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Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
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Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
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2
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Aymoz-Bressot T, Canis M, Meurisse F, Wijkhuisen A, Favier B, Mousseau G, Dupressoir A, Heidmann T, Bacquin A. Cell-Int: a cell-cell interaction assay to identify native membrane protein interactions. Life Sci Alliance 2024; 7:e202402844. [PMID: 39237366 PMCID: PMC11377309 DOI: 10.26508/lsa.202402844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024] Open
Abstract
Intercellular protein-protein interactions (PPIs) have pivotal roles in biological functions and diseases. Membrane proteins are therefore a major class of drug targets. However, studying such intercellular PPIs is challenging because of the properties of membrane proteins. Current methods commonly use purified or modified proteins that are not physiologically relevant and hence might mischaracterize interactions occurring in vivo. Here, we describe Cell-Int: a cell interaction assay for studying plasma membrane PPIs. The interaction signal is measured through conjugate formation between two populations of cells each expressing either a ligand or a receptor. In these settings, membrane proteins are in their native environment thus being physiologically relevant. Cell-Int has been applied to the study of diverse protein partners, and enables to investigate the inhibitory potential of blocking antibodies, as well as the retargeting of fusion proteins for therapeutic development. The assay was also validated for screening applications and could serve as a platform for identifying new protein interactors.
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Affiliation(s)
- Thibaud Aymoz-Bressot
- CNRS UMR9196, Laboratory of Molecular Physiology and Pathology of Endogenous and Infectious Retroviruses, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marie Canis
- CNRS UMR9196, Laboratory of Molecular Physiology and Pathology of Endogenous and Infectious Retroviruses, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- VIROXIS, Gustave Roussy, Villejuif, France
| | - Florian Meurisse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Paris, France
| | - Anne Wijkhuisen
- Université Paris-Saclay, CEA, INRAE, Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette, France
| | - Benoit Favier
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Paris, France
| | | | - Anne Dupressoir
- CNRS UMR9196, Laboratory of Molecular Physiology and Pathology of Endogenous and Infectious Retroviruses, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Thierry Heidmann
- CNRS UMR9196, Laboratory of Molecular Physiology and Pathology of Endogenous and Infectious Retroviruses, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- VIROXIS, Gustave Roussy, Villejuif, France
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3
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Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024; 25:668-687. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
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Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
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4
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Zhou X, Martell JD. DNA-Directed Activation of Photocatalytic Labeling at Cell-Cell Contact Sites. ACS Chem Biol 2024; 19:1935-1941. [PMID: 39226459 DOI: 10.1021/acschembio.4c00515] [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: 09/05/2024]
Abstract
Cell-cell interactions govern diverse biological activities, necessitating molecular tools for understanding and regulating these interactions. Photoredox chemistry can detect cell-cell interactions by anchoring photocatalysts on cellular membranes to generate reactive species that tag closely contacting cells. However, the activation of photocatalysts lacks precise spatial resolution for selectively labeling intercellular interfaces. Herein, we report a DNA-based approach to selectively activate photocatalytic reactions at cell-cell contacts. Two cell populations are coated with distinct DNA strands, which interact at intercellular contacts, mediating the site-specific turn-on of a Ru(bpy)3-type photocatalyst. We demonstrate high spatial specificity for intercellular chemical labeling in cultured mammalian cells. Furthermore, as a proof of concept, we activate the dynamic DNA catalyst at cell-cell contacts in response to customized DNA triggers. This study lays the foundation for designing versatile chemical tools with high spatial precision and programmable responsiveness, along with the temporal resolution afforded by photoirradiation, to investigate and manipulate cell-cell interactions.
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Affiliation(s)
- Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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5
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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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6
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Skawinski CLS, Shah PS. I'm Walking into Spiderwebs: Making Sense of Protein-Protein Interaction Data. J Proteome Res 2024; 23:2723-2732. [PMID: 38556766 PMCID: PMC11296932 DOI: 10.1021/acs.jproteome.3c00892] [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] [Indexed: 04/02/2024]
Abstract
Protein-protein interactions (PPIs) are at the heart of the molecular landscape permeating life. Proteomics studies can explore this protein interaction landscape using mass spectrometry (MS). Thanks to their high sensitivity, mass spectrometers can easily identify thousands of proteins within a single sample, but that same sensitivity generates tangled spiderwebs of data that hide biologically relevant findings. So, what does a researcher do when she finds herself walking into spiderwebs? In a field focused on discovery, MS data require rigor in their analysis, experimental validation, or a combination of both. In this Review, we provide a brief primer on MS-based experimental methods to identify PPIs. We discuss approaches to analyze the resulting data and remove the proteomic background. We consider the advantages between comprehensive and targeted studies. We also discuss how scoring might be improved through AI-based protein structure information. Women have been essential to the development of proteomics, so we will specifically highlight work by women that has made this field thrive in recent years.
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Affiliation(s)
| | - Priya S. Shah
- Department of Chemical Engineering, University of California – Davis, California
- Department of Microbiology and Molecular Genetics, University of California – Davis, California
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7
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Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, von Zastrow M, Krogan NJ, Hüttenhain R. A proximity proteomics pipeline with improved reproducibility and throughput. Mol Syst Biol 2024; 20:952-971. [PMID: 38951684 PMCID: PMC11297269 DOI: 10.1038/s44320-024-00049-2] [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: 04/07/2023] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024] Open
Abstract
Proximity labeling (PL) via biotinylation coupled with mass spectrometry (MS) captures spatial proteomes in cells. Large-scale processing requires a workflow minimizing hands-on time and enhancing quantitative reproducibility. We introduced a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. Combining this with optimized quantitative MS based on data-independent acquisition (DIA), we increased sample throughput and improved protein identification and quantification reproducibility. We applied this pipeline to delineate subcellular proteomes across various compartments. Using the 5HT2A serotonin receptor as a model, we studied temporal changes of proximal interaction networks induced by receptor activation. In addition, we modified the pipeline for reduced sample input to accommodate CRISPR-based gene knockout, assessing dynamics of the 5HT2A network in response to perturbation of selected interactors. This PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, enhancing throughput and reproducibility of standard protocols.
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Affiliation(s)
- Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Trupti Patil
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Aaron Marley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Prachi Khare
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Rasika Vartak
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94158, USA.
