linker molecule to paper, followed by enzyme-mediated conjugation of a protein of interest containing an enzyme-recognition tag. Here, this strategy was expanded by evaluating four different chemical and chemoenzymatic reactions and investigating paper loading efficiency and orthogonality. Enhanced green fluorescent protein (EGFP) was used as a model protein to allow quantification of protein loading via fluorescence imaging. Two approaches were identified that showed significantly increased loading efficiencies compared with the previously applied conjugation strategy. Additionally, all four methods were proven orthogonal to each other, allowing simultaneous immobilization of a mixture of proteins to a premodified assembly of two paper sheets.
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Affiliation(s)
- Ingo Bork
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Carolin S Dombrowsky
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Felix K Geyer
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Olga Avrutina
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
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2
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Bondarchuk T, Vaskiv D, Zhuravel E, Shyshlyk O, Hrynyshyn Y, Nedialko O, Pokholenko O, Pohribna A, Kuchuk O, Brovarets V, Zozulya S. Synthetic Amine Linkers for Efficient Sortagging. Bioconjug Chem 2024. [PMID: 38994647 DOI: 10.1021/acs.bioconjchem.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Enzymatic site-specific bioconjugation techniques, in particular sortase-mediated ligation, are increasingly used to generate conjugated proteins for a wide array of applications. Extension of the utility and practicality of sortagging for diverse purposes is critically dependent on further improvement of the efficiency of sortagging reactions with a wider structural variety of substrates. We present a comprehensive comparative mass spectrometry screening study of synthetic nonpeptidic incoming amine nucleophile substrates of Staphylococcus aureus Sortase A enzyme. We have identified the optimal structural motifs among the chemically diverse set of 452 model primary and secondary amine-containing sortagging substrates, and we demonstrate the utility of representative amine linkers for efficient C-terminal biotinylation of nanobodies.
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Affiliation(s)
- Tetiana Bondarchuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Diana Vaskiv
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Elena Zhuravel
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Oleh Shyshlyk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, Academician Kukhar Street 1, Kyiv 02094, Ukraine
| | - Yevhenii Hrynyshyn
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Oleksandr Nedialko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Oleksandr Pokholenko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01033, Ukraine
| | - Alla Pohribna
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Olga Kuchuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Volodymyr Brovarets
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, Academician Kukhar Street 1, Kyiv 02094, Ukraine
| | - Sergey Zozulya
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
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3
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Li P, Li H. A Handle-Free, All-Protein-Based Optical Tweezers Method to Probe Protein Folding-Unfolding Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:13721-13727. [PMID: 38899455 DOI: 10.1021/acs.langmuir.4c01711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Optical tweezers (OT) have evolved into powerful single molecule force spectroscopy tools to investigate protein folding-unfolding dynamics. To stretch a protein of interest using OT, the protein must be flanked with two double stranded DNA (dsDNA) handles. However, coupling dsDNA handles to the protein is often of low yield, representing a bottleneck in OT experiments. Here, we report a handle-free, all-protein-based OT method for investigating protein folding/unfolding dynamics. In this new method, we employed disordered elastin-like polypeptides (ELPs) as a molecular linker and the mechanically stable cohesin-dockerin (Coh-Doc) pair as the prey-bait system to enable the efficient capture and stretching of individual protein molecules. This novel approach was validated by using model proteins NuG2 and RTX-v, yielding experimental results comparable to those obtained by using the dsDNA handle approach. This new method provides a streamlined and efficient OT approach to investigate the folding-unfolding dynamics of proteins at the single molecule level, thus expanding the toolbox of OT-based single molecule force spectroscopy.
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Affiliation(s)
- Peiyun Li
- Department of ChemistryUniversity of British ColumbiaVancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of ChemistryUniversity of British ColumbiaVancouver, BC V6T 1Z1, Canada
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4
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Cui Z, Ayva CE, Liew YJ, Guo Z, Mutschler R, Dreier B, Fiorito MM, Walden P, Howard CB, Ely F, Plückthun A, Pretorius C, Ungerer JPJ, Buckle AM, Alexandrov K. mRNA Display Pipeline for Protein Biosensor Construction. ACS Sens 2024; 9:2846-2857. [PMID: 38807313 PMCID: PMC11218749 DOI: 10.1021/acssensors.3c02471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Despite the significant potential of protein biosensors, their construction remains a trial-and-error process. The most obvious approach for addressing this is to utilize modular biosensor architectures where specificity-conferring modalities can be readily generated to recognize new targets. Toward this goal, we established a workflow that uses mRNA display-based selection of hyper-stable monobody domains for the target of choice or ribosome display to select equally stable DARPins. These binders were integrated into a two-component allosteric biosensor architecture based on a calmodulin-reporter chimera. This workflow was tested by developing biosensors for liver toxicity markers such as cytosolic aspartate aminotransferase, mitochondrial aspartate aminotransferase, and alanine aminotransferase 1. We demonstrate that our pipeline consistently produced >103 unique binders for each target within a week. Our analysis revealed that the affinity of the binders for their targets was not a direct predictor of the binder's performance in a biosensor context. The interactions between the binding domains and the reporter module affect the biosensor activity and the dynamic range. We conclude that following binding domain selection, the multiplexed biosensor assembly and prototyping appear to be the most promising approach for identifying biosensors with the desired properties.
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Affiliation(s)
- Zhenling Cui
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Cagla Ergun Ayva
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Yi Jin Liew
- CSIRO
Health & Biosecurity, Westmead, New South Wales 2145,Australia
| | - Zhong Guo
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Roxane Mutschler
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Birgit Dreier
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Maria M Fiorito
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
| | - Christopher B Howard
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Andreas Plückthun
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Carel Pretorius
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacobus PJ Ungerer
- Department
of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty
of Health and Behavioural Sciences, The
University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Kirill Alexandrov
- ARC
Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre
for Agriculture and the Bioeconomy, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
- School
of Biology and Environmental Science, Queensland
University of Technology, Brisbane, Queensland 4001, Australia
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5
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Lokanathan Balaji S, De Bragança S, Balaguer-Pérez F, Northall S, Wilkinson OJ, Aicart-Ramos C, Seetaloo N, Sobott F, Moreno-Herrero F, Dillingham MS. DNA binding and bridging by human CtIP in the healthy and diseased states. Nucleic Acids Res 2024:gkae538. [PMID: 38922686 DOI: 10.1093/nar/gkae538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The human DNA repair factor CtIP helps to initiate the resection of double-stranded DNA breaks for repair by homologous recombination, in part through its ability to bind and bridge DNA molecules. However, CtIP is a natively disordered protein that bears no apparent similarity to other DNA-binding proteins and so the structural basis for these activities remains unclear. In this work, we have used bulk DNA binding, single molecule tracking, and DNA bridging assays to study wild-type and variant CtIP proteins to better define the DNA binding domains and the effects of mutations associated with inherited human disease. Our work identifies a monomeric DNA-binding domain in the C-terminal region of CtIP. CtIP binds non-specifically to DNA and can diffuse over thousands of nucleotides. CtIP-mediated bridging of distant DNA segments is observed in single-molecule magnetic tweezers experiments. However, we show that binding alone is insufficient for DNA bridging, which also requires tetramerization via the N-terminal domain. Variant CtIP proteins associated with Seckel and Jawad syndromes display impaired DNA binding and bridging activities. The significance of these findings in the context of facilitating DNA break repair is discussed.
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Affiliation(s)
- Shreya Lokanathan Balaji
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Francisco Balaguer-Pérez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Sarah Northall
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Oliver John Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Neeleema Seetaloo
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Mark Simon Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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6
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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7
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Makrydaki E, Donini R, Krueger A, Royle K, Moya Ramirez I, Kuntz DA, Rose DR, Haslam SM, Polizzi KM, Kontoravdi C. Immobilized enzyme cascade for targeted glycosylation. Nat Chem Biol 2024; 20:732-741. [PMID: 38321209 PMCID: PMC11142912 DOI: 10.1038/s41589-023-01539-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/21/2023] [Indexed: 02/08/2024]
Abstract
Glycosylation is a critical post-translational protein modification that affects folding, half-life and functionality. Glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. We describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro enabled by immobilized enzymes produced with a one-step immobilization/purification method. We reconstruct a reaction cascade mimicking a glycosylation pathway where promiscuity naturally exists to humanize a range of proteins derived from different cellular systems, yielding near-homogeneous glycoforms. Immobilized β-1,4-galactosyltransferase is used to enhance the galactosylation profile of three IgGs, yielding 80.2-96.3% terminal galactosylation. Enzyme recycling is demonstrated for a reaction time greater than 80 h. The platform is easy to implement, modular and reusable and can therefore produce homogeneous glycan structures derived from various hosts for functional and clinical evaluation.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Roberto Donini
- Department of Life Sciences, Imperial College London, London, UK
| | - Anja Krueger
- Department of Life Sciences, Imperial College London, London, UK
| | - Kate Royle
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ignacio Moya Ramirez
- Department of Chemical Engineering, Imperial College London, London, UK
- Departamento de Ingeniería Química, Universidad de Granada, Granada, Spain
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David R Rose
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK.
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London, UK.
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8
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Kawashima T, Nakamura M, Sakono M. A one-process production of completely biotinylated proteins in a T7 expression system. Biotechnol Appl Biochem 2024. [PMID: 38770738 DOI: 10.1002/bab.2598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
Streptavidin is a tetrameric protein with high specificity and affinity for biotin. The interaction between avidin and biotin has become a valuable tool in nanotechnology. In recent years, the site-specific biotin modification of proteins using biotin ligases, such as BirA, has attracted attention. This study established an in vivo method for achieving the complete biotinylation of target proteins using a single plasmid co-expressing BirA and its target proteins. Specifically, a biotin-modified protein was produced in Escherichia coli strain BL21(DE3) using a single plasmid containing genes encoding both BirA and a protein fused to BirA's substrate sequence, Avitag. This approach simplifies the production of biotinylated proteins in E. coli and allows the creation of various biotinylated protein types through gene replacement. Furthermore, the biotin modification rate of the obtained target protein could be evaluated using Native-PAGE without performing complicated isolation operations of biotinylated proteins. In Native-PAGE, biotin-modified proteins and unmodified proteins were confirmed as clearly different bands, and it was possible to easily derive the modification rate from the respective band intensities.
