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Xie X, Yang X, Zhang Y, Mao F, He Z, Sun Z, Zhang S, Liu X. Ready-to-use ratiometric bioluminescence immunosensor for detection of ochratoxin a in pepper. Biosens Bioelectron 2024; 259:116401. [PMID: 38761743 DOI: 10.1016/j.bios.2024.116401] [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: 01/25/2024] [Revised: 04/17/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Rapid, portable, and accurate detection tools for monitoring ochratoxin A (OTA) in food are essential for the guarantee of food safety and human health. Herein, as a proof-of-concept, this study proposed a ratiometric bioluminescence immunosensor (RBL-immunosensor) for homogeneous detection of OTA in pepper. The construct of the RBL-immunosensor consists of three components, including the large fragment of the split nanoluciferase (NanoLuc)-tagged nanobody (NLg), the small fragment of the split NanoLuc-tagged mimotope peptide heptamer (MPSm), and the calibrator luciferase (GeNL). The specific nanobody-mimotope peptide interaction between NLg and MPSm induces the reconstitution of the NanoLuc, which catalyzes the Nano-Glo substrate and produces a blue emission peak at 458 nm. Meanwhile, GeNL can produce a green emission peak at 518 nm upon substrate conversion via bioluminescent resonance energy transfer (BRET). Therefore, the concentration of OTA can be linked to the variation of the bioluminescence signal (λ458/λ518) measured by microplate reader and the variation of the blue/green ratio measured by smartphone via the competitive immunoreaction where OTA competes with MPSm to bind NLg. The immunosensor is ready-to-use and works by simply mixing the components in a one-step incubation of 10 min for readout. It has a limit of detection (LOD) of 0.98 ng/mL by a microplate reader and an LOD of 1.89 ng/mL by a smartphone. Good selectivity and accuracy were confirmed for the immunosensor by cross-reaction analysis and recovery experiments. The contents of OTA in 10 commercial pepper powder samples were tested by the RBL-immunosensor and validated by high-performance liquid chromatography. Hence, the ready-to-use RBL-immunosensor was demonstrated as a highly reliable tool for detection of OTA in food.
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Affiliation(s)
- Xiaoxia Xie
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xun Yang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yongli Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Fujing Mao
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhenyun He
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhichang Sun
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Sihang Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xing Liu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China.
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2
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Kamada Y, Ohnishi Y, Nakashima C, Fujii A, Terakawa M, Hamano I, Nakayamada U, Katoh S, Hirata N, Tateishi H, Fukuda R, Takahashi H, Lukacs GL, Okiyoneda T. HERC3 facilitates ERAD of select membrane proteins by recognizing membrane-spanning domains. J Cell Biol 2024; 223:e202308003. [PMID: 38722278 PMCID: PMC11082371 DOI: 10.1083/jcb.202308003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. Through a series of multiplex knockdown/knockout experiments with real-time kinetic measurements, we demonstrate that HERC3 operates independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to mediate the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 uniquely promotes CFTR ERAD. In vitro assay revealed that HERC3 directly interacts with the exposed membrane-spanning domains (MSDs) of CFTR but not with the MSDs embedded in liposomes. Therefore, HERC3 could play a role in the quality control of MSDs in the cytoplasm and might be crucial for the ERAD pathway of select membrane proteins.
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Affiliation(s)
- Yuka Kamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Yuko Ohnishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Chikako Nakashima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Aika Fujii
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Mana Terakawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ikuto Hamano
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Uta Nakayamada
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Saori Katoh
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Noriaki Hirata
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hazuki Tateishi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ryosuke Fukuda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), Ehime University, Matsuyama, Japan
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, Canada
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Tsukasa Okiyoneda
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
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3
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Liu A, Liu Y, Zhang W, Ye RD. Structural insights into ligand recognition and activation of the succinate receptor SUCNR1. Cell Rep 2024; 43:114381. [PMID: 38923454 DOI: 10.1016/j.celrep.2024.114381] [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: 04/18/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Succinate, a citric acid cycle intermediate, serves important functions in energy homeostasis and metabolic regulation. Extracellular succinate acts as a stress signal through succinate receptor (SUCNR1), a class A G protein-coupled receptor. Research on succinate signaling is hampered by the lack of high-resolution structures of the agonist-bound receptor. We present cryoelectron microscopy (cryo-EM) structures of SUCNR1-Gi complexes bound to succinate and its non-metabolite derivative cis-epoxysuccinate. Key determinants for the recognition of succinate in cis conformation include R2817.39 and Y832.64, while Y301.39 and R993.29 participate in the binding of both succinate and cis-epoxysuccinate. Extracellular loop 2, through F175ECL2 in its β-hairpin, forms a hydrogen bond with succinate and caps the binding pocket. At the receptor-Gi interface, agonist binding induces the rearrangement of a hydrophobic network on transmembrane (TM)5 and TM6, leading to TM signaling through TM3 and TM7. These findings extend our understanding of succinate recognition by SUCNR1, aiding the development of therapeutics for the succinate receptor.
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Affiliation(s)
- Aijun Liu
- Dongguan Songshan Lake Central Hospital, Dongguan Third People's Hospital, The Affiliated Dongguan Songshan Lake Central Hospital, Guangdong Medical University, Dongguan, Guangdong 523326, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China.
| | - Yezhou Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China
| | - Weijia Zhang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Richard D Ye
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China.
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4
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Lan T, Slezak T, Pu J, Zinkus-Boltz J, Adhikari S, Pekow JR, Taneja V, Zuniga J, Gómez-García IA, Regino-Zamarripa N, Ahmed M, Khader SA, Rubin DT, Kossiakoff AA, Dickinson BC. Development of Luminescent Biosensors for Calprotectin. ACS Chem Biol 2024; 19:1250-1259. [PMID: 38843544 DOI: 10.1021/acschembio.4c00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Calprotectin, a metal ion-binding protein complex, plays a crucial role in the innate immune system and has gained prominence as a biomarker for various intestinal and systemic inflammatory and infectious diseases, including inflammatory bowel disease (IBD) and tuberculosis (TB). Current clinical testing methods rely on enzyme-linked immunosorbent assays (ELISAs), limiting accessibility and convenience. In this study, we introduce the Fab-Enabled Split-luciferase Calprotectin Assay (FESCA), a novel quantitative method for calprotectin measurement. FESCA utilizes two new fragment antigen binding proteins (Fabs), CP16 and CP17, that bind to different epitopes of the calprotectin complex. These Fabs are fused with split NanoLuc luciferase fragments, enabling the reconstitution of active luciferase upon binding to calprotectin either in solution or in varied immobilized assay formats. FESCA's output luminescence can be measured with standard laboratory equipment as well as consumer-grade cell phone cameras. FESCA can detect physiologically relevant calprotectin levels across various sample types, including serum, plasma, and whole blood. Notably, FESCA can detect abnormally elevated native calprotectin from TB patients. In summary, FESCA presents a convenient, low-cost, and quantitative method for assessing calprotectin levels in various biological samples, with the potential to improve the diagnosis and monitoring of inflammatory diseases, especially in at-home or point-of-care settings.