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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8
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Gao S, Li R, Tai W, Song P, Hu Q, Yu L. Microsyringe-assisted visual volume detection based on phase separation: the case of chymosin milk-clotting activity study. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5105-5111. [PMID: 38993036 DOI: 10.1039/d4ay00670d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The constantly diverse demand scenarios for rapid on-site analysis have put forward high requirements for developing low-cost and user-friendly visual detection methods. Therefore, developing a visual detection method with simple operation and intuitive results has important practical value in the field of analysis and detection, but it is also challenging. In this work, we propose a microsyringe-assisted visual volume detection method based on phase separation, and apply it to analyze the milk-clotting activity of chymosin. Chymosin can cause phase separation of milk with whey in the mobile phase and curd in the gel state. The network structures of casein in curd can trap water molecules, resulting in separation of whey from curd gradually. Therefore, the analysis of chymosin milk-clotting activity can be realized according to the volume of whey measured using a portable microsyringe. This method shows a good linear correlation when the concentration of chymosin ranges from 1.02 U L-1 to 1020 U L-1 and the limit of detection of this method for chymosin is calculated to be 0.03 U mL-1. This work successfully realizes the visual analysis of chymosin milk-clotting activity based on the enzyme-triggered phase separation. It also shows great promise to be applied in other phase separation-based detection systems with the advantages of high accuracy, great portability and user-friendliness.
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Affiliation(s)
- Shan Gao
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
| | - Ruotong Li
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
| | - Wenjun Tai
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
| | - Ping Song
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qiongzheng Hu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, 250014, China.
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Li Yu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
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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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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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11
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Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, Zastrow MV, Krogan NJ, Hüttenhain R. A proximity proteomics pipeline with improved reproducibility and throughput. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.11.536358. [PMID: 37090610 PMCID: PMC10120663 DOI: 10.1101/2023.04.11.536358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Proximity labeling (PL) through biotinylation coupled with mass spectrometry (MS) has emerged as a powerful technique for capturing spatial proteomes within living cells. Large-scale sample processing for proximity proteomics requires a workflow that minimizes hands-on time while enhancing quantitative reproducibility. Here, we present a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. By combining this pipeline with an optimized quantitative MS acquisition method based on data-independent acquisition (DIA), we not only significantly increased sample throughput but also improved the reproducibility of protein identification and quantification. We applied this pipeline to delineate subcellular proteomes across various cellular compartments, including endosomes, late endosomes/lysosomes, the Golgi apparatus, and the plasma membrane. Moreover, employing 5HT2A serotonin receptor as a model, we investigated temporal changes of proximal interaction networks induced by the receptor's activation with serotonin. Finally, to demonstrate the applicability of our PL pipeline across multiple experimental conditions, we further modified the PL pipeline for reduced sample input amounts to accommodate CRISPR-based gene knockout, and assessed the dynamics of the 5HT2A network in response to the perturbation of selected proximal interactors. Importantly, the presented PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, increasing both throughput and reproducibility of standard protocols.
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Affiliation(s)
- Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiongyu Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trupti Patil
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aaron Marley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Prachi Khare
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rasika Vartak
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark Von Zastrow
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
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12
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Bertozzi CR, Ting AY. Directed evolution of genetically encoded LYTACs for cell-mediated delivery. Proc Natl Acad Sci U S A 2024; 121:e2320053121. [PMID: 38513100 PMCID: PMC10990137 DOI: 10.1073/pnas.2320053121] [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: 11/15/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here, we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin-like growth factor 2 (IGF2). After showing initial efficacy with wild-type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
| | - Joleen S. Cheah
- Department of Biology, Stanford University, Stanford, CA94305
| | - David S. Roberts
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305
- Parker Institute for Cancer Immunotherapy, San Francisco, CA94305
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
| | - Alice Y. Ting
- Department of Chemistry, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
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13
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Shi Y, Bashian EE, Hou Y, Wu P. Chemical immunology: Recent advances in tool development and applications. Cell Chem Biol 2024; 31:S2451-9456(24)00080-1. [PMID: 38508196 PMCID: PMC11393185 DOI: 10.1016/j.chembiol.2024.02.006] [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: 09/01/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.
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Affiliation(s)
- Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eleanor E Bashian
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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14
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Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
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Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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15
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Son S, Nagahama K, Lee J, Jung K, Kwak C, Kim J, Noh YW, Kim E, Lee S, Kwon HB, Heo WD. Real-time visualization of structural dynamics of synapses in live cells in vivo. Nat Methods 2024; 21:353-360. [PMID: 38191933 DOI: 10.1038/s41592-023-02122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 11/01/2023] [Indexed: 01/10/2024]
Abstract
The structural plasticity of synapses is crucial for regulating brain functions. However, currently available methods for studying synapse organization based on split fluorescent proteins (FPs) have been limited in assessing synaptic dynamics in vivo due to the irreversible binding of split FPs. Here, we develop 'SynapShot', a method for visualizing the structural dynamics of intact synapses by combining dimerization-dependent FPs (ddFPs) with engineered synaptic adhesion molecules. SynapShot allows real-time monitoring of reversible and bidirectional changes of synaptic contacts under physiological stimulation. The application of green and red ddFPs in SynapShot enables simultaneous visualization of two distinct populations of synapses. Notably, the red-shifted SynapShot is highly compatible with blue light-based optogenetic techniques, allowing for visualization of synaptic dynamics while precisely controlling specific signaling pathways. Furthermore, we demonstrate that SynapShot enables real-time monitoring of structural changes in synaptic contacts in the mouse brain during both primitive and higher-order behaviors.
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Affiliation(s)
- Seungkyu Son
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kenichiro Nagahama
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jinsu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kanghoon Jung
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Chuljung Kwak
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Woo Noh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea.
| | - Hyung-Bae Kwon
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea.
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16
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Wu J, Chu T, Hao J, Lin L. SpSrtA-Catalyzed Isopeptide Ligation on Lysine Residues. Microorganisms 2024; 12:179. [PMID: 38258005 PMCID: PMC10818881 DOI: 10.3390/microorganisms12010179] [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: 11/20/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Sortase-mediated ligation (SML) is widely used for protein bioconjugation. However, the sortase used in this strategy typically recognizes only the N-terminal oligoglycine, which is absent in most natural proteins. To broaden the spectrum of substrates compatible with SML, we focus on a novel sortase, sortase A from Streptococcus pneumoniae (SpSrtA), known for its expanded substrate specificity (N-terminal glycine, alanine, and serine). We present the first evidence showing that the reported SpSrtA mutant (SpSrtA*) can modify lysine residues in itself and other proteins. The modification sites of SpSrtA* were identified through LC-MS/MS analysis. Moreover, we discovered an optimal lysine-containing peptide tag by fusing it onto sfGFP, resulting in a labeling efficiency of 57%. Inspired by this, we applied the method to modify proteins on microorganism surfaces up to 13.5-fold. To enhance labeling efficiency, we fused the SpSrtA* onto a surface protein and achieved a 2.64-fold improvement. We further developed a high-throughput yeast display screening method for the directed evolution of SpSrtA*, achieving a 10-fold improvement in the labeling efficiency of this surface protein. Our study provides a novel strategy for modifying the lysine residues that will be a powerful addition to the protein bioconjugation toolbox.