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Affiliation(s)
- Takuma Kawashima
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Mitsuki Nakamura
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Masafumi Sakono
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
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9
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Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
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Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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10
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Shen J, Wu W, Wang K, Wu J, Liu B, Li C, Gong Z, Hong X, Fang H, Zhang X, Xu X. Chloroflexus aurantiacus acetyl-CoA carboxylase evolves fused biotin carboxylase and biotin carboxyl carrier protein to complete carboxylation activity. mBio 2024; 15:e0341423. [PMID: 38572988 PMCID: PMC11077971 DOI: 10.1128/mbio.03414-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Acetyl-CoA carboxylases (ACCs) convert acetyl-CoA to malonyl-CoA, a key step in fatty acid biosynthesis and autotrophic carbon fixation pathways. Three functionally distinct components, biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT), are either separated or partially fused in different combinations, forming heteromeric ACCs. However, an ACC with fused BC-BCCP and separate CT has not been identified, leaving its catalytic mechanism unclear. Here, we identify two BC isoforms (BC1 and BC2) from Chloroflexus aurantiacus, a filamentous anoxygenic phototroph that employs 3-hydroxypropionate (3-HP) bi-cycle rather than Calvin cycle for autotrophic carbon fixation. We reveal that BC1 possesses fused BC and BCCP domains, where BCCP could be biotinylated by E. coli or C. aurantiacus BirA on Lys553 residue. Crystal structures of BC1 and BC2 at 3.2 Å and 3.0 Å resolutions, respectively, further reveal a tetramer of two BC1-BC homodimers, and a BC2 homodimer, all exhibiting similar BC architectures. The two BC1-BC homodimers are connected by an eight-stranded β-barrel of the partially resolved BCCP domain. Disruption of β-barrel results in dissociation of the tetramer into dimers in solution and decreased biotin carboxylase activity. Biotinylation of the BCCP domain further promotes BC1 and CTβ-CTα interactions to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-HP via co-expression with a recombinant malonyl-CoA reductase in E. coli cells. This study revealed a heteromeric ACC that evolves fused BC-BCCP but separate CTα and CTβ to complete ACC activity.IMPORTANCEAcetyl-CoA carboxylase (ACC) catalyzes the rate-limiting step in fatty acid biosynthesis and autotrophic carbon fixation pathways across a wide range of organisms, making them attractive targets for drug discovery against various infections and diseases. Although structural studies on homomeric ACCs, which consist of a single protein with three subunits, have revealed the "swing domain model" where the biotin carboxyl carrier protein (BCCP) domain translocates between biotin carboxylase (BC) and carboxyltransferase (CT) active sites to facilitate the reaction, our understanding of the subunit composition and catalytic mechanism in heteromeric ACCs remains limited. Here, we identify a novel ACC from an ancient anoxygenic photosynthetic bacterium Chloroflexus aurantiacus, it evolves fused BC and BCCP domain, but separate CT components to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-hydroxypropionate (3-HP) via co-expression with recombinant malonyl-CoA reductase in E. coli cells. These findings expand the diversity and molecular evolution of heteromeric ACCs and provide a structural basis for potential applications in 3-HP biosynthesis.
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Affiliation(s)
- Jiejie Shen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Wenping Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Kangle Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Jingyi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Bing Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Chunyang Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Zijun Gong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Xin Hong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Han Fang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Xingwei Zhang
- The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Xiaoling Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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11
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Agdanowski MP, Castells-Graells R, Sawaya MR, Cascio D, Yeates TO, Arbing MA. X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. Acta Crystallogr F Struct Biol Commun 2024; 80:107-115. [PMID: 38767964 PMCID: PMC11134730 DOI: 10.1107/s2053230x2400414x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.
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Affiliation(s)
- Matthew P. Agdanowski
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roger Castells-Graells
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
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12
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Guo R, Dong X, Chen F, Ji T, He Q, Zhang J, Sheng Y, Liu Y, Yang S, Liang W, Song Y, Fang K, Zhang L, Hu G, Yao H. TEAD2 initiates ground-state pluripotency by mediating chromatin looping. EMBO J 2024; 43:1965-1989. [PMID: 38605224 PMCID: PMC11099042 DOI: 10.1038/s44318-024-00086-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 02/26/2024] [Accepted: 03/03/2024] [Indexed: 04/13/2024] Open
Abstract
The transition of mouse embryonic stem cells (ESCs) between serum/LIF and 2i(MEK and GSK3 kinase inhibitor)/LIF culture conditions serves as a valuable model for exploring the mechanisms underlying ground and confused pluripotent states. Regulatory networks comprising core and ancillary pluripotency factors drive the gene expression programs defining stable naïve pluripotency. In our study, we systematically screened factors essential for ESC pluripotency, identifying TEAD2 as an ancillary factor maintaining ground-state pluripotency in 2i/LIF ESCs and facilitating the transition from serum/LIF to 2i/LIF ESCs. TEAD2 exhibits increased binding to chromatin in 2i/LIF ESCs, targeting active chromatin regions to regulate the expression of 2i-specific genes. In addition, TEAD2 facilitates the expression of 2i-specific genes by mediating enhancer-promoter interactions during the serum/LIF to 2i/LIF transition. Notably, deletion of Tead2 results in reduction of a specific set of enhancer-promoter interactions without significantly affecting binding of chromatin architecture proteins, CCCTC-binding factor (CTCF), and Yin Yang 1 (YY1). In summary, our findings highlight a novel prominent role of TEAD2 in orchestrating higher-order chromatin structures of 2i-specific genes to sustain ground-state pluripotency.
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Affiliation(s)
- Rong Guo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaotao Dong
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Basic Medical Science, Henan University, Kaifeng, China
| | - Feng Chen
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Tianrong Ji
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiannan He
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Zhang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yingliang Sheng
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yanjiang Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shengxiong Yang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Weifang Liang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yawei Song
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ke Fang
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Gongcheng Hu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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13
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Garcia-Calvo E, García-García A, Rodríguez S, Martín R, García T. Exploring Gluten Assessment in Marketed Products through a Sandwich ELISA Methodology Based on Novel Recombinant Antibodies. Foods 2024; 13:1341. [PMID: 38731712 PMCID: PMC11083168 DOI: 10.3390/foods13091341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
This study presents the development of a sandwich ELISA method for gluten detection in foods, using recombinant Fab antibody fragments against gliadin. The Fabs were chemically biotinylated and immobilized on streptavidin-coated plates as capture antibodies, while alkaline phosphatase-conjugated Fabs were used as detection antibodies. Four different gliadin-binding Fabs were tested and the Fab pair Fab8E-4 and Fab-C showed the best compatibility. An indirect sandwich immunoassay, using unmodified Fab8E-4 for capture and Fab-C as the detection antibody, achieved a detection limit of 26 ng/mL of gliadin, corresponding to 10 mg/kg of gluten in foods. No cross-reactivity was observed against 60 gluten-free species commonly used in the food industry. Analysis of 50 commercial products demonstrated consistent results compared to the standard method for gluten detection. The complete lack of cross-reactivity of the developed immunoassay with oat products potentially provides an advantage over other gluten detection systems.
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Affiliation(s)
| | - Aina García-García
- Department of Nutrition and Food Sciences, School of Veterinary Sciences, Universidad Complutense de Madrid, 28040 Madrid, Spain; (E.G.-C.); (S.R.); (R.M.); (T.G.)
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14
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Lu C, Bevers J, Tyagi T, To H, Lin M, Ti S, Nakamura G, Lin W, Chen Y, Wu Y, Li H, Wu J, Wang F. AviTrap: A novel solution to achieve complete biotinylation. PLoS One 2024; 19:e0297122. [PMID: 38662671 PMCID: PMC11045115 DOI: 10.1371/journal.pone.0297122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/27/2023] [Indexed: 04/28/2024] Open
Abstract
Site specific biotinylation of AviTagged recombinant proteins using BirA enzyme is a widely used protein labeling technology. However, due to the incomplete biotinylation reactions and the lack of a purification method specific for the biotinylated proteins, it is challenging to purify the biotinylated sample when mixed with the non-biotinylated byproduct. Here, we have developed a monoclonal antibody that specifically recognizes the non-biotinylated AviTag but not the biotinylated sequence. After a ten-minute incubation with the resin that is conjugated with the antibody, the non-biotinylated AviTagged protein is trapped on the resin while the fully biotinylated material freely passes through. Therefore, our AviTrap (anti-AviTag antibody conjugated resin) provides an efficient solution for enriching biotinylated AviTagged proteins via a simple one-step purification.