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Affiliation(s)
- Tong Lan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Tomasz Slezak
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jinyue Pu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Julia Zinkus-Boltz
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sarbani Adhikari
- Section of Gastroenterology, Hepatology & Nutrition, University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, Illinois 60637 United States
| | - Joel R Pekow
- Section of Gastroenterology, Hepatology & Nutrition, University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, Illinois 60637 United States
| | - Vibha Taneja
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joaquin Zuniga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Mexico City 01389, Mexico
| | - Itzel A Gómez-García
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 07320, Mexico
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Mexico City 01389, Mexico
| | - Nora Regino-Zamarripa
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias, Mexico City 14080, Mexico
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Mexico City 01389, Mexico
| | - Mushtaq Ahmed
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shabaana A Khader
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - David T Rubin
- Section of Gastroenterology, Hepatology & Nutrition, University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, Illinois 60637 United States
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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5
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Lankford KP, Hulleman JD. Protocol for HiBiT tagging endogenous proteins using CRISPR-Cas9 gene editing. STAR Protoc 2024; 5:103000. [PMID: 38598333 PMCID: PMC11022101 DOI: 10.1016/j.xpro.2024.103000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/05/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
We present a method of in vitro/in vivo protein detection by pairing CRISPR-Cas9 genome editing with the NanoBiT system. We describe steps for cell culturing, in vitro CRISPR-Cas9 ribonucleoprotein delivery, cell monitoring, efficiency assessments, and edit analysis through HiBiT assays. We then detail procedures to determine edit specificity through genomic DNA analysis, small interfering RNA reverse transfection, and HiBiT blotting. This protocol is simple to execute and multifunctional, and it enables high-throughput screens on endogenous proteins to be conducted with ease.
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Affiliation(s)
- Kaylee P Lankford
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John D Hulleman
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, 2001 6(th) St. SE, Minneapolis, MN 55455, USA.
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6
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Guo X, Luo Z, Qi Y, Hei X, Zhang X, Cao X, Qian M, Zhao S, Hou Y, Chen X. Structure optimization of Cmpd-15 as negative allosteric modulators for the β 2-adrenergic receptor. Bioorg Med Chem 2024; 108:117787. [PMID: 38838580 DOI: 10.1016/j.bmc.2024.117787] [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: 03/28/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
19 derivatives of 1-benzyl-3-arylpyrazole-5-carboxamides (H1-H19) and 5 derivatives of 1-benzyl-5-arylpyrazole-3-carboxamides (J1-J5) have been designed and synthesized as potential negative allosteric modulators (NAMs) for the β2-adrenergic receptor (β2AR). The new pyrazole derivatives were screened on the classic G-protein dependent signaling pathway at β2AR. The majority of 1-benzyl-3-aryl-pyrazole-5-carboxamide derivatives show more potent allosteric antagonistic activity against β2AR than Cmpd-15, the first reported β2AR NAM. However, the 1-benzyl-5-arylpyrazole-3-carboxamide derivatives exhibit very poor or even no allosteric antagonistic activity for β2AR. Furthermore, the active pyrazole derivatives have relative better drug-like profiles than Cmpd-15. Taken together, we discovered a series of derivatives of 1-benzyl-3-arylpyrazole-5-carboxamides as a novel scaffold of β2AR NAM.
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Affiliation(s)
- Xue Guo
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Zhijie Luo
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Ying Qi
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Xiaoyuan Hei
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Xin Zhang
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Xuli Cao
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Mingcheng Qian
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Shuai Zhao
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Yanan Hou
- School of Pharmacy, Changzhou University, Jiangsu 213164, China
| | - Xin Chen
- School of Pharmacy, Changzhou University, Jiangsu 213164, China.
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7
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Dietze KA, Nguyen K, Pathni A, Fazekas F, Baker JM, Gebru E, Wang A, Sun W, Rosati E, Lum D, Rapoport AP, Fan X, Atanackovic D, Upadhayaya A, Luetkens T. Preventing trogocytosis by cathepsin B inhibition augments CAR T cell function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598379. [PMID: 38915559 PMCID: PMC11195252 DOI: 10.1101/2024.06.11.598379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has shown remarkable efficacy in cancer treatment. Still, most patients receiving CAR T cells relapse within 5 years of treatment. CAR-mediated trogocytosis (CMT) is a potential tumor escape mechanism in which cell surface proteins transfer from tumor cells to CAR T cells. CMT results in the emergence of antigen-negative tumor cells, which can evade future CAR detection, and antigen-positive CAR T cells, which is hypothesized to lead to CAR T cell fratricide and dysfunction. Using a system to selectively degrade trogocytosed antigen in CAR T cells, we show that the presence of trogocytosed antigen in CAR T cells directly causes CAR T cell fratricide and exhaustion. By performing a small molecule screening using a custom high throughput CMT-screening assay, we identified the cysteine protease cathepsin B (CTSB) as a key driver of CMT. We show that overexpression of cystatin A (CSTA), an endogenous human inhibitor of CTSB, reduces trogocytosis resulting in prolonged antitumor activity and increased CAR T cell expansion/persistence. Overall, we show that targeting CMT is an effective approach to enhance CAR T cell function, which may improve their clinical efficacy. One sentence summary CAR-mediated trogocytosis directly causes CAR T cell exhaustion and fratricide but can be prevented by inhibiting the cysteine protease cathepsin B through overexpression of human cystatins.