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Affiliation(s)
- Jiajia Wu
- Department of Chemistry, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tianyu Chu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Hao
- Department of Chemistry, Shanghai University, Shanghai 200444, China
| | - Liang Lin
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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17
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Xu X, Yin K, Xu S, Wang Z, Wu R. Mass spectrometry-based methods for investigating the dynamics and organization of the surfaceome: exploring potential clinical implications. Expert Rev Proteomics 2024; 21:99-113. [PMID: 38300624 PMCID: PMC10928381 DOI: 10.1080/14789450.2024.2314148] [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: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Cell-surface proteins are extremely important for many cellular events, such as regulating cell-cell communication and cell-matrix interactions. Aberrant alterations in surface protein expression, modification (especially glycosylation), and interactions are directly related to human diseases. Systematic investigation of surface proteins advances our understanding of protein functions, cellular activities, and disease mechanisms, which will lead to identifying surface proteins as disease biomarkers and drug targets. AREAS COVERED In this review, we summarize mass spectrometry (MS)-based proteomics methods for global analysis of cell-surface proteins. Then, investigations of the dynamics of surface proteins are discussed. Furthermore, we summarize the studies for the surfaceome interaction networks. Additionally, biological applications of MS-based surfaceome analysis are included, particularly highlighting the significance in biomarker identification, drug development, and immunotherapies. EXPERT OPINION Modern MS-based proteomics provides an opportunity to systematically characterize proteins. However, due to the complexity of cell-surface proteins, the labor-intensive workflow, and the limit of clinical samples, comprehensive characterization of the surfaceome remains extraordinarily challenging, especially in clinical studies. Developing and optimizing surfaceome enrichment methods and utilizing automated sample preparation workflow can expand the applications of surfaceome analysis and deepen our understanding of the functions of cell-surface proteins.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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18
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Yang JL, Yamada-Hunter SA, Labanieh L, Sotillo E, Cheah JS, Roberts DS, Mackall CL, Ting AY, Bertozzi CR. Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567117. [PMID: 38014030 PMCID: PMC10680704 DOI: 10.1101/2023.11.14.567117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin like growth factor 2 (IGF2). After showing initial efficacy with wild type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially-selective targeted protein degradation.
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Affiliation(s)
- Jonathan Lee Yang
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Sean A. Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louai Labanieh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Sotillo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joleen S. Cheah
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
| | - David S. Roberts
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94305, USA
| | - Alice Y. Ting
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Departments of Biology, and Genetics Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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19
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Fan X, Yan X, Han S. Enzyme-mediated proximity labeling for mapping molecular interactions. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2680-2683. [PMID: 37612532 DOI: 10.1007/s11427-023-2411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 08/25/2023]
Affiliation(s)
- Xinrui Fan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xinwen Yan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuo Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.
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20
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Nguyen PTT, Dinh TT, Tran-Van H. Construction of L-type lectin displaying Saccharomyces cerevisiae for Vibrio parahaemolyticus agglutination. Int Microbiol 2023:10.1007/s10123-023-00440-3. [PMID: 37889383 DOI: 10.1007/s10123-023-00440-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
The utilization of Aga1P anchor protein in the display system for expressing heterologous proteins on the surface of Saccharomyces cerevisiae has been shown to be an ideal approach. This system has the ability to improve the expression of target proteins beyond the cell surface, resulting in increased activity and stability of the expression system. Recent studies have demonstrated that a new L-type lectin from Litopenaeus vannamei (LvLTLC1) has been found to possess the capability of agglutinating Vibrio parahaemolyticus, a pathogen responsible for causing acute hepatopancreatic necrosis disease (AHPND) in shrimp. In this study, LvLTLC1 protein was designed to be expressed on the surface of S. cerevisiae via Aga1P anchor. The expression of LvLTLC1 protein on the surface of S. cerevisiae::pYIP-LvLTLC1-Aga1P was confirmed through the use of analytical techniques including SDS-PAGE, dot blot, and fluorescent immunoassay with LvLTC1-specific antibody. Subsequently, the newly generated yeast strain was evaluated for its ability to agglutinate V. parahaemolyticus and A. hydrophila. The obtained results indicated that S. cerevisiae expressing LvLTLC1 protein on its surface had the ability to agglutinate both AHPND-causing V. parahaemolyticus and A. hydrophila. This newly generated yeast strain could be served as a feed supplement for controlling bacteria in general and AHPND in particular.
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Affiliation(s)
- Phuong-Thao Thi Nguyen
- Department of Molecular and Environmental Biotechnology; Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Faculty of Agriculture and Food Technology, Tien Giang University, My Tho, Vietnam
| | - Thuan-Thien Dinh
- Department of Molecular and Environmental Biotechnology; Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hieu Tran-Van
- Department of Molecular and Environmental Biotechnology; Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
- Vietnam National University, Ho Chi Minh City, Vietnam.
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21
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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22
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Liu Z, Jillette N, Robson P, Cheng AW. Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold. Nucleic Acids Res 2023; 51:e77. [PMID: 37395412 PMCID: PMC10415119 DOI: 10.1093/nar/gkad547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
RNA processing and metabolism are subjected to precise regulation in the cell to ensure integrity and functions of RNA. Though targeted RNA engineering has become feasible with the discovery and engineering of the CRISPR-Cas13 system, simultaneous modulation of different RNA processing steps remains unavailable. In addition, off-target events resulting from effectors fused with dCas13 limit its application. Here we developed a novel platform, Combinatorial RNA Engineering via Scaffold Tagged gRNA (CREST), which can simultaneously execute multiple RNA modulation functions on different RNA targets. In CREST, RNA scaffolds are appended to the 3' end of Cas13 gRNA and their cognate RNA binding proteins are fused with enzymatic domains for manipulation. Taking RNA alternative splicing, A-to-G and C-to-U base editing as examples, we developed bifunctional and tri-functional CREST systems for simultaneously RNA manipulation. Furthermore, by fusing two split fragments of the deaminase domain of ADAR2 to dCas13 and/or PUFc respectively, we reconstituted its enzyme activity at target sites. This split design can reduce nearly 99% of off-target events otherwise induced by a full-length effector. The flexibility of the CREST framework will enrich the transcriptome engineering toolbox for the study of RNA biology.