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Affiliation(s)
- Cheng Lu
- Department of Protein Sciences, Genentech Inc., South San Francisco, CA, United States of America
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Jack Bevers
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Tulika Tyagi
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Hao To
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - May Lin
- Department of Protein Sciences, Genentech Inc., South San Francisco, CA, United States of America
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Shu Ti
- Department of Protein Sciences, Genentech Inc., South San Francisco, CA, United States of America
| | - Gerry Nakamura
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - WeiYu Lin
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Yongmei Chen
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Yan Wu
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Hong Li
- Department of Protein Sciences, Genentech Inc., South San Francisco, CA, United States of America
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
| | - Jiansheng Wu
- Protein Sciences, Wuxi Biologics, San Francisco, CA, United States of America
| | - Feng Wang
- Department of Protein Sciences, Genentech Inc., South San Francisco, CA, United States of America
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, United States of America
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15
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Madarati H, DeYoung V, Singh K, Sparring T, Kwong AC, Fredenburgh JC, Teney C, Koschinsky ML, Boffa MB, Weitz JI, Kretz CA. Optimization of plasma-based BioID identifies plasminogen as a ligand of ADAMTS13. Sci Rep 2024; 14:9073. [PMID: 38643218 PMCID: PMC11032339 DOI: 10.1038/s41598-024-59672-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/13/2024] [Indexed: 04/22/2024] Open
Abstract
ADAMTS13, a disintegrin and metalloprotease with a thrombospondin type 1 motif, member 13, regulates the length of Von Willebrand factor (VWF) multimers and their platelet-binding activity. ADAMTS13 is constitutively secreted as an active protease and is not inhibited by circulating protease inhibitors. Therefore, the mechanisms that regulate ADAMTS13 protease activity are unknown. We performed an unbiased proteomics screen to identify ligands of ADAMTS13 by optimizing the application of BioID to plasma. Plasma BioID identified 5 plasma proteins significantly labeled by the ADAMTS13-birA* fusion, including VWF and plasminogen. Glu-plasminogen, Lys-plasminogen, mini-plasminogen, and apo(a) bound ADAMTS13 with high affinity, whereas micro-plasminogen did not. None of the plasminogen variants or apo(a) bound to a C-terminal truncation variant of ADAMTS13 (MDTCS). The binding of plasminogen to ADAMTS13 was attenuated by tranexamic acid or ε-aminocaproic acid, and tranexamic acid protected ADAMTS13 from plasmin degradation. These data demonstrate that plasminogen is an important ligand of ADAMTS13 in plasma by binding to the C-terminus of ADAMTS13. Plasmin proteolytically degrades ADAMTS13 in a lysine-dependent manner, which may contribute to its regulation. Adapting BioID to identify protein-interaction networks in plasma provides a powerful new tool to study protease regulation in the cardiovascular system.
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Affiliation(s)
- Hasam Madarati
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Veronica DeYoung
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Kanwal Singh
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Taylor Sparring
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Andrew C Kwong
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - James C Fredenburgh
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Cherie Teney
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Marlys L Koschinsky
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
| | - Michael B Boffa
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Robarts Research Institute, The University of Western Ontario, London, ON, Canada
| | - Jeffrey I Weitz
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Colin A Kretz
- Department of Medicine, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada.
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16
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Cronan JE. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. Proteins 2024; 92:435-448. [PMID: 37997490 PMCID: PMC10932917 DOI: 10.1002/prot.26642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase- and biotin-acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin-responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl-AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl-AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity-dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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17
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Veggiani G, Sidhu SS. Generation and Selection of Synthetic Human Antibody Libraries via Phage Display. Cold Spring Harb Protoc 2024; 2024:108347. [PMID: 37295821 DOI: 10.1101/pdb.prot108347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthetic antibody libraries enable the development of antibodies that can recognize virtually any antigen, with affinity and specificity profiles that are superior to those of natural antibodies. By using highly stable and optimized frameworks, synthetic antibody libraries can be rapidly generated by precisely designing synthetic DNA, allowing absolute control over the position and chemical diversity introduced while expanding the sequence space for antigen recognition. Here, we describe a detailed protocol for the generation of highly diverse synthetic antibody phage display libraries based on a single framework, with diversity genetically incorporated by using finely designed mutagenic oligonucleotides. This general method enables the facile construction of large antibody libraries with precisely tunable features, resulting in the rapid development of recombinant antibodies for virtually any antigen.
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Affiliation(s)
- Gianluca Veggiani
- The Anvil Institute, Kitchener, Ontario N2G 1H6, Canada
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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18
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Merino-Cacho L, Barroso-Gomila O, Hernández-Sánchez S, Ramirez J, Mayor U, Sutherland JD, Barrio R. Biotin-Based Strategies to Explore the World of Ubiquitin and Ubiquitin-Like Modifiers. Chembiochem 2024; 25:e202300746. [PMID: 38081789 DOI: 10.1002/cbic.202300746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/07/2023] [Indexed: 01/06/2024]
Abstract
A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non-modified cellular substrates, and protease-mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin-based tools developed for this purpose (for example BioUbLs, UbL-ID, BioE3, BioID), taking advantage of the strong affinity of biotin-streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass-spectrometry-based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL-ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.
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Affiliation(s)
- Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Sandra Hernández-Sánchez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
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19
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Marini-Rapoport O, Fernández-Quintero ML, Keswani T, Zong G, Shim J, Pedersen LC, Mueller GA, Patil SU. Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies. Clin Exp Immunol 2024; 216:25-35. [PMID: 38346116 PMCID: PMC10929694 DOI: 10.1093/cei/uxae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/08/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In peanut allergy, Arachis hypogaea 2 (Ara h 2) and Arachis hypogaea 6 (Ara h 6) are two clinically relevant peanut allergens with known structural and sequence homology and demonstrated cross-reactivity. We have previously utilized X-ray crystallography and epitope binning to define the epitopes on Ara h 2. We aimed to quantitatively characterize the cross-reactivity between Ara h 2 and Ara h 6 on a molecular level using human monoclonal antibodies (mAbs) and structural characterization of allergenic epitopes. We utilized mAbs cloned from Ara h 2 positive single B cells isolated from peanut-allergic, oral immunotherapy-treated patients to quantitatively analyze cross-reactivity between recombinant Ara h 2 (rAra h 2) and Ara h 6 (rAra h 6) proteins using biolayer interferometry and indirect inhibitory ELISA. Molecular dynamics simulations assessed time-dependent motions and interactions in the antibody-antigen complexes. Three epitopes-conformational epitopes 1.1 and 3, and the sequential epitope KRELRNL/KRELMNL-are conserved between Ara h 2 and Ara h 6, while two more conformational and three sequential epitopes are not. Overall, mAb affinity was significantly lower to rAra h 6 than it was to rAra h 2. This difference in affinity was primarily due to increased dissociation of the antibodies from rAra h 6, a phenomenon explained by the higher conformational flexibility of the Ara h 6-antibody complexes in comparison to Ara h 2-antibody complexes. Our results further elucidate the cross-reactivity of peanut 2S albumins on a molecular level and support the clinical immunodominance of Ara h 2.
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Affiliation(s)
- Orlee Marini-Rapoport
- Harvard University, Cambridge, MA, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tarun Keswani
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Guangning Zong
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jane Shim
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Sarita U Patil
- Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
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20
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Cloots E, Guilbert P, Provost M, Neidhardt L, Van de Velde E, Fayazpour F, De Sutter D, Savvides SN, Eyckerman S, Janssens S. Activation of goblet-cell stress sensor IRE1β is controlled by the mucin chaperone AGR2. EMBO J 2024; 43:695-718. [PMID: 38177501 PMCID: PMC10907643 DOI: 10.1038/s44318-023-00015-y] [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: 06/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Intestinal goblet cells are secretory cells specialized in the production of mucins, and as such are challenged by the need for efficient protein folding. Goblet cells express Inositol-Requiring Enzyme-1β (IRE1β), a unique sensor in the unfolded protein response (UPR), which is part of an adaptive mechanism that regulates the demands of mucin production and secretion. However, how IRE1β activity is tuned to mucus folding load remains unknown. We identified the disulfide isomerase and mucin chaperone AGR2 as a goblet cell-specific protein that crucially regulates IRE1β-, but not IRE1α-mediated signaling. AGR2 binding to IRE1β disrupts IRE1β oligomerization, thereby blocking its downstream endonuclease activity. Depletion of endogenous AGR2 from goblet cells induces spontaneous IRE1β activation, suggesting that alterations in AGR2 availability in the endoplasmic reticulum set the threshold for IRE1β activation. We found that AGR2 mutants lacking their catalytic cysteine, or displaying the disease-associated mutation H117Y, were no longer able to dampen IRE1β activity. Collectively, these results demonstrate that AGR2 is a central chaperone regulating the goblet cell UPR by acting as a rheostat of IRE1β endonuclease activity.
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Affiliation(s)
- Eva Cloots
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Ghent University, 9052, Ghent, Belgium
| | - Phaedra Guilbert
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Ghent University, 9052, Ghent, Belgium
| | - Mathias Provost
- Unit for Structural Biology, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, 9052, Ghent, Belgium
| | - Lisa Neidhardt
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Evelien Van de Velde
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Ghent University, 9052, Ghent, Belgium
| | - Farzaneh Fayazpour
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Ghent University, 9052, Ghent, Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, VIB Center for Inflammation Research, 9052, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, 9052, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, 9052, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium
| | - Sophie Janssens
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, 9052, Ghent, Belgium.
- Department of Pediatrics and Internal Medicine, Ghent University, 9052, Ghent, Belgium.
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21
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Di Vincenzo R, Beutel J, Arnold P, Wang Y, Damm D, Tannig P, Lux A, Temchura V, Eichler J, Überla K. Oriented display of HIV-1 Env trimers by a novel coupling strategy enhances B cell activation and phagocytosis. Front Immunol 2024; 15:1344346. [PMID: 38390320 PMCID: PMC10882061 DOI: 10.3389/fimmu.2024.1344346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Conformationally stabilized Env trimers have been developed as antigens for the induction of neutralizing antibodies against HIV-1. However, the non-glycosylated immunodominant base of these soluble antigens may compete with the neutralizing antibody response. This has prompted attempts to couple Env trimers to organic or inorganic nanoparticles with the base facing towards the carrier. Such a site-directed coupling could not only occlude the base of the trimer, but also enhance B cell activation by repetitive display. Methods To explore the effect of an ordered display of HIV-1 Env on microspheres on the activation of Env-specific B cells we used Bind&Bite, a novel covalent coupling approach for conformationally sensitive antigens based on heterodimeric coiled-coil peptides. By engineering a trimeric HIV-1 Env protein with a basic 21-aa peptide (Peptide K) extension at the C-terminus, we were able to covalently biotinylate the antigen in a site-directed fashion using an acidic complementary peptide (Peptide E) bearing a reactive site and a biotin molecule. This allowed us to load our antigen onto streptavidin beads in an oriented manner. Results Microspheres coated with HIV-1 Env through our Bind&Bite system showed i) enhanced binding by conformational anti-HIV Env broadly neutralizing antibodies (bNAbs), ii) reduced binding activity by antibodies directed towards the base of Env, iii) higher Env-specific B cell activation, and iv) were taken-up more efficiently after opsonization compared to beads presenting HIV-1 Env in an undirected orientation. Discussion In comparison to site-directed biotinylation via the Avi-tag, Bind&Bite, offers greater flexibility with regard to alternative covalent protein modifications, allowing selective modification of multiple proteins via orthogonal coiled-coil peptide pairs. Thus, the Bind&Bite coupling approach via peptide K and peptide E described in this study offers a valuable tool for nanoparticle vaccine design where surface conjugation of correctly folded antigens is required.