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Affiliation(s)
- Kenneth A. Dietze
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kiet Nguyen
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
| | - Aashli Pathni
- Biological Sciences Graduate Program, University of Maryland, College Park, MD, USA
| | - Frank Fazekas
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
| | - Jillian M. Baker
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Etse Gebru
- Department of Medicine and Transplant/Cell Therapy Program, University of Maryland School of Medicine and Marlene and Stewart Greenebaum Comprehensive Cancer Center
| | - Alexander Wang
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wenxiang Sun
- Preclinical Research Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ethan Rosati
- Preclinical Research Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - David Lum
- Preclinical Research Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Aaron P. Rapoport
- Department of Medicine and Transplant/Cell Therapy Program, University of Maryland School of Medicine and Marlene and Stewart Greenebaum Comprehensive Cancer Center
| | - Xiaoxuan Fan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Djordje Atanackovic
- Department of Medicine and Transplant/Cell Therapy Program, University of Maryland School of Medicine and Marlene and Stewart Greenebaum Comprehensive Cancer Center
| | - Arpita Upadhayaya
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Tim Luetkens
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine and Transplant/Cell Therapy Program, University of Maryland School of Medicine and Marlene and Stewart Greenebaum Comprehensive Cancer Center
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8
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Sasaki M, Kato D, Murakami K, Yoshida H, Takase S, Otsubo T, Ogiwara H. Targeting dependency on a paralog pair of CBP/p300 against de-repression of KREMEN2 in SMARCB1-deficient cancers. Nat Commun 2024; 15:4770. [PMID: 38839769 PMCID: PMC11153594 DOI: 10.1038/s41467-024-49063-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex, is the causative gene of rhabdoid tumors and epithelioid sarcomas. Here, we identify a paralog pair of CBP and p300 as a synthetic lethal target in SMARCB1-deficient cancers by using a dual siRNA screening method based on the "simultaneous inhibition of a paralog pair" concept. Treatment with CBP/p300 dual inhibitors suppresses growth of cell lines and tumor xenografts derived from SMARCB1-deficient cells but not from SMARCB1-proficient cells. SMARCB1-containing SWI/SNF complexes localize with H3K27me3 and its methyltransferase EZH2 at the promotor region of the KREMEN2 locus, resulting in transcriptional downregulation of KREMEN2. By contrast, SMARCB1 deficiency leads to localization of H3K27ac, and recruitment of its acetyltransferases CBP and p300, at the KREMEN2 locus, resulting in transcriptional upregulation of KREMEN2, which cooperates with the SMARCA1 chromatin remodeling complex. Simultaneous inhibition of CBP/p300 leads to transcriptional downregulation of KREMEN2, followed by apoptosis induction via monomerization of KREMEN1 due to a failure to interact with KREMEN2, which suppresses anti-apoptotic signaling pathways. Taken together, our findings indicate that simultaneous inhibitors of CBP/p300 could be promising therapeutic agents for SMARCB1-deficient cancers.
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Affiliation(s)
- Mariko Sasaki
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daiki Kato
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Karin Murakami
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shohei Takase
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tsuguteru Otsubo
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hideaki Ogiwara
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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9
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Jin S, Guo S, Xu Y, Li X, Wu C, He X, Pan B, Xin W, Zhang H, Hu W, Yin Y, Zhang T, Wu K, Yuan Q, Xu HE, Xie X, Jiang Y. Structural basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor. Cell Discov 2024; 10:58. [PMID: 38830850 PMCID: PMC11148045 DOI: 10.1038/s41421-024-00670-3] [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: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 06/05/2024] Open
Abstract
The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the extracellular region of the receptor and the N-terminus of the peptide, and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa by the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptide recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide peptide receptors.
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Affiliation(s)
| | - Shimeng Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xin Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Canrong Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Wenwen Xin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Heng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wen Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Tianwei Zhang
- Lingang Laboratory, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kai Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qingning Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Xin Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, China.
| | - Yi Jiang
- Lingang Laboratory, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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10
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Liang S, Liu A, Liu Y, Wang F, Zhou Y, Long Y, Wang T, Liu Z, Ren R, Ye RD. Structural basis for EROS binding to human phagocyte NADPH oxidase NOX2. Proc Natl Acad Sci U S A 2024; 121:e2320388121. [PMID: 38805284 PMCID: PMC11161758 DOI: 10.1073/pnas.2320388121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/11/2024] [Indexed: 05/30/2024] Open
Abstract
Essential for reactive oxygen species (EROS) protein is a recently identified molecular chaperone of NOX2 (gp91phox), the catalytic subunit of phagocyte NADPH oxidase. Deficiency in EROS is a recently identified cause for chronic granulomatous disease, a genetic disorder with recurrent bacterial and fungal infections. Here, we report a cryo-EM structure of the EROS-NOX2-p22phox heterotrimeric complex at an overall resolution of 3.56Å. EROS and p22phox are situated on the opposite sides of NOX2, and there is no direct contact between them. EROS associates with NOX2 through two antiparallel transmembrane (TM) α-helices and multiple β-strands that form hydrogen bonds with the cytoplasmic domain of NOX2. EROS binding induces a 79° upward bend of TM2 and a 48° backward rotation of the lower part of TM6 in NOX2, resulting in an increase in the distance between the two hemes and a shift of the binding site for flavin adenine dinucleotide (FAD). These conformational changes are expected to compromise superoxide production by NOX2, suggesting that the EROS-bound NOX2 is in a protected state against activation. Phorbol myristate acetate, an activator of NOX2 in vitro, is able to induce dissociation of NOX2 from EROS with concurrent increase in FAD binding and superoxide production in a transfected COS-7 model. In differentiated neutrophil-like HL-60, the majority of NOX2 on the cell surface is dissociated with EROS. Further studies are required to delineate how EROS dissociates from NOX2 during its transport to cell surface, which may be a potential mechanism for regulation of NOX2 activation.
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Affiliation(s)
- Shiyu Liang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Aijun Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
- Dongguan Songshan Lake Central Hospital, Dongguan Third People’s Hospital, Dongguan, Guangdong523326, China
| | - Yezhou Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen518132, China
| | - Fuxing Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Youli Zhou
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Yuanzhengyang Long
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Tao Wang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen518132, China
- Key Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Nanshan District, Shenzhen518055, China
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai200438, China
| | - Richard D. Ye
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
- The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong518000, China
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11
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Droppelmann CA, Campos-Melo D, Noches V, McLellan C, Szabla R, Lyons TA, Amzil H, Withers B, Kaplanis B, Sonkar KS, Simon A, Buratti E, Junop M, Kramer JM, Strong MJ. Mitigation of TDP-43 toxic phenotype by an RGNEF fragment in amyotrophic lateral sclerosis models. Brain 2024; 147:2053-2068. [PMID: 38739752 PMCID: PMC11146434 DOI: 10.1093/brain/awae078] [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: 08/30/2023] [Revised: 01/24/2024] [Accepted: 02/08/2024] [Indexed: 05/16/2024] Open
Abstract
Aggregation of the RNA-binding protein TAR DNA binding protein (TDP-43) is a hallmark of TDP-proteinopathies including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As TDP-43 aggregation and dysregulation are causative of neuronal death, there is a special interest in targeting this protein as a therapeutic approach. Previously, we found that TDP-43 extensively co-aggregated with the dual function protein GEF (guanine exchange factor) and RNA-binding protein rho guanine nucleotide exchange factor (RGNEF) in ALS patients. Here, we show that an N-terminal fragment of RGNEF (NF242) interacts directly with the RNA recognition motifs of TDP-43 competing with RNA and that the IPT/TIG domain of NF242 is essential for this interaction. Genetic expression of NF242 in a fruit fly ALS model overexpressing TDP-43 suppressed the neuropathological phenotype increasing lifespan, abolishing motor defects and preventing neurodegeneration. Intracerebroventricular injections of AAV9/NF242 in a severe TDP-43 murine model (rNLS8) improved lifespan and motor phenotype, and decreased neuroinflammation markers. Our results demonstrate an innovative way to target TDP-43 proteinopathies using a protein fragment with a strong affinity for TDP-43 aggregates and a mechanism that includes competition with RNA sequestration, suggesting a promising therapeutic strategy for TDP-43 proteinopathies such as ALS and FTD.