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Affiliation(s)
- Zukai Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Albert Wu Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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23
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [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] [Indexed: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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24
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Huang W, Yuan H, Yang H, Ma X, Huang S, Zhang H, Huang S, Chen G, Ouyang G. Green synthesis of stable hybrid biocatalyst using a hydrogen-bonded, π-π-stacking supramolecular assembly for electrochemical immunosensor. Nat Commun 2023; 14:3644. [PMID: 37339954 DOI: 10.1038/s41467-023-39364-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
Rational integration of native enzymes and nanoscaffold is an efficient means to access robust biocatalyst, yet remains on-going challenges due to the trade-off between fragile enzymes and harsh assembling conditions. Here, we report a supramolecular strategy enabling the in situ fusion of fragile enzymes into a robust porous crystal. A c2-symmetric pyrene tecton with four formic acid arms is utilized as the building block to engineer this hybrid biocatalyst. The decorated formic acid arms afford the pyrene tectons high dispersibility in minute amount of organic solvent, and permit the hydrogen-bonded linkage of discrete pyrene tectons to an extended supramolecular network around an enzyme in almost organic solvent-free aqueous solution. This hybrid biocatalyst is covered by long-range ordered pore channels, which can serve as the gating to sieve the catalytic substrate and thus enhance the biocatalytic selectivity. Given the structural integration, a supramolecular biocatalyst-based electrochemical immunosensor is developed, enabling the pg/mL detection of cancer biomarker.
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Affiliation(s)
- Wei Huang
- School of Chemical Engineering and Technology, Sun Yat-sen University, 519082, Zhuhai, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, China
| | - Haitao Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University), 518020, Shenzhen, China
| | - Huangsheng Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xiaomin Ma
- Cryo-EM Center, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shuyao Huang
- Instrumental Analysis and Research Center, Sun Yat-sen University, 510275, Guangzhou, China
| | - Hongjie Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, China
| | - Siming Huang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, 511436, Guangzhou, China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 510275, Guangzhou, China.
| | - Gangfeng Ouyang
- School of Chemical Engineering and Technology, Sun Yat-sen University, 519082, Zhuhai, China.
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25
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Ban Ž, Barišić A, Crnolatac I, Kazazić S, Škulj S, Savini F, Bertoša B, Barišić I, Piantanida I. Highly selective preparation of N-terminus Horseradish peroxidase-DNA conjugate with fully retained enzymatic activity: HRP-DNA structure - activity relation. Enzyme Microb Technol 2023; 168:110257. [PMID: 37209508 DOI: 10.1016/j.enzmictec.2023.110257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Within the last decade, the field of bio-nanoengineering has achieved significant advances allowing us to generate, e.g., nanoscaled molecular machineries with arbitrary shapes. To unleash the full potential of novel methods such as DNA origami technology, it is important to functionalise complex molecules and nanostructures precisely. Thus, considerable attention has been given to site-selective modifications of proteins allowing further incorporation of various functionalities. Here, we describe a method for the covalent attachment of oligonucleotides to the glycosylated horseradish peroxidase protein (HRP) with high N-terminus selectivity and significant yield while conserving the enzymatic activity. This two-step process includes a pH-controlled metal-free diazotransfer reaction using imidazole-1-sulfonyl azide hydrogen sulfate, which at pH 8.5 results in an N-terminal azide-functionalized protein, followed by the Cu-free click SPAAC reaction to dibenzocyclooctyne- (DBCO) modified oligonucleotides. The reaction conditions were optimised to achieve maximum yield and the best performance. The resulting protein-oligonucleotide conjugates (HRP-DNA) were characterised by electrophoresis and mass spectrometry (MS). Native-PAGE experiments demonstrated different migration patterns for HRP-DNA and the azido-modified protein allowing zymogram experiments. Structure-activity relationships of novel HRP-DNA conjugates were assessed using molecular dynamics simulations, characterising the molecular interactions that define the structural and dynamical properties of the obtained protein-oligonucleotide conjugates (POC).
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Saša Kazazić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Ivan Barišić
- AIT Austrian Institute of Technology,Vienna, Austria.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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26
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A multifunctional peroxidase-based reaction for imaging, sensing and networking of spatial biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119428. [PMID: 36610614 DOI: 10.1016/j.bbamcr.2022.119428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
Peroxidase is a heme-containing enzyme that reduces hydrogen peroxide to water by extracting electron(s) from aromatic compounds via a sequential turnover reaction. This reaction can generate various aromatic radicals in the form of short-lived "spray" molecules. These can be either covalently attached to proximal proteins or polymerized via radical-radical coupling. Recent studies have shown that these peroxidase-generated radicals can be utilized as effective tools for spatial research in biological systems, including imaging studies aimed at the spatial localization of proteins using electron microscopy, spatial proteome mapping, and spatial sensing of metabolites (e.g., heme and hydrogen peroxide). This review may facilitate the wider utilization of these peroxidase-based methods for spatial discovery in cellular biology.
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27
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Zhuo Y, Robleto VL, Marchese A. Proximity Labeling to Identify β-Arrestin1 Binding Partners Downstream of Ligand-Activated G Protein-Coupled Receptors. Int J Mol Sci 2023; 24:3285. [PMID: 36834700 PMCID: PMC9967311 DOI: 10.3390/ijms24043285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
β-arrestins are multifaceted adaptor proteins that regulate various aspects of G protein-coupled receptor (GPCR) signaling. β-arrestins are recruited to agonist-activated and phosphorylated GPCRs at the plasma membrane, thereby preventing G protein coupling, while also targeting GPCRs for internalization via clathrin-coated pits. In addition, β-arrestins can activate various effector molecules to prosecute their role in GPCR signaling; however, the full extent of their interacting partners remains unknown. To discover potentially novel β-arrestin interacting partners, we used APEX-based proximity labeling coupled with affinity purification and quantitative mass spectrometry. We appended APEX in-frame to the C-terminus of β-arrestin1 (βarr1-APEX), which we show does not impact its ability to support agonist-stimulated internalization of GPCRs. By using coimmunoprecipitation, we show that βarr1-APEX interacts with known interacting proteins. Furthermore, following agonist stimulation βarr1-APEX labeled known βarr1-interacting partners as assessed by streptavidin affinity purification and immunoblotting. Aliquots were prepared in a similar manner and analyzed by tandem mass tag labeling and high-content quantitative mass spectrometry. Several proteins were found to be increased in abundance following GPCR stimulation. Biochemical experiments confirmed two novel proteins that interact with β-arrestin1, which we predict are novel ligand-stimulated βarr1 interacting partners. Our study highlights that βarr1-APEX-based proximity labeling represents a valuable approach to identifying novel players involved in GPCR signaling.