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Affiliation(s)
- Riccardo Di Vincenzo
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jannis Beutel
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yu Wang
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dominik Damm
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pierre Tannig
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anja Lux
- Chair of Genetics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Vladimir Temchura
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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22
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Lee D, Min D. Single-molecule tethering methods for membrane proteins. Methods Enzymol 2024; 694:263-284. [PMID: 38492954 DOI: 10.1016/bs.mie.2023.12.013] [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: 03/18/2024]
Abstract
Molecular tethering of a single membrane protein between the glass surface and a magnetic bead is essential for studying the structural dynamics of membrane proteins using magnetic tweezers. However, the force-induced bond breakage of the widely-used digoxigenin-antidigoxigenin tether complex has imposed limitations on its stable observation. In this chapter, we describe the procedures of constructing highly stable single-molecule tethering methods for membrane proteins. These methods are established using dibenzocyclooctyne click chemistry, traptavidin-biotin binding, SpyCatcher-SpyTag conjugation, and SnoopCatcher-SnoopTag conjugation. The molecular tethering approaches allow for more stable observation of structural transitions in membrane proteins under force.
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Affiliation(s)
- Daehyo Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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23
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Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen T, Li J, Lister R. A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Res 2024; 52:474-491. [PMID: 38000387 PMCID: PMC10783489 DOI: 10.1093/nar/gkad1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct 'effector' chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and, by testing it against existing multi-effector targeting systems, demonstrate its comparable efficacy. Furthermore, we demonstrate the importance of the spatial ordering of the recruited effectors for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.
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Affiliation(s)
- Tessa Swain
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Saskia Freytag
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ji Kevin Li
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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24
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Stevens TA, Tomaleri GP, Hazu M, Wei S, Nguyen VN, DeKalb C, Voorhees RM, Pleiner T. A nanobody-based strategy for rapid and scalable purification of human protein complexes. Nat Protoc 2024; 19:127-158. [PMID: 37974029 DOI: 10.1038/s41596-023-00904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/18/2023] [Indexed: 11/19/2023]
Abstract
The isolation of proteins in high yield and purity is a major bottleneck for the analysis of their three-dimensional structure, function and interactome. Here, we present a streamlined workflow for the rapid production of proteins or protein complexes using lentiviral transduction of human suspension cells, combined with highly specific nanobody-mediated purification and proteolytic elution. Application of the method requires prior generation of a plasmid coding for a protein of interest (POI) fused to an N- or C-terminal GFP or ALFA peptide tag using a lentiviral plasmid toolkit we have designed. The plasmid is then used to generate human suspension cell lines stably expressing the tagged fusion protein by lentiviral transduction. By leveraging the picomolar affinity of the GFP and ALFA nanobodies for their respective tags, the POI can be specifically captured from the resulting cell lysate even when expressed at low levels and under a variety of conditions, including detergents and mild denaturants. Finally, rapid and specific elution of the POI (in its tagged or untagged form) under native conditions is achieved within minutes at 4 °C, using the engineered SUMO protease SENPEuB. We demonstrate the wide applicability of the method by purifying multiple challenging soluble and membrane protein complexes to high purity from human cells. Our strategy is also directly compatible with many widely used GFP-expression plasmids, cell lines and transgenic model organisms. Finally, our method is faster than alternative approaches, requiring only 8 d from plasmid to purified protein, and results in substantially improved yields and purity.
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Affiliation(s)
- Taylor Anthony Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sophia Wei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Charlene DeKalb
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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25
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Ghosh A, Yang C, Lloyd K, Meijers R. High-Throughput Protein Expression Screening of Cell-Surface Protein Ectodomains. Methods Mol Biol 2024; 2810:301-316. [PMID: 38926287 DOI: 10.1007/978-1-0716-3878-1_19] [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: 06/28/2024]
Abstract
Cell-surface receptors can be difficult to express and purify for structural and biochemical studies due to low expression levels, misfolding, aggregation, and instability. Cell-surface receptor ectodomains are more amenable to large-scale production, but this requires designing and testing various truncation constructs. However, since each protein is unique, testing these constructs individually for many targets is a time-consuming process. In this context, we present a high-throughput ELISA fluorescence approach that allows the rapid assessment of numerous recombinant constructs simultaneously. Cell-surface ectodomains are expressed in small scale, enzymatically biotinylated, and detected using a C-terminal His-tag. As an example, we tested the expression of truncation constructs for the neurexin, neuroligin, and latrophilin families and show that the small-scale ELISA allowed us to prioritize well-expressing construct for large-scale production. By employing this method, one can efficiently detect clones with low expression levels, streamlining the process and saving valuable time in identifying optimal candidates for further study.
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Affiliation(s)
- Anita Ghosh
- Institute for Protein Innovation (IPI), Boston, MA, USA
| | - Chang Yang
- Institute for Protein Innovation (IPI), Boston, MA, USA
| | - Kenneth Lloyd
- Institute for Protein Innovation (IPI), Boston, MA, USA
| | - Rob Meijers
- Institute for Protein Innovation (IPI), Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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26
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Immink LE, Guthmiller JJ. Isolation of Rare Antigen-Specific Memory B Cells via Antigen Tetramers. Methods Mol Biol 2024; 2826:95-115. [PMID: 39017888 DOI: 10.1007/978-1-0716-3950-4_8] [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: 07/18/2024]
Abstract
Immunological memory, which sets the foundation for the adaptive immune response, plays a key role in disease protection and prevention. Obtaining a deeper understanding of the mechanisms underlying this phenomenon can aide in research aimed to improve vaccines and therapies. Memory B cells (MBCs) are a fundamental component of immunological memory but can exist in rare populations that prove challenging to study. By combining fluorescent antigen tetramers with multiple enrichment processes, a highly streamlined method for identifying and sorting antigen-specific MBCs from human blood and lymphoid tissues can be achieved. With the output of this process being viable cells, there is a multitude of downstream operations that can be used in conjunction with the antigen-specific cell sorting outlined in this chapter. Single-cell RNA-sequencing paired with B cell repertoire sequencing, which can be linked to distinct antigens in a high-throughput fashion, is a downstream application widely used in disease and vaccination research. Incorporation of this protocol can lead to a variety of applications and a diversity of outcomes aiding in a deeper understanding of how immunological memory not only forms but is recalled and impacted by infection and vaccination.
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Affiliation(s)
- Lauren E Immink
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jenna J Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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27
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Kang M, Wang Z, Ge X. One-step production of fully biotinylated and glycosylated human Fc gamma receptors. Biotechnol Prog 2024; 40:e3392. [PMID: 37734055 PMCID: PMC10922510 DOI: 10.1002/btpr.3392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Initiating and regulating humoral immunity, Fc gamma receptors (FcγRs) have been identified both as therapeutics and as drug targets, and thus production of biologically active FcγRs is highly demanded for biopharmaceutical development. Focusing on low-affinity FcγRs IIA (131H/R allotypes), IIB, and IIIA (176F/V), this study used human 293-F cells to achieve correct post-translational modifications (PTMs) including biotinylation, N-glycosylation, and disulfides. Approaches involving co-expression of FcγR-AviTag and Escherichia coli biotin ligase BirA, endoplasmic reticulum retention, stable and transient transfections, and optimization of transgene ratio were investigated. Protein electrophoresis under reducing and non-reducing conditions, enzymatic deglycosylation, streptavidin pull-down assays, and binding kinetic analysis collectively indicated that the produced FcγR ectodomains were fully biotinylated, N-glycosylated, had formed disulfide bond, and exhibited expected binding affinities toward IgG1 trastuzumab and its Fc mutants. A clear trade-off between production yield and PTM quality was also observed. Achieving multiple types of PTMs completely by one-step cell culture should have applications for the production of a variety of complex proteins of biomedical importance.
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Affiliation(s)
- Minhyo Kang
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Present address: Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC Canada
| | - Zening Wang
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, TX, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, CA, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, TX, USA
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28
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Ma X, Leon B, Ornelas E, Dovala D, Tandeske L, Luu C, Pardee G, Widger S, Solomon JM, Beckwith REJ, Moser H, Clifton MC, Wartchow CA. Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon. Sci Rep 2023; 13:22088. [PMID: 38086859 PMCID: PMC10716131 DOI: 10.1038/s41598-023-48606-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
The design of cereblon-binding molecular glues (MGs) that selectively recruit a desired protein while excluding teratogenic SALL4 is an area of significant interest when designing therapeutic agents. Previous studies show that SALL4 is degraded in the presence of IKZF1 degraders pomalidomide, and to a lesser extent by CC-220. To expand our understanding of the molecular basis for the interaction of SALL4 with cereblon, we performed biophysical and structural studies demonstrating that SALL4 zinc finger domains one and two (ZF1-2) interact with cereblon (CRBN) in a unique manner. ZF1 interacts with the N-terminal domain of cereblon and ZF2 binds as expected in the C-terminal IMiD-binding domain. Both ZF1 and ZF2 contribute to the potency of the interaction of ZF1-2 with CRBN:MG complexes and the affinities of SALL4 ZF1-2 for the cereblon:CC-220 complex are less potent than for the corresponding pomalidomide complex. Structural analysis provides a rationale for understanding the reduced affinity of SALL4 for cereblon in the presence of CC-220, which engages both ZF1 and ZF2. These studies further our understanding of the molecular glue-mediated interactions of zinc finger-based proteins with cereblon and may provide structural tools for the prospective design of compounds with reduced binding and degradation of SALL4.