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Affiliation(s)
- Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Crystal McLellan
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Robert Szabla
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Taylor A Lyons
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Hind Amzil
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Benjamin Withers
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Brianna Kaplanis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Kirti S Sonkar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, 34149 Trieste, Italy
| | - Anne Simon
- Department of Biology, Faculty of Science, Western University, London, Ontario N6A 5B7, Canada
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, 34149 Trieste, Italy
| | - Murray Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
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12
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Deventer MH, Persson M, Norman C, Liu H, Connolly MJ, Daéid NN, McKenzie C, Gréen H, Stove CP. In vitro cannabinoid activity profiling of generic ban-evading brominated synthetic cannabinoid receptor agonists and their analogs. Drug Test Anal 2024; 16:616-628. [PMID: 37903509 DOI: 10.1002/dta.3592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023]
Abstract
Following the enactment of a generic ban in China in 2021, the synthetic cannabinoid market has been evolving, now encompassing even wider structural diversity. Compounds carrying a brominated core such as ADB-5'Br-BUTINACA (ADMB-B-5Br-INACA) and tail-less analogs, such as ADB-5'Br-INACA (ADMB-5Br-INACA), MDMB-5'Br-INACA, and ADB-INACA (ADMB-INACA), have been detected since late 2021. This study investigated the cannabinoid receptor (CB) activation potential of synthesized (S)-enantiomers of these substances, as well as of two predicted analogs MDMB-5'Br-BUTINACA (MDMB-B-5Br-INACA) and ADB-5'F-BUTINACA (ADMB-B-5F-INACA), using CB1 and CB2 β-arrestin 2 recruitment assays and a CB1 intracellular calcium release assay. Surprisingly, the tail-less (S)-ADB-5'Br-INACA and (S)-MDMB-5'Br-INACA retained CB activity, albeit with a decreased potency compared to their tailed counterparts (S)-ADB-5'Br-BUTINACA and (S)-MDMB-5'Br-BUTINACA, respectively, which were potent and efficacious CB1 agonists. Also, at CB2, tail-less analogs showed a lower potency but increased efficacy. Removing the bromine substitution ((S)-ADB-INACA) resulted in a reduced activity at CB1; however, this effect was less prominent at CB2. Looking at tailed analogs, replacing the bromine with a fluorine substitution ((S)-ADB-5'F-BUTINACA) resulted in an increased potency and efficacy at both receptors. Furthermore, as ADB-5'Br-INACA and MDMB-5'Br-INACA have been frequently detected together in Scottish prisons, this study also evaluated the CB1 receptor activation potential of different mixtures of their respective reference standards, showing no unexpected cannabimimetic effect of combining both substances. Lastly, two powders seized by Belgian Customs and confirmed to contain ADB-5'Br-INACA and MDMB-5'Br-INACA, respectively, were assessed for CB activity. Based on the comparison with their reference standards, varying degrees of purity were suspected.
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Affiliation(s)
- Marie H Deventer
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Mattias Persson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Caitlyn Norman
- Leverhulme Research Centre for Forensic Science, School of Science and Engineering, University of Dundee, Dundee, UK
| | | | | | - Niamh Nic Daéid
- Leverhulme Research Centre for Forensic Science, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Craig McKenzie
- Leverhulme Research Centre for Forensic Science, School of Science and Engineering, University of Dundee, Dundee, UK
- Chiron AS, Trondheim, Norway
| | - Henrik Gréen
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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13
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Ahmed WS, Geethakumari AM, Sultana A, Fatima A, Philip AM, Uddin SMN, Biswas KH. A slow but steady nanoLuc: R162A mutation results in a decreased, but stable, nanoLuc activity. Int J Biol Macromol 2024; 269:131864. [PMID: 38692549 DOI: 10.1016/j.ijbiomac.2024.131864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
NanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays, including gene expression analysis, protein-protein interaction, and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remain elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in living cells and in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in live cell and in vitro assays performed using lysates prepared from cells expressing the proteins and with the furimazine substrate. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity. SIGNIFICANCE: Bioluminescence has been extensively utilized in developing a variety of biological and biomedical assays. In this regard, engineering of brighter bioluminescent proteins, i.e. luciferases, has played a significant role. This is acutely exemplified by the engineering of the NLuc luciferase, which is small in size and displays much enhanced bioluminescence and thermal stability compared to previously available luciferases. While enhanced bioluminescent activity is desirable in a multitude of biological and biomedical assays, it would also be useful to develop variants of the protein that display a prolonged bioluminescence activity. This is specifically relevant in designing assays that require bioluminescence for extended periods, such as in the case of biosensors designed for monitoring slow enzymatic or cellular signaling reactions, without necessitating multiple rounds of luciferase substrate addition or any specialized reagents that result in increased assay costs. In the current manuscript, we report a mutant NLuc that possesses a stable and prolonged bioluminescence activity, albeit lower than the wild-type NLuc, and envisage a wider application of the mutant NLuc in designing biosensors for monitoring slower biological and biomedical events.
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Affiliation(s)
- Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Angelin M Philip
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - S M Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar.
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14
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Zubčić K, Franić D, Pravica M, Hof PR, Šimić G, Boban M. Effects of heterologous human tau protein expression in yeast models of proteotoxic stress response. CNS Neurosci Ther 2024; 30:e14304. [PMID: 37341072 PMCID: PMC11163194 DOI: 10.1111/cns.14304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The primary histological characteristic of Alzheimer's disease is the presence of neurofibrillary tangles, which are large aggregates of tau protein. Aging is the primary risk factor for the development of Alzheimer's disease, however, the underlying causes of tau protein aggregation and toxicity are unclear. AIMS Here we investigated tau aggregation and toxicity under the conditions of compromised protein homeostasis. METHODS We used heterologous expression of human tau protein in the unicellular eukaryote yeast Saccharomyces cerevisiae with evolutionarily conserved protein quality control pathways and examined tau-dependent toxicity and aggregation using growth assays, fluorescence microscopy, and a split luciferase-based reporter NanoBiT. RESULTS Tau protein expressed in yeast under mild proteotoxic stress, or in mutants with impaired pathways for proteotoxic stress response, did not lead to synthetic toxicity or the formation of obvious aggregates. Chronologically old cells also did not develop observable tau aggregates. Our examination of tau oligomerization in living cells using NanoBiT reporter suggests that tau does not form significant levels of oligomers under basal conditions or under mild proteotoxic stress. CONCLUSION Together our data suggest that human tau protein does not represent a major burden to the protein quality control system in yeast cells.