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Affiliation(s)
| | | | - Adriano Marchese
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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28
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Zhou G, Wan WW, Wang W. Modular Peroxidase-Based Reporters for Detecting Protease Activity and Protein Interactions with Temporal Gating. J Am Chem Soc 2022; 144:22933-22940. [PMID: 36511757 PMCID: PMC10026560 DOI: 10.1021/jacs.2c08280] [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] [Indexed: 12/15/2022]
Abstract
Enzymatic reporters have been widely applied to study various biological processes because they can amplify signal through enzymatic reactions and provide good sensitivity. However, there is still a need for modular motifs for designing a series of enzymatic reporters. Here, we report a modular peroxidase-based motif, named CLAPon, that features acid-base coil-caged enhanced ascorbate peroxidase (APEX). We demonstrate the modularity of CLAPon by designing a series of reporters for detecting protease activity and protein-protein interactions (PPIs). CLAPon for protease activity showed a 390-fold fluorescent signal increase upon tobacco etch virus protease cleavage. CLAPon for PPI detection (PPI-CLAPon) has two variants, PPI-CLAPon1.0 and 1.1. PPI-CLAPon1.0 showed a signal-to-noise ratio (SNR) of up to 107 for high-affinity PPI pairs and enabled imaging with sub-cellular spatial resolution. However, the more sensitive PPI-CLAPon1.1 is required for detecting low-affinity PPI pairs. PPI-CLAPon1.0 was further engineered to a reporter with light-dependent temporal gating, called LiPPI-CLAPon1.0, which can detect a 3-min calcium-dependent PPI with an SNR of 17. LiPPI-CLAPon enables PPI detection within a specific time window with rapid APEX activation and diverse readout. Lastly, PPI-CLAPon1.0 was designed to have chemical gating, providing more versatility to complement the LiPPI-CLAPon. These CLAPon-based reporter designs can be broadly applied to study various signaling processes that involve protease activity and PPIs and provide a versatile platform to design various genetically encoded reporters.
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Affiliation(s)
- Guanwei Zhou
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Wei Wan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Corresponding Author: Wenjing Wang,
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29
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Bechtel TJ, Bertoch JM, Olow AK, Duich M, White CH, Reyes-Robles T, Fadeyi OO, Oslund RC. Proteomic mapping of intercellular synaptic environments via flavin-dependent photoredox catalysis. Org Biomol Chem 2022; 21:98-106. [PMID: 36477737 DOI: 10.1039/d2ob02103j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Receptor-ligand interactions play essential signaling roles within intercellular contact regions. This is particularly important within the context of the immune synapse where protein communication at the surface of physically interacting T cells and antigen-presenting cells regulate downstream immune signaling responses. To identify protein microenvironments within immunological synapses, we combined a flavin-dependent photocatalytic labeling strategy with quantitative mass spectrometry-based proteomics. Using α-PD-L1 or α-PD-1 single-domain antibody (VHH)-based photocatalyst targeting modalities, we profiled protein microenvironments within the intercellular region of an immune synapse-forming co-culture system. In addition to enrichment of both PD-L1 and PD-1 with either targeting modality, we also observed enrichment of both known immune synapse residing receptor-ligand pairs and surface proteins, as well as previously unknown synapse residing proteins.
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Affiliation(s)
- Tyler J Bechtel
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Jayde M Bertoch
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Aleksandra K Olow
- Genetics and Pharmacogenomics, Merck & Co., Inc., South San Francisco, CA, 94080, USA
| | - Margaret Duich
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Cory H White
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | | | | | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
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30
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Li R, Fan L, Chen S, Wang L, Cui Y, Ma G, Zhang X, Liu Z. Zwitterionic Sulfhydryl Sulfobetaine Stabilized Platinum Nanoparticles for Enhanced Dopamine Detection and Antitumor Ability. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55201-55216. [PMID: 36458592 DOI: 10.1021/acsami.2c15863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, three kinds of molecules were used to modify the surface of platinum nanoparticles (Pt NPs) to tune their surface charge. Zwitterionic thiol-functionalized sulfobetaine (SH-SB) stabilized Pt NPs (SH-SB/Pt NPs) had the highest oxidase activity and peroxidase activity in the prepared platinum nanozymes due to the generation of reactive oxygen species. In addition, a colorimetric dopamine detection method was established based on the peroxidase activity of SH-SB/Pt NPs. This method had a wide range (0-120 μM), a low detection limit (0.244 μM), and high specificity. More importantly, SH-SB/Pt NPs displayed little hemolysis and good stability in the presence of proteins. SH-SB/Pt NPs demonstrated high cytotoxicity in vitro and good antitumor ability in vivo, which was attributed to the photothermal conversion ability of SH-SB/Pt NPs and the generation of reactive oxygen species in the acidic environment. The surface modification of nanozymes using zwitterionic molecules opens a new method to improve the catalytic activity and antitumor ability of nanozymes.
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Affiliation(s)
- Ruyu Li
- State Key Laboratory of Metastable Materials Science and Technology, Hebei Key Laboratory of Nano-biotechnology, Hebei Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao066004, China
| | - Liyuan Fan
- State Key Laboratory of Metastable Materials Science and Technology, Hebei Key Laboratory of Nano-biotechnology, Hebei Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao066004, China
| | - Shengfu Chen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang310027, China
| | - Longgang Wang
- State Key Laboratory of Metastable Materials Science and Technology, Hebei Key Laboratory of Nano-biotechnology, Hebei Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao066004, China
| | - Yanshuai Cui
- Hebei University of Environmental Engineering, Qinhuangdao066102, China
| | - Guanglong Ma
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, SouthamptonSO166YD, United Kingdom
| | - Xiaoyu Zhang
- State Key Laboratory of Metastable Materials Science and Technology, Hebei Key Laboratory of Nano-biotechnology, Hebei Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao066004, China
| | - Zhiwei Liu
- State Key Laboratory of Metastable Materials Science and Technology, Hebei Key Laboratory of Nano-biotechnology, Hebei Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao066004, China
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31
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Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling. Mol Cell Proteomics 2022; 21:100422. [PMID: 36198386 PMCID: PMC9650050 DOI: 10.1016/j.mcpro.2022.100422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular biomolecular complexes including protein-protein, protein-RNA, and protein-DNA interactions regulate and execute most biological functions. In particular in brain, protein-protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell-cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte-neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.
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Affiliation(s)
- Boby Mathew
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, Connecticut, USA; Department of Psychiatry, Yale University, New Haven, Connecticut, USA.