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Affiliation(s)
- Xiaolei Ma
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Barbara Leon
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Elizabeth Ornelas
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Dustin Dovala
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Laura Tandeske
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Catherine Luu
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Gwynn Pardee
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Stephania Widger
- Discovery Sciences, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Jonathan M Solomon
- Discovery Sciences, Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Rohan E J Beckwith
- Discovery Sciences, Novartis Biomedical Research, Cambridge, MA, 02139, USA
| | - Heinz Moser
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Matthew C Clifton
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA
| | - Charles A Wartchow
- Global Discovery Chemistry, Novartis Biomedical Research, Emeryville, CA, 94608, USA.
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29
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Mahata D, Mukherjee D, Biswas D, Basak S, Basak AJ, Jamir I, Pandey N, Khatoon H, Samanta D, Basak A, Mukherjee G. Activation and differentiation of cognate T cells by a dextran-based antigen-presenting system for cancer immunotherapy. Eur J Immunol 2023; 53:e2350528. [PMID: 37698527 DOI: 10.1002/eji.202350528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/14/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
Immunotherapeutic modulation of antigen-specific T-cell responses instead of the whole repertoire helps avoid immune-related adverse events. We have developed an artificial antigen-presenting system (aAPS) where multiple copies of a multimeric peptide-MHC class I complex presenting a murine class I MHC restricted ovalbumin-derived peptide (signal 1), along with a costimulatory ligand (signal 2) are chemically conjugated to a dextran backbone. Cognate naive CD8+ T cells, when treated with this aAPS underwent significant expansion and showed an activated phenotype. Furthermore, elevated expression of effector cytokines led to the differentiation of these cells to cytotoxic T lymphocytes which resulted in target cell lysis, indicative of the functional efficacy of the aAPS. CD8+ T cells with decreased proliferative potential due to repeated antigenic stimulation could also be re-expanded by the developed aAPS. Thus, the developed aAPS warrants further engineering for future application as a rapidly customizable personalized immunotherapeutic agent, incorporating patient-specific MHC-restricted tumor antigens and different costimulatory signals to modulate both naive and antigen-experienced but exhausted tumor-specific T cells in cancer.
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Affiliation(s)
- Dhrubajyoti Mahata
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Debangshu Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Debarati Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Shyam Basak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Aditya Jyoti Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Imlilong Jamir
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Nidhi Pandey
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Huma Khatoon
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Amit Basak
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Gayatri Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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30
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Menzies SK, Arinto-Garcia R, Amorim FG, Cardoso IA, Abada C, Crasset T, Durbesson F, Edge RJ, El-Kazzi P, Hall S, Redureau D, Stenner R, Boldrini-França J, Sun H, Roldão A, Alves PM, Harrison RA, Vincentelli R, Berger I, Quinton L, Casewell NR, Schaffitzel C. ADDovenom: Thermostable Protein-Based ADDomer Nanoparticles as New Therapeutics for Snakebite Envenoming. Toxins (Basel) 2023; 15:673. [PMID: 38133177 PMCID: PMC10747859 DOI: 10.3390/toxins15120673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Snakebite envenoming can be a life-threatening medical emergency that requires prompt medical intervention to neutralise the effects of venom toxins. Each year up to 138,000 people die from snakebites and threefold more victims suffer life-altering disabilities. The current treatment of snakebite relies solely on antivenom-polyclonal antibodies isolated from the plasma of hyperimmunised animals-which is associated with numerous deficiencies. The ADDovenom project seeks to deliver a novel snakebite therapy, through the use of an innovative protein-based scaffold as a next-generation antivenom. The ADDomer is a megadalton-sized, thermostable synthetic nanoparticle derived from the adenovirus penton base protein; it has 60 high-avidity binding sites to neutralise venom toxins. Here, we outline our experimental strategies to achieve this goal using state-of-the-art protein engineering, expression technology and mass spectrometry, as well as in vitro and in vivo venom neutralisation assays. We anticipate that the approaches described here will produce antivenom with unparalleled efficacy, safety and affordability.
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Affiliation(s)
- Stefanie K. Menzies
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Raquel Arinto-Garcia
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fernanda Gobbi Amorim
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Iara Aimê Cardoso
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Camille Abada
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Thomas Crasset
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Rebecca J. Edge
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Priscila El-Kazzi
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Damien Redureau
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Richard Stenner
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Johara Boldrini-França
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Huan Sun
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - António Roldão
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula M. Alves
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Robert A. Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Imre Berger
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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31
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Debatis M, Danz H, Tremblay JM, Gaspie K, Kudej RK, Vigdorovich V, Sather N, Jaskiewicz JJ, Tzipori S, Shoemaker CB. Enteric pharmacokinetics of monomeric and multimeric camelid nanobody single-domain antibodies. PLoS One 2023; 18:e0291937. [PMID: 38011121 PMCID: PMC10681176 DOI: 10.1371/journal.pone.0291937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/10/2023] [Indexed: 11/29/2023] Open
Abstract
Single-domain antibodies (sdAbs) derived from Camelidae heavy-chain-only antibodies (also called nanobodies or VHHs) have advantages over conventional antibodies in terms of their small size and stability to pH and temperature extremes, their ability to express well in microbial hosts, and to be functionally multimerized for enhanced properties. For these reasons, VHHs are showing promise as enteric disease therapeutics, yet little is known as to their pharmacokinetics (PK) within the digestive tract. To improve understanding of enteric VHH PK, we investigated the functional and structural stability of monomeric and multimeric camelid VHH-agents following in vitro incubation with intestinal extracts (chyme) from rabbits and pigs or fecal extracts from human sources, and in vivo in rabbits. The results showed that unstructured domains such as epitopic tags and flexible spacers composed of different amino acid sequences were rapidly degraded by enteric proteases while the functional core VHHs were much more stable to these treatments. Individual VHHs were widely variable in their functional stability to GI tract proteases. Some VHH-based agents which neutralize enteric Shiga toxin Stx2 displayed a functional stability to chyme incubations comparable to that of Stx2-neutralizing IgG and IgA mAbs, thus indicating that selected nanobodies can approach the functional stability of conventional immunoglobulins. Enteric PK data obtained from in vitro incubation studies were consistent with similar incubations performed in vivo in rabbit surgical gut loops. These findings have broad implications for enteric use of VHH-based agents, particularly VHH fusion proteins.
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Affiliation(s)
- Michelle Debatis
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Hillary Danz
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Jacqueline M. Tremblay
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Kimberly Gaspie
- Division of Animal Resources, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Raymond K. Kudej
- Department of Clinical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States of America
| | - Noah Sather
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA, United States of America
| | - Justyna J. Jaskiewicz
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Charles B. Shoemaker
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
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32
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Barroso-Gomila O, Merino-Cacho L, Muratore V, Perez C, Taibi V, Maspero E, Azkargorta M, Iloro I, Trulsson F, Vertegaal ACO, Mayor U, Elortza F, Polo S, Barrio R, Sutherland JD. BioE3 identifies specific substrates of ubiquitin E3 ligases. Nat Commun 2023; 14:7656. [PMID: 37996419 PMCID: PMC10667490 DOI: 10.1038/s41467-023-43326-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
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Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Coralia Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Fredrik Trulsson
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
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Zuo J, Chen H, Li H. Two molecule force spectroscopy on ligand-receptor interactions. NANOSCALE 2023; 15:16581-16589. [PMID: 37740375 DOI: 10.1039/d3nr03428c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Many biological processes involve the rupture of multiple ligand-receptors or multivalent ligand-receptors. It is challenging to study the rupture of such parallelly arranged multiple ligand-receptors due to the difficulties in engineering such systems in a well-controlled fashion. Here we report the use of two-molecule force spectroscopy to investigate the rupture of two parallelly arranged monomeric streptavidin (mSA)-biotin complexes. By using SpyCatcher-SpyTag chemistry, we successfully engineered a molecular twin of biotin, in which two biotins are arranged in parallel. By reacting mSA with twin biotin, we constructed parallelly arranged two mSA-biotin complexes for force spectroscopy experiments. The incorporation of single molecule fingerprint domains into our mSA-biotin dimers allowed us to identify and assign the rupture events of the parallelly arranged mSA-biotin complexes without any ambiguity in the two-molecule force spectroscopy experiments. Our results revealed that the rupture force of the parallel dimer mSA-biotin is 172 pN at a pulling speed of 400 nm s-1, which is about 1.6 times of that of single mSA-biotin (105 pN). Furthermore, our findings indicate that the two mSA-biotin behave as non-interacting, independent ligand-receptors. The strategy we demonstrated here can be extended to other ligand-receptors and may open up an avenue toward rigorously testing the theoretic predictions proposed in various models regarding the rupture of multiple parallel ligand-receptors.
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Affiliation(s)
- Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hui Chen
- Department of Chemical Engineering, Nanjing Forestry University, Nanjing, Jiangsu, P. R. China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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Paiva ACF, Lemos AR, Busse P, Martins MT, Silva DO, Freitas MC, Santos SP, Freire F, Barrey EJ, Manival X, Koetzner L, Heinrich T, Wegener A, Grädler U, Bandeiras TM, Schwarz D, Sousa PMF. Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance. BIOSENSORS 2023; 13:913. [PMID: 37887106 PMCID: PMC10605449 DOI: 10.3390/bios13100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Modern drug discovery relies on combinatorial screening campaigns to find drug molecules targeting specific disease-associated proteins. The success of such campaigns often relies on functional and structural information of the selected therapeutic target, only achievable once its purification is mastered. With the aim of bypassing the protein purification process to gain insights on the druggability, ligand binding, and/or characterization of protein-protein interactions, herein, we describe the Extract2Chip method. This approach builds on the immobilization of site-specific biotinylated proteins of interest, directly from cellular extracts, on avidin-coated sensor chips to allow for the characterization of molecular interactions via surface plasmon resonance (SPR). The developed method was initially validated using Cyclophilin D (CypD) and subsequently applied to other drug discovery projects in which the targets of interest were difficult to express, purify, and crystallize. Extract2Chip was successfully applied to the characterization of Yes-associated protein (YAP): Transcriptional enhancer factor TEF (TEAD1) protein-protein interaction inhibitors, in the validation of a ternary complex assembly composed of Dyskerin pseudouridine synthase 1 (DKC1) and RuvBL1/RuvBL2, and in the establishment of a fast-screening platform to select the most suitable NUAK family SNF1-like kinase 2 (NUAK2) surrogate for binding and structural studies. The described method paves the way for a potential revival of the many drug discovery campaigns that have failed to deliver due to the lack of suitable and sufficient protein supply.