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Affiliation(s)
- Klara Zubčić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Dina Franić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mihaela Pravica
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's DiseaseFriedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Goran Šimić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mirta Boban
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
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15
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Wu H, Hoare BL, Handley TNG, Akhter Hossain M, Bathgate RAD. Development of a synthetic relaxin-3/INSL5 chimeric peptide ligand for NanoBiT complementation binding assays. Biochem Pharmacol 2024; 224:116238. [PMID: 38677442 DOI: 10.1016/j.bcp.2024.116238] [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: 01/16/2024] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
INSL5 and relaxin-3 are relaxin family peptides with important roles in gut and brain function, respectively. They mediate their actions through the class A GPCRs RXFP4 and RXFP3. RXFP4 has been proposed to be a therapeutic target for colon motility disorders whereas RXFP3 targeting could be effective for neurological conditions such as anxiety. Validation of these targets has been limited by the lack of specific ligands and the availability of robust ligand-binding assays for their development. In this study, we have utilized NanoBiT complementation to develop a SmBiT-conjugated tracer for use with LgBiT-fused RXFP3 and RXFP4. The low affinity between LgBiT:SmBiT should result in a low non-specific luminescence signal and enable the quantification of binding without the tedious separation of non-bound ligands. We used solid-phase peptide synthesis to produce a SmBiT-labelled RXFP3/4 agonist, R3/I5, where SmBiT was conjugated to the B-chain N-terminus via a PEG12 linker. Both SmBiT-R3/I5 and R3/I5 were synthesized and purified in high purity and yield. Stable HEK293T cell lines expressing LgBiT-RXFP3 and LgBiT-RXFP4 were produced and demonstrated normal signaling in response to the synthetic R3/I5 peptide. Binding was first characterized in whole-cell binding kinetic assays validating that the SmBiT-R3/I5 bound to both cell lines with nanomolar affinity with minimal non-specific binding without bound and free SmBiT-R3/I5 separation. We then optimized membrane binding assays, demonstrating easy and robust analysis of both saturation and competition binding from frozen membranes. These assays therefore provide an appropriate rigorous binding assay for the high-throughput analysis of RXFP3 and RXFP4 ligands.
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Affiliation(s)
- Hongkang Wu
- The Florey, University of Melbourne, Victoria, Australia
| | | | | | - Mohammed Akhter Hossain
- The Florey, University of Melbourne, Victoria, Australia; School of Chemistry, University of Melbourne, Victoria, Australia; Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, Australia.
| | - Ross A D Bathgate
- The Florey, University of Melbourne, Victoria, Australia; Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, Australia.
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16
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Rosenblum SL, Soueid DM, Giambasu G, Vander Roest S, Pasternak A, DiMauro EF, Simov V, Garner AL. Live cell screening to identify RNA-binding small molecule inhibitors of the pre-let-7-Lin28 RNA-protein interaction. RSC Med Chem 2024; 15:1539-1546. [PMID: 38784453 PMCID: PMC11110735 DOI: 10.1039/d4md00123k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/16/2024] [Indexed: 05/25/2024] Open
Abstract
Dysregulation of the networking of RNA-binding proteins (RBPs) and RNAs drives many human diseases, including cancers, and the targeting of RNA-protein interactions (RPIs) has emerged as an exciting area of RNA-targeted drug discovery. Accordingly, methods that enable the discovery of cell-active small molecule modulators of RPIs are needed to propel this emerging field forward. Herein, we describe the application of live-cell assay technology, RNA interaction with protein-mediated complementation assay (RiPCA), for high-throughput screening to identify small molecule inhibitors of the pre-let-7d-Lin28A RPI. Utilizing a combination of RNA-biased small molecules and virtual screening hits, we discovered an RNA-binding small molecule that can disrupt the pre-let-7-Lin28 interaction demonstrating the potential of RiPCA for advancing RPI-targeted drug discovery.
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Affiliation(s)
- Sydney L Rosenblum
- Program in Chemical Biology, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
| | - Dalia M Soueid
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan 1600 Huron Parkway, NCRC B520 Ann Arbor MI 48109 USA
| | - George Giambasu
- Computational Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Steve Vander Roest
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
| | | | - Erin F DiMauro
- Discovery Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Vladimir Simov
- Discovery Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Amanda L Garner
- Program in Chemical Biology, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan 1600 Huron Parkway, NCRC B520 Ann Arbor MI 48109 USA
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17
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Russo F, Civili B, Winssinger N. Bright Red Bioluminescence from Semisynthetic NanoLuc (sNLuc). ACS Chem Biol 2024; 19:1035-1039. [PMID: 38717306 PMCID: PMC11106743 DOI: 10.1021/acschembio.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Red-shifted bioluminescence is highly desirable for diagnostic and imaging applications. Herein, we report a semisynthetic NanoLuc (sNLuc) based on complementation of a split NLuc (LgBiT) with a synthetic peptide (SmBiT) functionalized with a fluorophore for BRET emission. We observed exceptional BRET ratios with diverse fluorophores, notably in the red (I674/I450 > 14), with a brightness that is sufficient for naked eye detection in blood or through tissues. To exemplify its utility, LgBiT was fused to a miniprotein that binds HER2 (affibody, ZHER2), and the selective detection of HER2+ SK-BR-3 cells over HER2- HeLa cells was demonstrated.
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Affiliation(s)
- Francesco Russo
- Department of Organic Chemistry,
Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Beatrice Civili
- Department of Organic Chemistry,
Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
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18
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Wu Y, Jensen N, Rossner MJ, Wehr MC. Exploiting Cell-Based Assays to Accelerate Drug Development for G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:5474. [PMID: 38791511 PMCID: PMC11121687 DOI: 10.3390/ijms25105474] [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: 04/22/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are relevant targets for health and disease as they regulate various aspects of metabolism, proliferation, differentiation, and immune pathways. They are implicated in several disease areas, including cancer, diabetes, cardiovascular diseases, and mental disorders. It is worth noting that about a third of all marketed drugs target GPCRs, making them prime pharmacological targets for drug discovery. Numerous functional assays have been developed to assess GPCR activity and GPCR signaling in living cells. Here, we review the current literature of genetically encoded cell-based assays to measure GPCR activation and downstream signaling at different hierarchical levels of signaling, from the receptor to transcription, via transducers, effectors, and second messengers. Singleplex assay formats provide one data point per experimental condition. Typical examples are bioluminescence resonance energy transfer (BRET) assays and protease cleavage assays (e.g., Tango or split TEV). By contrast, multiplex assay formats allow for the parallel measurement of multiple receptors and pathways and typically use molecular barcodes as transcriptional reporters in barcoded assays. This enables the efficient identification of desired on-target and on-pathway effects as well as detrimental off-target and off-pathway effects. Multiplex assays are anticipated to accelerate drug discovery for GPCRs as they provide a comprehensive and broad identification of compound effects.