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32
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Skeeters SS, Camp T, Fan H, Zhang K. The expanding role of split protein complementation in opsin-free optogenetics. Curr Opin Pharmacol 2022; 65:102236. [PMID: 35609383 PMCID: PMC9308681 DOI: 10.1016/j.coph.2022.102236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
A comprehensive understanding of signaling mechanisms helps interpret fundamental biological processes and restore cell behavior from pathological conditions. Signaling outcome depends not only on the activity of each signaling component but also on their dynamic interaction in time and space, which remains challenging to probe by biochemical and cell-based assays. Opsin-based optogenetics has transformed neural science research with its spatiotemporal modulation of the activity of excitable cells. Motivated by this advantage, opsin-free optogenetics extends the power of light to a larger spectrum of signaling molecules. This review summarizes commonly used opsin-free optogenetic strategies, presents a historical overview of split protein complementation, and highlights the adaptation of split protein recombination as optogenetic sensors and actuators.
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33
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Oslund RC, Reyes-Robles T, White CH, Tomlinson JH, Crotty KA, Bowman EP, Chang D, Peterson VM, Li L, Frutos S, Vila-Perelló M, Vlerick D, Cromie K, Perlman DH, Ingale S, Hara SDO, Roberts LR, Piizzi G, Hett EC, Hazuda DJ, Fadeyi OO. Detection of cell-cell interactions via photocatalytic cell tagging. Nat Chem Biol 2022; 18:850-858. [PMID: 35654846 DOI: 10.1038/s41589-022-01044-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.
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Affiliation(s)
- Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
| | | | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Jake H Tomlinson
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Kelly A Crotty
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Edward P Bowman
- Discovery Research, Merck & Co., Inc., San Francisco, CA, USA
| | - Dan Chang
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | - Lixia Li
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | | | - David H Perlman
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Sampat Ingale
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | | | - Lee R Roberts
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.,Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA
| | - Olugbeminiyi O Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
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34
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Kuťák D, Melo L, Schroeder F, Jelic-Matošević Z, Mutter N, Bertoša B, Barišić I. CATANA: an online modelling environment for proteins and nucleic acid nanostructures. Nucleic Acids Res 2022; 50:W152-W158. [PMID: 35544315 PMCID: PMC9252799 DOI: 10.1093/nar/gkac350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.
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Affiliation(s)
- David Kuťák
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia.,Visitlab, Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Lucas Melo
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Fabian Schroeder
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Zoe Jelic-Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Natalie Mutter
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
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35
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Proximity labeling methods for proteomic analysis of membrane proteins. J Proteomics 2022; 264:104620. [DOI: 10.1016/j.jprot.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
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36
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Buksh BF, Knutson SD, Oakley JV, Bissonnette NB, Oblinsky DG, Schwoerer MP, Seath CP, Geri JB, Rodriguez-Rivera FP, Parker DL, Scholes GD, Ploss A, MacMillan DWC. μMap-Red: Proximity Labeling by Red Light Photocatalysis. J Am Chem Soc 2022; 144:6154-6162. [PMID: 35363468 PMCID: PMC9843638 DOI: 10.1021/jacs.2c01384] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Modern proximity labeling techniques have enabled significant advances in understanding biomolecular interactions. However, current tools primarily utilize activation modes that are incompatible with complex biological environments, limiting our ability to interrogate cell- and tissue-level microenvironments in animal models. Here, we report μMap-Red, a proximity labeling platform that uses a red-light-excited SnIV chlorin e6 catalyst to activate a phenyl azide biotin probe. We validate μMap-Red by demonstrating photonically controlled protein labeling in vitro through several layers of tissue, and we then apply our platform in cellulo to label EGFR microenvironments and validate performance with STED microscopy and quantitative proteomics. Finally, to demonstrate labeling in a complex biological sample, we deploy μMap-Red in whole mouse blood to profile erythrocyte cell-surface proteins. This work represents a significant methodological advance toward light-based proximity labeling in complex tissue environments and animal models.
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Affiliation(s)
- Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - James V Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Noah B Bissonnette
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Michael P Schwoerer
- Department of Molecular Biology, Princeton University, Princeton, New Jersey08544, United States
| | - Ciaran P Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Jacob B Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | | | - Dann L Parker
- Discovery Chemistry, Merck & Co., Kenilworth, New Jersey07033, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey08544, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey08544, United States
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37
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Cho KF, Gillespie SM, Kalogriopoulos NA, Quezada MA, Jacko M, Monje M, Ting AY. A light-gated transcriptional recorder for detecting cell-cell contacts. eLife 2022; 11:e70881. [PMID: 35311648 PMCID: PMC8937215 DOI: 10.7554/elife.70881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/25/2022] [Indexed: 01/21/2023] Open
Abstract
Technologies for detecting cell-cell contacts are powerful tools for studying a wide range of biological processes, from neuronal signaling to cancer-immune interactions within the tumor microenvironment. Here, we report TRACC (Transcriptional Readout Activated by Cell-cell Contacts), a GPCR-based transcriptional recorder of cellular contacts, which converts contact events into stable transgene expression. TRACC is derived from our previous protein-protein interaction recorders, SPARK (Kim et al., 2017) and SPARK2 (Kim et al., 2019), reported in this journal. TRACC incorporates light gating via the light-oxygen-voltage-sensing (LOV) domain, which provides user-defined temporal control of tool activation and reduces background. We show that TRACC detects cell-cell contacts with high specificity and sensitivity in mammalian cell culture and that it can be used to interrogate interactions between neurons and glioma, a form of brain cancer.
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Affiliation(s)
- Kelvin F Cho
- Cancer Biology Program, Stanford UniversityStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Shawn M Gillespie
- Cancer Biology Program, Stanford UniversityStanfordUnited States
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
| | | | - Michael A Quezada
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
| | | | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford UniversityStanfordUnited States
- Department of Pathology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford UniversityStanfordUnited States
- Department of Neurosurgery, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Chemistry, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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38
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Kirkemo LL, Elledge SK, Yang J, Byrnes JR, Glasgow JE, Blelloch R, Wells JA. Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells. eLife 2022; 11:73982. [PMID: 35257663 PMCID: PMC8983049 DOI: 10.7554/elife.73982] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Characterization of cell surface proteome differences between cancer and healthy cells is a valuable approach for the identification of novel diagnostic and therapeutic targets. However, selective sampling of surface proteins for proteomics requires large samples (>10e6 cells) and long labeling times. These limitations preclude analysis of material-limited biological samples or the capture of rapid surface proteomic changes. Here, we present two labeling approaches to tether exogenous peroxidases (APEX2 and HRP) directly to cells, enabling rapid, small-scale cell surface biotinylation without the need to engineer cells. We used a novel lipidated DNA-tethered APEX2 (DNA-APEX2), which upon addition to cells promoted cell agnostic membrane-proximal labeling. Alternatively, we employed horseradish peroxidase (HRP) fused to the glycan-binding domain of wheat germ agglutinin (WGA-HRP). This approach yielded a rapid and commercially inexpensive means to directly label cells containing common N-Acetylglucosamine (GlcNAc) and sialic acid glycans on their surface. The facile WGA-HRP method permitted high surface coverage of cellular samples and enabled the first comparative surface proteome characterization of cells and cell-derived small extracellular vesicles (EVs), leading to the robust quantification of 953 cell and EV surface annotated proteins. We identified a newly recognized subset of EV-enriched markers, as well as proteins that are uniquely upregulated on Myc oncogene-transformed prostate cancer EVs. These two cell-tethered enzyme surface biotinylation approaches are highly advantageous for rapidly and directly labeling surface proteins across a range of material-limited sample types.