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Affiliation(s)
- Ana C. F. Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana R. Lemos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philipp Busse
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Madalena T. Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
| | - Diana O. Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Evelyne J. Barrey
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, F-54000 Nancy, France;
| | - Lisa Koetzner
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ansgar Wegener
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Tiago M. Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Daniel Schwarz
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Pedro M. F. Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Porębska N, Ciura K, Chorążewska A, Zakrzewska M, Otlewski J, Opaliński Ł. Multivalent protein-drug conjugates - An emerging strategy for the upgraded precision and efficiency of drug delivery to cancer cells. Biotechnol Adv 2023; 67:108213. [PMID: 37453463 DOI: 10.1016/j.biotechadv.2023.108213] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/20/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
With almost 20 million new cases per year, cancer constitutes one of the most important challenges for public health systems. Unlike traditional chemotherapy, targeted anti-cancer strategies employ sophisticated therapeutics to precisely identify and attack cancer cells, limiting the impact of drugs on healthy cells and thereby minimizing the unwanted side effects of therapy. Protein drug conjugates (PDCs) are a rapidly growing group of targeted therapeutics, composed of a cancer-recognition factor covalently coupled to a cytotoxic drug. Several PDCs, mainly in the form of antibody-drug conjugates (ADCs) that employ monoclonal antibodies as cancer-recognition molecules, are used in the clinic and many PDCs are currently in clinical trials. Highly selective, strong and stable interaction of the PDC with the tumor marker, combined with efficient, rapid endocytosis of the receptor/PDC complex and its subsequent effective delivery to lysosomes, is critical for the efficacy of targeted cancer therapy with PDCs. However, the bivalent architecture of contemporary clinical PDCs is not optimal for tumor receptor recognition or PDCs internalization. In this review, we focus on multivalent PDCs, which represent a rapidly evolving and highly promising therapeutics that overcome most of the limitations of current bivalent PDCs, enhancing the precision and efficiency of drug delivery to cancer cells. We present an expanding set of protein scaffolds used to generate multivalent PDCs that, in addition to folding into well-defined multivalent molecular structures, enable site-specific conjugation of the cytotoxic drug to ensure PDC homogeneity. We provide an overview of the architectures of multivalent PDCs developed to date, emphasizing their efficacy in the targeted treatment of various cancers.
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Affiliation(s)
- Natalia Porębska
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Krzysztof Ciura
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Aleksandra Chorążewska
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Małgorzata Zakrzewska
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Jacek Otlewski
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland
| | - Łukasz Opaliński
- Faculty of Biotechnology, Department of Protein Engineering, University of Wroclaw, Joliot-Curie 14a, Wroclaw 50-383, Poland.
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36
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Peissert F, Pedotti M, Corbellari R, Simonelli L, De Gasparo R, Tamagnini E, Plüss L, Elsayed A, Matasci M, De Luca R, Cassaniti I, Sammartino JC, Piralla A, Baldanti F, Neri D, Varani L. Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300088. [PMID: 37829677 PMCID: PMC10566804 DOI: 10.1002/gch2.202300088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 10/14/2023]
Abstract
Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.
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Affiliation(s)
| | - Mattia Pedotti
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | | | - Luca Simonelli
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Raoul De Gasparo
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Elia Tamagnini
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Louis Plüss
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
| | | | | | | | - Irene Cassaniti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Jose’ Camilla Sammartino
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Antonio Piralla
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Fausto Baldanti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
- Department of Clinical Surgical Diagnostic and Pediatric SciencesUniversità degli Studi di PaviaPavia27100Italy
| | - Dario Neri
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
- Philogen SpALocalità Bellaria 35Sovicille (SI)53018Italy
| | - Luca Varani
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
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Lende SSF, Barnkob NM, Hansen RW, Bansia H, Vestergaard M, Rothemejer FH, Worsaae A, Brown D, Pedersen ML, Rahimic AHF, Juhl AK, Gjetting T, Østergaard L, Georges AD, Vuillard LM, Schleimann MH, Koefoed K, Tolstrup M. Discovery of neutralizing SARS-CoV-2 antibodies enriched in a unique antigen specific B cell cluster. PLoS One 2023; 18:e0291131. [PMID: 37729215 PMCID: PMC10511142 DOI: 10.1371/journal.pone.0291131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
Despite development of effective SARS-CoV-2 vaccines, a sub-group of vaccine non-responders depends on therapeutic antibodies or small-molecule drugs in cases of severe disease. However, perpetual viral evolution has required continuous efficacy monitoring as well as exploration of new therapeutic antibodies, to circumvent resistance mutations arising in the viral population. We performed SARS-CoV-2-specific B cell sorting and subsequent single-cell sequencing on material from 15 SARS-CoV-2 convalescent participants. Through screening of 455 monoclonal antibodies for SARS-CoV-2 variant binding and virus neutralization, we identified a cluster of activated B cells highly enriched for SARS-CoV-2 neutralizing antibodies. Epitope binning and Cryo-EM structure analysis identified the majority of neutralizing antibodies having epitopes overlapping with the ACE2 receptor binding motif (class 1 binders). Extensive functional antibody characterization identified two potent neutralizing antibodies, one retaining SARS-CoV-1 neutralizing capability, while both bind major common variants of concern and display prophylactic efficacy in vivo. The transcriptomic signature of activated B cells harboring broadly binding neutralizing antibodies with therapeutic potential identified here, may be a guide in future efforts of rapid therapeutic antibody discovery.
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Affiliation(s)
- Stine Sofie Frank Lende
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
| | | | - Frederik Holm Rothemejer
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Deijona Brown
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
| | - Maria Lange Pedersen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Anna Karina Juhl
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
| | - Torben Gjetting
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
- Antibody Technology, Novo Nordisk A/S, Måløv, Denmark
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amédée Des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, United States of America
- PhD Programs in Biochemistry, and Chemistry, Graduate Center, City University of New York, New York, NY, United States of America
| | | | | | | | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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38
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Ciută AD, Nosol K, Kowal J, Mukherjee S, Ramírez AS, Stieger B, Kossiakoff AA, Locher KP. Structure of human drug transporters OATP1B1 and OATP1B3. Nat Commun 2023; 14:5774. [PMID: 37723174 PMCID: PMC10507018 DOI: 10.1038/s41467-023-41552-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The organic anion transporting polypeptides OATP1B1 and OATP1B3 are membrane proteins that mediate uptake of drugs into the liver for subsequent conjugation and biliary excretion, a key step in drug elimination from the human body. Polymorphic variants of these transporters can cause reduced drug clearance and adverse drug effects such as statin-induced rhabdomyolysis, and co-administration of OATP substrates can lead to damaging drug-drug interaction. Despite their clinical relevance in drug disposition and pharmacokinetics, the structure and mechanism of OATPs are unknown. Here we present cryo-EM structures of human OATP1B1 and OATP1B3 bound to synthetic Fab fragments and in functionally distinct states. A single estrone-3-sulfate molecule is bound in a pocket located in the C-terminal half of OATP1B1. The shape and chemical nature of the pocket rationalize the preference for diverse organic anions and allow in silico docking of statins. The structure of OATP1B3 is determined in a drug-free state but reveals a bicarbonate molecule bound to the conserved signature motif and a histidine residue that is prevalent in OATPs exhibiting pH-dependent activity.
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Affiliation(s)
- Anca-Denise Ciută
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Kamil Nosol
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Ana S Ramírez
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bruno Stieger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.
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Alteen MG, Deme JC, Alvarez CP, Loppnau P, Hutchinson A, Seitova A, Chandrasekaran R, Silva Ramos E, Secker C, Alqazzaz M, Wanker EE, Lea SM, Arrowsmith CH, Harding RJ. Delineation of functional subdomains of Huntingtin protein and their interaction with HAP40. Structure 2023; 31:1121-1131.e6. [PMID: 37390814 PMCID: PMC10527579 DOI: 10.1016/j.str.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
The huntingtin (HTT) protein plays critical roles in numerous cellular pathways by functioning as a scaffold for its many interaction partners and HTT knock out is embryonic lethal. Interrogation of HTT function is complicated by the large size of this protein so we studied a suite of structure-rationalized subdomains to investigate the structure-function relationships within the HTT-HAP40 complex. Protein samples derived from the subdomain constructs were validated using biophysical methods and cryo-electron microscopy, revealing they are natively folded and can complex with validated binding partner, HAP40. Derivatized versions of these constructs enable protein-protein interaction assays in vitro, with biotin tags, and in cells, with luciferase two-hybrid assay-based tags, which we use in proof-of-principle analyses to further interrogate the HTT-HAP40 interaction. These open-source biochemical tools enable studies of fundamental HTT biochemistry and biology, will aid the discovery of macromolecular or small-molecule binding partners and help map interaction sites across this large protein.