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Affiliation(s)
- Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Niels Jensen
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Moritz J. Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C. Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
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19
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Bensaude O, Barbosa I, Morillo L, Dikstein R, Le Hir H. Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly. Nat Commun 2024; 15:4209. [PMID: 38760352 PMCID: PMC11101648 DOI: 10.1038/s41467-024-48371-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
Exon junction complexes are deposited at exon-exon junctions during splicing. They are primarily known to activate non-sense mediated degradation of transcripts harbouring premature stop codons before the last intron. According to a popular model, exon-junction complexes accompany mRNAs to the cytoplasm where the first translating ribosome pushes them out. However, they are also removed by uncharacterized, translation-independent mechanisms. Little is known about kinetic and transcript specificity of these processes. Here we tag core subunits of exon-junction complexes with complementary split nanoluciferase fragments to obtain sensitive and quantitative assays for complex formation. Unexpectedly, exon-junction complexes form large stable mRNPs containing stalled ribosomes. Complex assembly and disassembly rates are determined after an arrest in transcription and/or translation. 85% of newly deposited exon-junction complexes are disassembled by a translation-dependent mechanism. However as this process is much faster than the translation-independent one, only 30% of the exon-junction complexes present in cells at steady state require translation for disassembly. Deep RNA sequencing shows a bias of exon-junction complex bound transcripts towards microtubule and centrosome coding ones and demonstrate that the lifetimes of exon-junction complexes are transcript-specific. This study provides a dynamic vision of exon-junction complexes and uncovers their unexpected stable association with ribosomes.
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Affiliation(s)
- Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Lucia Morillo
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
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20
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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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21
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Lin H, Riching K, Lai MP, Lu D, Cheng R, Qi X, Wang J. Lysineless HiBiT and NanoLuc Tagging Systems as Alternative Tools Monitoring Targeted Protein Degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594249. [PMID: 38798562 PMCID: PMC11118299 DOI: 10.1101/2024.05.14.594249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Target protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, leveraging the cell's intrinsic machinery to selectively degrade disease-associated proteins. Proteolysis-Targeting Chimeras (PROTACs) exemplify this strategy, exploiting heterobifunctional molecules to induce ubiquitination and subsequent degradation of target proteins. The clinical advancement of PROTACs underscores their potential in therapeutic intervention, with numerous projects progressing through clinical stages. However, monitoring subtle changes in protein abundance induced by TPD molecules demands highly sensitive assays. Nano-luciferase (nLuc) fusion proteins, or the NanoBiT technology derived from it, offer a robust screening platform due to their high sensitivity and stability. Despite these advantages, concerns have arisen regarding potential degradation artifacts introduced by tagging systems due to the presence of lysine residues on them, prompting the development of alternative tools. In this study, we introduce HiBiT-RR and nLuc K0 , variants devoid of lysine residues, to mitigate such artifacts. Our findings demonstrate that HiBiT-RR maintains similar sensitivity and binding affinity with the original HiBiT. Moreover, the comparison between nLuc WT and nLuc K0 constructs reveals variations in degradation patterns induced by certain PROTAC molecules, emphasizing the importance of choosing appropriate tagging systems to ensure the reliability of experimental outcomes in studying protein degradation processes.
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22
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Salinas P, Bibak S, Cantos R, Tremiño L, Jerez C, Mata-Balaguer T, Contreras A. Studies on the PII-PipX-NtcA Regulatory Axis of Cyanobacteria Provide Novel Insights into the Advantages and Limitations of Two-Hybrid Systems for Protein Interactions. Int J Mol Sci 2024; 25:5429. [PMID: 38791467 PMCID: PMC11121479 DOI: 10.3390/ijms25105429] [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: 04/05/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Yeast two-hybrid approaches, which are based on fusion proteins that must co-localise to the nucleus to reconstitute the transcriptional activity of GAL4, have greatly contributed to our understanding of the nitrogen interaction network of cyanobacteria, the main hubs of which are the trimeric PII and the monomeric PipX regulators. The bacterial two-hybrid system, based on the reconstitution in the E. coli cytoplasm of the adenylate cyclase of Bordetella pertussis, should provide a relatively faster and presumably more physiological assay for cyanobacterial proteins than the yeast system. Here, we used the bacterial two-hybrid system to gain additional insights into the cyanobacterial PipX interaction network while simultaneously assessing the advantages and limitations of the two most popular two-hybrid systems. A comprehensive mutational analysis of PipX and bacterial two-hybrid assays were performed to compare the outcomes between yeast and bacterial systems. We detected interactions that were previously recorded in the yeast two-hybrid system as negative, as well as a "false positive", the self-interaction of PipX, which is rather an indirect interaction that is dependent on PII homologues from the E. coli host, a result confirmed by Western blot analysis with relevant PipX variants. This is, to our knowledge, the first report of the molecular basis of a false positive in the bacterial two-hybrid system.
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Affiliation(s)
| | | | | | | | | | | | - Asunción Contreras
- Departamento. de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (P.S.); (S.B.); (R.C.); (L.T.); (C.J.); (T.M.-B.)
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23
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Won HI, Zinga S, Kandror O, Akopian T, Wolf ID, Schweber JTP, Schmid EW, Chao MC, Waldor M, Rubin EJ, Zhu J. Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy. Nat Commun 2024; 15:4065. [PMID: 38744895 PMCID: PMC11094019 DOI: 10.1038/s41467-024-48506-8] [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: 02/14/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
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Affiliation(s)
- Harim I Won
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Samuel Zinga
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Olga Kandror
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tatos Akopian
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jessica T P Schweber
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ernst W Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, 02115, USA
| | - Michael C Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Maya Waldor
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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24
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Chen X, Crawford MC, Xiong Y, Shaik AB, Suazo KF, Penkalapati MS, Williams JH, Andressen T, Swenson RE, Meier JL. Paralogue-selective degradation of the lysine acetyltransferase EP300. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592353. [PMID: 38746397 PMCID: PMC11092752 DOI: 10.1101/2024.05.03.592353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transcriptional coactivators EP300 and CREBBP are critical regulators of gene expression that share high sequence identity but exhibit non-redundant functions in basal and pathological contexts. Here, we report the development of a bifunctional small molecule, MC-1, capable of selectively degrading EP300 over CREBBP. Using a potent aminopyridine-based inhibitor of the EP300/CREBBP catalytic domain in combination with a VHL ligand, we demonstrate that MC-1 preferentially degrades EP300 in a proteasome-dependent manner. Mechanistic studies reveal that selective degradation cannot be predicted solely by target engagement or ternary complex formation, suggesting additional factors govern paralogue-specific degradation. MC-1 inhibits cell proliferation in a subset of cancer cell lines and provides a new tool to investigate the non-catalytic functions of EP300 and CREBBP. Our findings expand the repertoire of EP300/CREBBP-targeting chemical probes and offer insights into the determinants of selective degradation of highly homologous proteins.