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Affiliation(s)
- Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jiuling Yang
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Robert Blelloch
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
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39
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Dionne U, Gingras AC. Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome. Front Mol Biosci 2022; 9:852911. [PMID: 35309513 PMCID: PMC8930824 DOI: 10.3389/fmolb.2022.852911] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.
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Affiliation(s)
- Ugo Dionne
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Anne-Claude Gingras,
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40
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Mair A, Bergmann DC. Advances in enzyme-mediated proximity labeling and its potential for plant research. PLANT PHYSIOLOGY 2022; 188:756-768. [PMID: 34662401 PMCID: PMC8825456 DOI: 10.1093/plphys/kiab479] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/21/2021] [Indexed: 06/12/2023]
Abstract
Cellular processes rely on the intimate interplay of different molecules, including DNA, RNA, proteins, and metabolites. Obtaining and integrating data on their abundance and dynamics at high temporal and spatial resolution are essential for our understanding of plant growth and development. In the past decade, enzymatic proximity labeling (PL) has emerged as a powerful tool to study local protein and nucleotide ensembles, discover protein-protein and protein-nucleotide interactions, and resolve questions about protein localization and membrane topology. An ever-growing number and continuous improvement of enzymes and methods keep broadening the spectrum of possible applications for PL and make it more accessible to different organisms, including plants. While initial PL experiments in plants required high expression levels and long labeling times, recently developed faster enzymes now enable PL of proteins on a cell type-specific level, even with low-abundant baits, and in different plant species. Moreover, expanding the use of PL for additional purposes, such as identification of locus-specific gene regulators or high-resolution electron microscopy may now be in reach. In this review, we give an overview of currently available PL enzymes and their applications in mammalian cell culture and plants. We discuss the challenges and limitations of PL methods and highlight open questions and possible future directions for PL in plants.
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Affiliation(s)
- Andrea Mair
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Dominique C Bergmann
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, California 94305, USA
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41
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Lee J, Liao H, Wang Q, Han J, Han J, Shin HE, Ge M, Park W, Li F. Exploration of nanozymes in viral diagnosis and therapy. EXPLORATION (BEIJING, CHINA) 2022; 2:20210086. [PMID: 37324577 PMCID: PMC10191057 DOI: 10.1002/exp.20210086] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/21/2021] [Indexed: 06/15/2023]
Abstract
Nanozymes are nanomaterials with similar catalytic activities to natural enzymes. Compared with natural enzymes, they have numerous advantages, including higher physiochemical stability, versatility, and suitability for mass production. In the past decade, the synthesis of nanozymes and their catalytic mechanisms have advanced beyond the simple replacement of natural enzymes, allowing for fascinating applications in various fields such as biosensing and disease treatment. In particular, the exploration of nanozymes as powerful toolkits in diagnostic viral testing and antiviral therapy has attracted growing attention. It can address the great challenges faced by current natural enzyme-based viral testing technologies, such as high cost and storage difficulties. Therefore, nanozyme can provide a novel nanozyme-based antiviral therapeutic regime with broader availability and generalizability that are keys to fighting a pandemic such as COVID-19. Herein, we provide a timely review of the state-of-the-art nanozymes regarding their catalytic activities, as well as a focused discussion on recent research into the use of nanozymes in viral testing and therapy. The remaining challenges and future perspectives will also be outlined. Ultimately, this review will inform readers of the current knowledge of nanozymes and inspire more innovative studies to push forward the frontier of this field.
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Affiliation(s)
- Jiyoung Lee
- Institute of PharmaceuticsCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiangP. R. China
| | - Hongwei Liao
- Institute of PharmaceuticsCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiangP. R. China
| | - Qiyue Wang
- Institute of PharmaceuticsCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiangP. R. China
| | - Jieun Han
- Department of Biomedical‐Chemical Engineering and BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
- Department of BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
| | - Jun‐Hyeok Han
- Department of Biomedical‐Chemical Engineering and BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
- Department of BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
- Department of Biological ScienceKorea UniversitySeoulRepublic of Korea
| | - Ha Eun Shin
- Department of Biomedical‐Chemical Engineering and BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
- Department of BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
| | - Minghua Ge
- Zhejiang Provincial People's Hospital HangzhouHangzhouP. R. China
| | - Wooram Park
- Department of Biomedical‐Chemical Engineering and BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
- Department of BiotechnologyThe Catholic University of KoreaBucheonGyeonggiRepublic of Korea
| | - Fangyuan Li
- Institute of PharmaceuticsCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiangP. R. China
- Hangzhou Institute of Innovative MedicineCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouP. R. China
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42
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Kushner JS, Liu G, Eisert RJ, Bradshaw GA, Pitt GS, Hinson JT, Kalocsay M, Marx SO. Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics. Circ Res 2022; 130:273-287. [PMID: 35050691 PMCID: PMC8852690 DOI: 10.1161/circresaha.121.319810] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity purification and mass spectrometry, have revealed many macromolecular complexes in cardiomyocytes and the vasculature. Yet these methods often fail to identify in vivo or transient protein-protein interactions. To capture these interactions in living cells and animals with subsequent mass spectrometry identification, enzyme-catalyzed proximity labeling techniques have been developed in the past decade. Although the application of this methodology to cardiovascular research is still in its infancy, the field is developing rapidly, and the promise is substantial. In this review, we outline important concepts and discuss how proximity proteomics has been applied to study physiological and pathophysiological processes relevant to the cardiovascular system.