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Affiliation(s)
- Matthew G Alteen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; POINT Biopharma, 22 St Clair Avenue E Suite 1201, Toronto, ON M4T 2S3, Canada
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Claudia P Alvarez
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; SCIEX, 71 Four Valley Dr, Vaughan, ON L4K 4V8, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Renu Chandrasekaran
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Mona Alqazzaz
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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40
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Patel PN, Dickey TH, Diouf A, Salinas ND, McAleese H, Ouahes T, Long CA, Miura K, Lambert LE, Tolia NH. Structure-based design of a strain transcending AMA1-RON2L malaria vaccine. Nat Commun 2023; 14:5345. [PMID: 37660103 PMCID: PMC10475129 DOI: 10.1038/s41467-023-40878-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/14/2023] [Indexed: 09/04/2023] Open
Abstract
Apical membrane antigen 1 (AMA1) is a key malaria vaccine candidate and target of neutralizing antibodies. AMA1 binds to a loop in rhoptry neck protein 2 (RON2L) to form the moving junction during parasite invasion of host cells, and this complex is conserved among apicomplexan parasites. AMA1-RON2L complex immunization achieves higher growth inhibitory activity than AMA1 alone and protects mice against Plasmodium yoelii challenge. Here, three single-component AMA1-RON2L immunogens were designed that retain the structure of the two-component AMA1-RON2L complex: one structure-based design (SBD1) and two insertion fusions. All immunogens elicited high antibody titers with potent growth inhibitory activity, yet these antibodies did not block RON2L binding to AMA1. The SBD1 immunogen induced significantly more potent strain-transcending neutralizing antibody responses against diverse strains of Plasmodium falciparum than AMA1 or AMA1-RON2L complex vaccination. This indicates that SBD1 directs neutralizing antibody responses to strain-transcending epitopes in AMA1 that are independent of RON2L binding. This work underscores the importance of neutralization mechanisms that are distinct from RON2 blockade. The stable single-component SBD1 immunogen elicits potent strain-transcending protection that may drive the development of next-generation vaccines for improved malaria and apicomplexan parasite control.
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Affiliation(s)
- Palak N Patel
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thayne H Dickey
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Nichole D Salinas
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Holly McAleese
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tarik Ouahes
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carole A Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Lynn E Lambert
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Niraj H Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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41
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Lučić I, Héluin L, Jiang PL, Castro Scalise AG, Wang C, Franz A, Heyd F, Wahl MC, Liu F, Plested AJR. CaMKII autophosphorylation can occur between holoenzymes without subunit exchange. eLife 2023; 12:e86090. [PMID: 37566455 PMCID: PMC10468207 DOI: 10.7554/elife.86090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
The dodecameric protein kinase CaMKII is expressed throughout the body. The alpha isoform is responsible for synaptic plasticity and participates in memory through its phosphorylation of synaptic proteins. Its elaborate subunit organization and propensity for autophosphorylation allow it to preserve neuronal plasticity across space and time. The prevailing hypothesis for the spread of CaMKII activity, involving shuffling of subunits between activated and naive holoenzymes, is broadly termed subunit exchange. In contrast to the expectations of previous work, we found little evidence for subunit exchange upon activation, and no effect of restraining subunits to their parent holoenzymes. Rather, mass photometry, crosslinking mass spectrometry, single molecule TIRF microscopy and biochemical assays identify inter-holoenzyme phosphorylation (IHP) as the mechanism for spreading phosphorylation. The transient, activity-dependent formation of groups of holoenzymes is well suited to the speed of neuronal activity. Our results place fundamental limits on the activation mechanism of this kinase.
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Affiliation(s)
- Iva Lučić
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Léonie Héluin
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Pin-Lian Jiang
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Alejandro G Castro Scalise
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Cong Wang
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
| | - Andreas Franz
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular CrystallographyBerlinGermany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
- Charité-Universitätsmedizin BerlinBerlinGermany
| | - Andrew JR Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu BerlinBerlinGermany
- Leibniz-Forschungsinstitut für Molekulare PharmakologieBerlinGermany
- NeuroCure, Charité UniversitätsmedizinBerlinGermany
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42
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Huisman BD, Guan N, Rückert T, Garner L, Singh NK, McMichael AJ, Gillespie GM, Romagnani C, Birnbaum ME. High-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation. Nat Commun 2023; 14:4809. [PMID: 37558657 PMCID: PMC10412585 DOI: 10.1038/s41467-023-40220-1] [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: 09/23/2022] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
HLA-E is a non-classical class I MHC protein involved in innate and adaptive immune recognition. While recent studies have shown HLA-E can present diverse peptides to NK cells and T cells, the HLA-E repertoire recognized by CD94/NKG2x has remained poorly defined, with only a limited number of peptide ligands identified. Here we screen a yeast-displayed peptide library in the context of HLA-E to identify 500 high-confidence unique peptides that bind both HLA-E and CD94/NKG2A or CD94/NKG2C. Utilizing the sequences identified via yeast display selections, we train prediction algorithms and identify human and cytomegalovirus (CMV) proteome-derived, HLA-E-presented peptides capable of binding and signaling through both CD94/NKG2A and CD94/NKG2C. In addition, we identify peptides which selectively activate NKG2C+ NK cells. Taken together, characterization of the HLA-E-binding peptide repertoire and identification of NK activity-modulating peptides present opportunities for studies of NK cell regulation in health and disease, in addition to vaccine and therapeutic design.
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Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Ning Guan
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | - Lee Garner
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nishant K Singh
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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43
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Choe H, Antee T, Ge X. Substrate derived sequences act as subsite-blocking motifs in protease inhibitory antibodies. Protein Sci 2023; 32:e4691. [PMID: 37278099 PMCID: PMC10285753 DOI: 10.1002/pro.4691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023]
Abstract
Proteases are involved in many physiologic processes, and dysregulated proteolysis is basis of a variety of diseases. Specific inhibition of pathogenetic proteases via monoclonal antibodies therefore holds significant therapeutic promise. Inspired by the competitive mechanism utilized by many naturally occurring and man-made protease inhibitors, we hypothesized that substrate-like peptide sequences can act as protease subsite blocking motifs if they occupy only one side of the reaction center. To test this hypothesis, a degenerate codon library representing MMP-14 substrate profiles at P1-P5' positions was constructed in the context of an anti-MMP-14 Fab by replacing its inhibitory motif in CDR-H3 with MMP-14 substrate repertoires. After selection for MMP-14 active-site binders by phage panning, results indicated that diverse substrate-like sequences conferring antibodies inhibitory potencies were enriched in the isolated clones. Optimal residues at each of P1-P5' positions were then identified, and the corresponding mutation combinations showed improved characteristics as effective inhibitors of MMP-14. Insights on efficient library designs for inhibitory peptide motifs were further discussed. Overall, this study proved the concept that substrate-derived sequences were able to behave as the inhibitory motifs in protease-specific antibodies. With accumulating data available on protease substrate profiles, we expect the approach described here can be broadly applied to facilitate the generation of antibody inhibitors targeting biomedically important proteases.
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Affiliation(s)
- Hyunjun Choe
- Institute of Molecular MedicineUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
- Present address:
Arrowhead PharmaceuticalsMadisonWIUSA
| | - Tara Antee
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
| | - Xin Ge
- Institute of Molecular MedicineUniversity of Texas Health Science Center at HoustonHoustonTexasUSA
- Department of Chemical and Environmental EngineeringUniversity of California RiversideRiversideCaliforniaUSA
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44
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Bauer A, Klassa S, Herbst A, Maccioni C, Abhamon W, Segueni N, Kaluzhny Y, Hunter MC, Halin C. Optimization and Characterization of Novel ALCAM-Targeting Antibody Fragments for Transepithelial Delivery. Pharmaceutics 2023; 15:1841. [PMID: 37514028 PMCID: PMC10385607 DOI: 10.3390/pharmaceutics15071841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Activated leukocyte cell adhesion molecule (ALCAM) is a cell adhesion molecule that supports T cell activation, leukocyte migration, and (lymph)angiogenesis and has been shown to contribute to the pathology of various immune-mediated disorders, including asthma and corneal graft rejection. In contrast to monoclonal antibodies (mAbs) targeting ALCAM's T cell expressed binding partner CD6, no ALCAM-targeting mAbs have thus far entered clinical development. This is likely linked with the broad expression of ALCAM on many different cell types, which increases the risk of eliciting unwanted treatment-induced side effects upon systemic mAb application. Targeting ALCAM in surface-exposed tissues, such as the lungs or the cornea, by a topical application could circumvent this issue. Here, we report the development of various stability- and affinity-improved anti-ALCAM mAb fragments with cross-species reactivity towards mouse, rat, monkey, and human ALCAM. Fragments generated in either mono- or bivalent formats potently blocked ALCAM-CD6 interactions in a competition ELISA, but only bivalent fragments efficiently inhibited ALCAM-ALCAM interactions in a leukocyte transmigration assay. The different fragments displayed a clear size-dependence in their ability to penetrate the human corneal epithelium. Furthermore, intranasal delivery of anti-ALCAM fragments reduced leukocyte infiltration in a mouse model of asthma, confirming ALCAM as a target for topical application in the lungs.