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Affiliation(s)
- Xuemin Chen
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | | | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Anver Basha Shaik
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Kiall F. Suazo
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | | | | | - Thorkell Andressen
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | - Rolf E. Swenson
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
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25
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Dombrowsky CS, Happel D, Habermann J, Hofmann S, Otmi S, Cohen B, Kolmar H. A Conditionally Activated Cytosol-Penetrating Antibody for TME-Dependent Intracellular Cargo Delivery. Antibodies (Basel) 2024; 13:37. [PMID: 38804305 PMCID: PMC11130931 DOI: 10.3390/antib13020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
Currently, therapeutic and diagnostic applications of antibodies are primarily limited to cell surface-exposed and extracellular proteins. However, research has been conducted on cell-penetrating peptides (CPP), as well as cytosol-penetrating antibodies, to overcome these limitations. In this context, a heparin sulfate proteoglycan (HSPG)-binding antibody was serendipitously discovered, which eventually localizes to the cytosol of target cells. Functional characterization revealed that the tested antibody has beneficial cytosol-penetrating capabilities and can deliver cargo proteins (up to 70 kDa) to the cytosol. To achieve tumor-specific cell targeting and cargo delivery through conditional activation of the cell-penetrating antibody in the tumor microenvironment, a single-chain Fc fragment (scFv) and a VL domain were isolated as masking units. Several in vitro assays demonstrated that fusing the masking protein with a cleavable linker to the cell penetration antibody results in the inactivation of antibody cell binding and internalization. Removal of the mask via MMP-9 protease cleavage, a protease that is frequently overexpressed in the tumor microenvironment (TME), led to complete regeneration of binding and cytosol-penetrating capabilities. Masked and conditionally activated cytosol-penetrating antibodies have the potential to serve as a modular platform for delivering protein cargoes addressing intracellular targets in tumor cells.
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Affiliation(s)
- Carolin Sophie Dombrowsky
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Jan Habermann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sarah Hofmann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sasi Otmi
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Benny Cohen
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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26
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Suzuki N, Konuma T, Ikegami T, Akashi S. Biophysical insights into the dimer formation of human Sirtuin 2. Protein Sci 2024; 33:e4994. [PMID: 38647411 PMCID: PMC11034489 DOI: 10.1002/pro.4994] [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: 12/27/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild-type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52-357) forms a homodimer in a concentration-dependent manner with a dimer-monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non-dimerizing mutants exhibited deacetylation activity for the N-terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292-306, which lacks a SIRT2-specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X-ray structure of the mutant Δ292-306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.
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Affiliation(s)
- Noa Suzuki
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
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27
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Lefevre TJ, Wei W, Mukhaleva E, Meda Venkata SP, Chandan NR, Abraham S, Li Y, Dessauer CW, Vaidehi N, Smrcka AV. Stabilization of interdomain interactions in G protein α subunits as a determinant of Gα i subtype signaling specificity. J Biol Chem 2024; 300:107211. [PMID: 38522511 PMCID: PMC11066577 DOI: 10.1016/j.jbc.2024.107211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
Highly homologous members of the Gαi family, Gαi1-3, have distinct tissue distributions and physiological functions, yet their biochemical and functional properties are very similar. We recently identified PDZ-RhoGEF (PRG) as a novel Gαi1 effector that is poorly activated by Gαi2. In a proteomic proximity labeling screen we observed a strong preference for Gαi1 relative to Gαi2 with respect to engagement of a broad range of potential targets. We investigated the mechanistic basis for this selectivity using PRG as a representative target. Substitution of either the helical domain (HD) from Gαi1 into Gαi2 or substitution of a single amino acid, A230 in Gαi2 with the corresponding D in Gαi1, largely rescues PRG activation and interactions with other potential Gαi targets. Molecular dynamics simulations combined with Bayesian network models revealed that in the GTP bound state, separation at the HD-Ras-like domain (RLD) interface is more pronounced in Gαi2 than Gαi1. Mutation of A230 to D in Gαi2 stabilizes HD-RLD interactions via ionic interactions with R145 in the HD which in turn modify the conformation of Switch III. These data support a model where D229 in Gαi1 interacts with R144 and stabilizes a network of interactions between HD and RLD to promote protein target recognition. The corresponding A230 in Gαi2 is unable to stabilize this network leading to an overall lower efficacy with respect to target interactions. This study reveals distinct mechanistic properties that could underly differential biological and physiological consequences of activation of Gαi1 or Gαi2 by G protein-coupled receptors.
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Affiliation(s)
- Tyler J Lefevre
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Wenyuan Wei
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Naincy R Chandan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Genentech, South San Francisco, California, USA
| | - Saji Abraham
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yong Li
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, Texas, USA
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, Texas, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Alan V Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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28
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Ando S, Tanaka K, Matsumoto M, Oyama Y, Tomabechi Y, Yamagata A, Shirouzu M, Nakagawa R, Okimoto N, Taiji M, Sato K, Ohama T. The luciferase-based in vivo protein-protein interaction assay revealed that CHK1 promotes PP2A and PME-1 interaction. J Biol Chem 2024; 300:107277. [PMID: 38588804 PMCID: PMC11098961 DOI: 10.1016/j.jbc.2024.107277] [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: 12/21/2023] [Revised: 03/12/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
Protein phosphatase 2A (PP2A) is an essential serine/threonine protein phosphatase, and its dysfunction is involved in the onset of cancer and neurodegenerative disorders. PP2A functions as a trimeric holoenzyme whose composition is regulated by the methyl-esterification (methylation) of the PP2A catalytic subunit (PP2Ac). Protein phosphatase methylesterase-1 (PME-1) is the sole PP2Ac methylesterase, and the higher PME-1 expression is observed in various cancer and neurodegenerative diseases. Apart from serving as a methylesterase, PME-1 acts as a PP2A inhibitory protein, binding directly to PP2Ac and suppressing its activity. The intricate function of PME-1 hinders drug development by targeting the PME-1/PP2Ac axis. This study applied the NanoBiT system, a bioluminescence-based protein interaction assay, to elucidate the molecular mechanism that modulates unknown PME-1/PP2Ac protein-protein interaction (PPI). Compound screening identified that the CHK1 inhibitors inhibited PME-1/PP2Ac association without affecting PP2Ac methylation levels. CHK1 directly phosphorylates PP2Ac to promote PME-1 association. Phospho-mass spectrometry identified multiple phospho-sites on PP2Ac, including the Thr219, that affect PME-1 interaction. An anti-phospho-Thr219 PP2Ac antibody was generated and showed that CHK1 regulates the phosphorylation levels of this site in cells. On the contrary, in vitro phosphatase assay showed that CHK1 is the substrate of PP2A, and PME-1 hindered PP2A-mediated dephosphorylation of CHK1. Our data provides novel insights into the molecular mechanisms governing the PME-1/PP2Ac PPI and the triad relationship between PP2A, PME-1, and CHK1.