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Affiliation(s)
- Jared S. Kushner
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Guoxia Liu
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Robyn J. Eisert
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Gary A. Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Geoffrey S. Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College
| | - J. Travis Hinson
- Cardiology Center, UConn Health, Farmington, CT
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Marian Kalocsay
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Steven O. Marx
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
- Department of Molecular Pharmacology and Therapeutics, Columbia University, Vagelos College of Physicians and Surgeons
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43
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Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods Cell Biol 2022; 169:237-266. [PMID: 35623704 PMCID: PMC10782847 DOI: 10.1016/bs.mcb.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study of protein complexes and protein-protein interactions is of great importance due to their fundamental roles in cellular function. Proximity labeling, often coupled with mass spectrometry, has become a powerful and versatile tool for studying protein-protein interactions by enriching and identifying proteins in the vicinity of a specified protein-of-interest. Here, we describe and compare traditional approaches to investigate protein-protein interactions to current day state-of-the-art proximity labeling methods. We focus on the wide array of proximity labeling strategies and underscore studies using diverse model systems to address numerous biological questions. In addition, we highlight current advances in mass spectrometry-based technology that exhibit promise in improving the depth and breadth of the data acquired in proximity labeling experiments. In all, we show the diversity of proximity labeling strategies and emphasize the broad range of applications and biological inquiries that can be addressed using this technology.
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Affiliation(s)
- Conrad T Pfeiffer
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC, United States.
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44
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Škulj S, Barišić A, Mutter N, Spadiut O, Barišić I, Bertoša B. Effect of N-glycosylation on horseradish peroxidase structural and dynamical properties. Comput Struct Biotechnol J 2022; 20:3096-3105. [PMID: 35782731 PMCID: PMC9233188 DOI: 10.1016/j.csbj.2022.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022] Open
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45
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Siva Sankar D, Dengjel J. Protein complexes and neighborhoods driving autophagy. Autophagy 2021; 17:2689-2705. [PMID: 33183148 PMCID: PMC8526019 DOI: 10.1080/15548627.2020.1847461] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023] Open
Abstract
Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms.Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
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Affiliation(s)
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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46
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Kimmel J, Kehrer J, Frischknecht F, Spielmann T. Proximity-dependent biotinylation approaches to study apicomplexan biology. Mol Microbiol 2021; 117:553-568. [PMID: 34587292 DOI: 10.1111/mmi.14815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
In the last 10 years, proximity-dependent biotinylation (PDB) techniques greatly expanded the ability to study protein environments in the living cell that range from specific protein complexes to entire compartments. This is achieved by using enzymes such as BirA* and APEX that are fused to proteins of interest and biotinylate proteins in their proximity. PDB techniques are now also increasingly used in apicomplexan parasites. In this review, we first give an overview of the main PDB approaches and how they compare with other techniques that address similar questions. PDB is particularly valuable to detect weak or transient protein associations under physiological conditions and to study cellular structures that are difficult to purify or have a poorly understood protein composition. We also highlight new developments such as novel smaller or faster-acting enzyme variants and conditional PDB approaches, providing improvements in both temporal and spatial resolution which may offer broader application possibilities useful in apicomplexan research. In the second part, we review work using PDB techniques in apicomplexan parasites and how this expanded our knowledge about these medically important parasites.
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Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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47
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Kushner J, Papa A, Marx SO. Use of Proximity Labeling in Cardiovascular Research. JACC Basic Transl Sci 2021; 6:598-609. [PMID: 34368510 PMCID: PMC8326230 DOI: 10.1016/j.jacbts.2021.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 10/31/2022]
Abstract
Protein-protein interactions are of paramount importance in regulating normal cardiac physiology. Methodologies to elucidate these interactions in vivo have been limited. Recently, proximity-dependent biotinylation, with the use of BioID, TurboID, and ascorbate peroxidase, has been developed to uncover cellular neighborhoods and novel protein-protein interactions. These cutting-edge techniques have enabled the identification of subcellular localizations of specific proteins and the neighbors or interacting proteins within these subcellular regions. In contrast to classic methods such as affinity purification and subcellular fractionation, these techniques add covalently bound tags in living cells, such that spatial relationships and interaction networks are not disrupted. Recently, these methodologies have been used to identify novel protein-protein interactions relevant to the cardiovascular system. In this review, we discuss the development and current use of proximity biotin-labeling for cardiovascular research.
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Affiliation(s)
- Jared Kushner
- Division of Cardiology, Department of Medicine, Columbia University, Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Arianne Papa
- Department of Physiology and Cellular Biophysics, Columbia University, Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Steven O. Marx
- Division of Cardiology, Department of Medicine, Columbia University, Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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48
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Strategies for monitoring cell-cell interactions. Nat Chem Biol 2021; 17:641-652. [PMID: 34035514 DOI: 10.1038/s41589-021-00790-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023]
Abstract
Multicellular organisms depend on physical cell-cell interactions to control physiological processes such as tissue formation, neurotransmission and immune response. These intercellular binding events can be both highly dynamic in their duration and complex in their composition, involving the participation of many different surface and intracellular biomolecules. Untangling the intricacy of these interactions and the signaling pathways they modulate has greatly improved insight into the biological processes that ensue upon cell-cell engagement and has led to the development of protein- and cell-based therapeutics. The importance of monitoring physical cell-cell interactions has inspired the development of several emerging approaches that effectively interrogate cell-cell interfaces with molecular-level detail. Specifically, the merging of chemistry- and biology-based technologies to deconstruct the complexity of cell-cell interactions has provided new avenues for understanding cell-cell interaction biology and opened opportunities for therapeutic development.
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49
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Tripartite synaptomics: Cell-surface proximity labeling in vivo. Neurosci Res 2021; 173:14-21. [PMID: 34019951 DOI: 10.1016/j.neures.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 11/23/2022]
Abstract
The astrocyte is a central glial cell and plays a critical role in the architecture and activity of neuronal circuits and brain functions through forming a tripartite synapse with neurons. Emerging evidence suggests that dysfunction of tripartite synaptic connections contributes to a variety of psychiatric and neurodevelopmental disorders. Furthermore, recent advancements with transcriptome profiling, cell biological and physiological approaches have provided new insights into the molecular mechanisms into how astrocytes control synaptogenesis in the brain. In addition to these findings, we have recently developed in vivo cell-surface proximity-dependent biotinylation (BioID) approaches, TurboID-surface and Split-TurboID, to comprehensively understand the molecular composition between astrocytes and neuronal synapses. These proteomic approaches have discovered a novel molecular framework for understanding the tripartite synaptic cleft that arbitrates neuronal circuit formation and function. Here, this short review highlights novel in vivo cell-surface BioID approaches and recent advances in this rapidly evolving field, emphasizing how astrocytes regulate excitatory and inhibitory synapse formation in vitro and in vivo.
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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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