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Affiliation(s)
- Aline Bauer
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - Sven Klassa
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - Anja Herbst
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - Cristina Maccioni
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - William Abhamon
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - Noria Segueni
- Artimmune SAS, 13 Avenue Buffon, 45100 Orleans, France
| | - Yulia Kaluzhny
- MatTek Corporation, 200 Homer Avenue, Ashland, MA 01721, USA
| | - Morgan Campbell Hunter
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
| | - Cornelia Halin
- Institute of Pharmaceutical Sciences, ETH Zurich, 1-5/10 Vladimir-Prelog-Weg, 8093 Zurich, Switzerland
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45
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Zhao Y, Caron C, Chan YY, Lee CK, Xu X, Zhang J, Masubuchi T, Wu C, Bui JD, Hui E. cis-B7:CD28 interactions at invaginated synaptic membranes provide CD28 co-stimulation and promote CD8 + T cell function and anti-tumor immunity. Immunity 2023; 56:1187-1203.e12. [PMID: 37160118 PMCID: PMC10330546 DOI: 10.1016/j.immuni.2023.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/30/2023] [Accepted: 04/07/2023] [Indexed: 05/11/2023]
Abstract
B7 ligands (CD80 and CD86), expressed by professional antigen-presenting cells (APCs), activate the main co-stimulatory receptor CD28 on T cells in trans. However, in peripheral tissues, APCs expressing B7 ligands are relatively scarce. This raises the questions of whether and how CD28 co-stimulation occurs in peripheral tissues. Here, we report that CD8+ T cells displayed B7 ligands that interacted with CD28 in cis at membrane invaginations of the immunological synapse as a result of membrane remodeling driven by phosphoinositide-3-kinase (PI3K) and sorting-nexin-9 (SNX9). cis-B7:CD28 interactions triggered CD28 signaling through protein kinase C theta (PKCθ) and promoted CD8+ T cell survival, migration, and cytokine production. In mouse tumor models, loss of T cell-intrinsic cis-B7:CD28 interactions decreased intratumoral T cells and accelerated tumor growth. Thus, B7 ligands on CD8+ T cells can evoke cell-autonomous CD28 co-stimulation in cis in peripheral tissues, suggesting cis-signaling as a general mechanism for boosting T cell functionality.
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Affiliation(s)
- Yunlong Zhao
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Christine Caron
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ya-Yuan Chan
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Calvin K Lee
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Xiaozheng Xu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jibin Zhang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Takeya Masubuchi
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Enfu Hui
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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46
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Keeble AH, Wood DP, Howarth M. Design and Evolution of Enhanced Peptide-Peptide Ligation for Modular Transglutaminase Assembly. Bioconjug Chem 2023. [PMID: 37289810 DOI: 10.1021/acs.bioconjchem.3c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Robust and precise tools are needed to enhance the functionality and resilience of synthetic nanoarchitectures. Here, we have employed directed evolution and rational design to build a fast-acting molecular superglue from a bacterial adhesion protein. We have generated the SnoopLigase2 coupling system, a genetically encoded route for efficient transamidation between SnoopTag2 and DogTag2 peptides. Each peptide was selected for rapid reaction by phage display screening. The optimized set allows more than 99% completion and is compatible with diverse buffers, pH values, and temperatures, accelerating the reaction over 1000-fold. SnoopLigase2 directs a specific reaction in the mammalian secretory pathway, allowing covalent display on the plasma membrane. Transglutaminase 2 (TG2) has a network of interactions and substrates amidst the mammalian cell surface and extracellular matrix. We expressed a modified TG2 with resistance to oxidative inactivation and minimal self-reactivity. SnoopLigase2 enables TG2 functionalization with transforming growth factor alpha (TGFα) in routes that would be impossible through genetic fusion. The TG2:TGFα conjugate retained transamidase activity, stably anchored TGFα for signal activation in the extracellular environment, and reprogrammed cell behavior. This modular toolbox should create new opportunities for molecular assembly, both for novel biomaterials and complex cellular environments.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Dominic P Wood
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
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47
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Wei E, Bou-Nader C, Perry ML, Fattah R, Zhang J, Leppla SH, Bothra A. S9.6 Antibody-Enzyme Conjugates for the Detection of DNA-RNA Hybrids. Bioconjug Chem 2023; 34:834-844. [PMID: 37194248 DOI: 10.1021/acs.bioconjchem.2c00609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Diagnosis of infectious agents is increasingly done by the detection of unique nucleic acid sequences, typically using methods such as PCR that specifically amplify these sequences. A largely neglected alternative approach is to use antibodies that recognize nucleic acids. The unique monoclonal antibody S9.6 recognizes DNA-RNA hybrids in a largely sequence-independent manner. S9.6 has been used in several cases for the analysis of nucleic acids. Extending our recent determination of the structure of S9.6 Fab bound to a DNA-RNA hybrid, we have developed reagents and methods for the sensitive detection of specific DNA and RNA sequences. To facilitate the use in diagnostics, we conjugated the S9.6 Fab to the highly active and well-characterized reporter enzyme human-secreted embryonic alkaline phosphatase (SEAP). Two approaches were utilized for conjugation. The first used sortase A (SrtA), which generates a covalent peptide bond between short amino acid sequences added to recombinantly produced S9.6 Fab and SEAP. The second approach was to genetically fuse the S9.6 Fab and SEAP so that the two are produced as a single molecule. Using these two antibody-SEAP proteins, we developed a simplified ELISA format for the identification of synthetic DNA-RNA hybrids, which can be optimized for detecting nucleic acids of pathogens, as well as for other applications. We successfully used this immunosorbent assay, HC-S, to identify DNA-RNA hybrids in solution with high specificity and sensitivity.
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Affiliation(s)
- Elena Wei
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda Maryland 20892, United States
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Megan L Perry
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda Maryland 20892, United States
| | - Rasem Fattah
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda Maryland 20892, United States
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda Maryland 20892, United States
| | - Ankur Bothra
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda Maryland 20892, United States
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48
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Blanc M, Lettl C, Guérin J, Vieille A, Furler S, Briand-Schumacher S, Dreier B, Bergé C, Plückthun A, Vadon-Le Goff S, Fronzes R, Rousselle P, Fischer W, Terradot L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 2023; 19:e1011368. [PMID: 37155700 DOI: 10.1371/journal.ppat.1011368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/18/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The bacterial human pathogen Helicobacter pylori produces a type IV secretion system (cagT4SS) to inject the oncoprotein CagA into gastric cells. The cagT4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shape N-terminal domains (CagIN) prolonged by globular C-terminal domains (CagIC). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagIC with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagIC were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagIC plays a key role in cagT4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cagT4SS, a crucial risk factor for gastric cancer development.
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Affiliation(s)
- Marine Blanc
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jérémy Guérin
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Anaïs Vieille
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Sven Furler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Rémi Fronzes
- European Institute of Chemistry and Biology, CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Univ. Bordeaux, Pessac, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
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49
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Srinivasan K, Erramilli SK, Chakravarthy S, Gonzalez A, Kossiakoff A, Noinaj N. Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum. Structure 2023; 31:595-606.e5. [PMID: 36977410 PMCID: PMC10164082 DOI: 10.1016/j.str.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/21/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023]
Abstract
Roughly 95% of the proteins that make up the chloroplast must be imported from the cytoplasm. The machinery responsible for the translocation of these cargo proteins is called the translocon at the outer membrane of chloroplast (TOC). The TOC core consists of three proteins, Toc34, Toc75, and Toc159; no high-resolution structure has been solved of fully assembled TOC from plants. Efforts toward determining the structure of the TOC have been hindered almost entirely by difficulties in producing sufficient yields for structural studies. In this study, we introduce an innovative method that utilizes synthetic antigen binding fragments (sABs) to isolate TOC directly from wild-type plant biomass including A. thaliana and P. sativum. Binding between the sABs and the POTRA domains was characterized by size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS), X-ray crystallography, and isothermal titration calorimetry. We also demonstrate the isolation of the TOC from P. sativum, laying the framework for large-scale isolation and purification of TOC for functional and structural studies.
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Affiliation(s)
- Karthik Srinivasan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Adrian Gonzalez
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Anthony Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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50
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Alsoussi WB, Malladi SK, Zhou JQ, Liu Z, Ying B, Kim W, Schmitz AJ, Lei T, Horvath SC, Sturtz AJ, McIntire KM, Evavold B, Han F, Scheaffer SM, Fox IF, Mirza SF, Parra-Rodriguez L, Nachbagauer R, Nestorova B, Chalkias S, Farnsworth CW, Klebert MK, Pusic I, Strnad BS, Middleton WD, Teefey SA, Whelan SPJ, Diamond MS, Paris R, O'Halloran JA, Presti RM, Turner JS, Ellebedy AH. SARS-CoV-2 Omicron boosting induces de novo B cell response in humans. Nature 2023; 617:592-598. [PMID: 37011668 DOI: 10.1038/s41586-023-06025-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
The primary two-dose SARS-CoV-2 mRNA vaccine series are strongly immunogenic in humans, but the emergence of highly infectious variants necessitated additional doses and the development of vaccines aimed at the new variants1-4. SARS-CoV-2 booster immunizations in humans primarily recruit pre-existing memory B cells5-9. However, it remains unclear whether the additional doses induce germinal centre reactions whereby re-engaged B cells can further mature, and whether variant-derived vaccines can elicit responses to variant-specific epitopes. Here we show that boosting with an mRNA vaccine against the original monovalent SARS-CoV-2 mRNA vaccine or the bivalent B.1.351 and B.1.617.2 (Beta/Delta) mRNA vaccine induced robust spike-specific germinal centre B cell responses in humans. The germinal centre response persisted for at least eight weeks, leading to significantly more mutated antigen-specific bone marrow plasma cell and memory B cell compartments. Spike-binding monoclonal antibodies derived from memory B cells isolated from individuals boosted with either the original SARS-CoV-2 spike protein, bivalent Beta/Delta vaccine or a monovalent Omicron BA.1-based vaccine predominantly recognized the original SARS-CoV-2 spike protein. Nonetheless, using a more targeted sorting approach, we isolated monoclonal antibodies that recognized the BA.1 spike protein but not the original SARS-CoV-2 spike protein from individuals who received the mRNA-1273.529 booster; these antibodies were less mutated and recognized novel epitopes within the spike protein, suggesting that they originated from naive B cells. Thus, SARS-CoV-2 booster immunizations in humans induce robust germinal centre B cell responses and can generate de novo B cell responses targeting variant-specific epitopes.
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Affiliation(s)
- Wafaa B Alsoussi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Sameer Kumar Malladi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Baoling Ying
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Stephen C Horvath
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Alexandria J Sturtz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Katherine M McIntire
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Birk Evavold
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Fangjie Han
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Suzanne M Scheaffer
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Isabella F Fox
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Senaa F Mirza
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Luis Parra-Rodriguez
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Christopher W Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael K Klebert
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Iskra Pusic
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin S Strnad
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | | | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
- Infectious Disease Clinical Research Unit, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
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