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Affiliation(s)
- Sana Ando
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Keiko Tanaka
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Maharu Matsumoto
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuki Oyama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuri Tomabechi
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan; Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan; Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
| | - Koichi Sato
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan; Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Takashi Ohama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan; Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan.
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29
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Tian X, Zhang Y, Ai HW. ATP-Independent Water-Soluble Luciferins Enable Non-Invasive High-Speed Video-Rate Bioluminescence Imaging of Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591933. [PMID: 38746394 PMCID: PMC11092570 DOI: 10.1101/2024.04.30.591933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
NanoLuc luciferase and its derivatives are attractive bioluminescent reporters recognized for their efficient photon production and ATP independence. However, utilizing them for in vivo imaging poses notable challenges. Low substrate solubility has been a prominent problem, limiting in vivo brightness, while substrate instability hampers consistent results and handling. To address these issues, we developed a range of caged PEGylated luciferins with improved stability and water solubility of up to 25 mM, resulting in substantial bioluminescence increases in mouse models. This advancement has created the brightest and most sensitive luciferase-luciferin combination, enabling high-speed video-rate imaging of freely moving mice with brain-expressed luciferase. Furthermore, we developed a bioluminescent Ca 2+ indicator with exceptional sensitivity to physiological Ca 2+ changes and paired it with a new substrate to showcase non-invasive, video-rate imaging of Ca 2+ activity in a defined brain region in awake mice. These innovative substrates and the Ca 2+ indicator are poised to become invaluable resources for biological and biomedical fields.
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30
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Sherman DJ, Liu L, Mamrosh JL, Xie J, Ferbas J, Lomenick B, Ladinsky MS, Verma R, Rulifson IC, Deshaies RJ. The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics. Proc Natl Acad Sci U S A 2024; 121:e2318619121. [PMID: 38657050 PMCID: PMC11067037 DOI: 10.1073/pnas.2318619121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024] Open
Abstract
Nonalcoholic fatty liver disease, recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery 20 y ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
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Affiliation(s)
| | - Lei Liu
- Amgen Research, South San Francisco, CA94080
| | | | | | | | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
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31
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Zheng YS, Liu YL, Xu ZG, He C, Guo ZY. Is myeloid-derived growth factor a ligand of the sphingosine-1-phosphate receptor 2? Biochem Biophys Res Commun 2024; 706:149766. [PMID: 38484568 DOI: 10.1016/j.bbrc.2024.149766] [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: 02/25/2024] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Secretory myeloid-derived growth factor (MYDGF) exerts beneficial effects on organ repair, probably via a plasma membrane receptor; however, the identity of the expected receptor has remained elusive. In a recent study, MYDGF was reported as an agonist of the sphingosine-1-phosphate receptor 2 (S1PR2), an A-class G protein-coupled receptor that mediates the functions of the signaling lipid, sphingosine-1-phosphate (S1P). In the present study, we conducted living cell-based functional assays to test whether S1PR2 is a receptor for MYDGF. In the NanoLuc Binary Technology (NanoBiT)-based β-arrestin recruitment assay and the cAMP-response element (CRE)-controlled NanoLuc reporter assay, S1P could efficiently activate human S1PR2 overexpressed in human embryonic kidney (HEK) 293T cells; however, recombinant human MYDGF, overexpressed either from Escherichia coli or HEK293 cells, had no detectable effect. Thus, the results demonstrated that human MYDGF is not a ligand of human S1PR2. Considering the high conservation of MYDGF and S1PR2 in evolution, MYDGF is also probably not a ligand of S1PR2 in other vertebrates.
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Affiliation(s)
- Yong-Shan Zheng
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Shanghai Institute of Biological Products Co., Ltd., Shanghai, China
| | - Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeng-Guang Xu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cheng He
- Shanghai Institute of Biological Products Co., Ltd., Shanghai, China.
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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32
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Jerez C, Llop A, Salinas P, Bibak S, Forchhammer K, Contreras A. Analysing the Cyanobacterial PipX Interaction Network Using NanoBiT Complementation in Synechococcus elongatus PCC7942. Int J Mol Sci 2024; 25:4702. [PMID: 38731921 PMCID: PMC11083307 DOI: 10.3390/ijms25094702] [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: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The conserved cyanobacterial protein PipX is part of a complex interaction network with regulators involved in essential processes that include metabolic homeostasis and ribosome assembly. Because PipX interactions depend on the relative levels of their different partners and of the effector molecules binding to them, in vivo studies are required to understand the physiological significance and contribution of environmental factors to the regulation of PipX complexes. Here, we have used the NanoBiT complementation system to analyse the regulation of complex formation in Synechococcus elongatus PCC 7942 between PipX and each of its two best-characterized partners, PII and NtcA. Our results confirm previous in vitro analyses on the regulation of PipX-PII and PipX-NtcA complexes by 2-oxoglutarate and on the regulation of PipX-PII by the ATP/ADP ratio, showing the disruption of PipX-NtcA complexes due to increased levels of ADP-bound PII in Synechococcus elongatus. The demonstration of a positive role of PII on PipX-NtcA complexes during their initial response to nitrogen starvation or the impact of a PipX point mutation on the activity of PipX-PII and PipX-NtcA reporters are further indications of the sensitivity of the system. This study reveals additional regulatory complexities in the PipX interaction network, opening a path for future research on cyanobacteria.
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Affiliation(s)
- Carmen Jerez
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (C.J.); (A.L.); (P.S.); (S.B.)
- Interfaculty Institute of Microbiology and Infection Biology, University Tübingen, 72076 Tübingen, Germany;
| | - Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (C.J.); (A.L.); (P.S.); (S.B.)
| | - Paloma Salinas
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (C.J.); (A.L.); (P.S.); (S.B.)
| | - Sirine Bibak
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (C.J.); (A.L.); (P.S.); (S.B.)
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Biology, University Tübingen, 72076 Tübingen, Germany;
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (C.J.); (A.L.); (P.S.); (S.B.)
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33
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Piccolo D, Zarouchlioti C, Bellingham J, Guarascio R, Ziaka K, Molday RS, Cheetham ME. A Proximity Complementation Assay to Identify Small Molecules That Enhance the Traffic of ABCA4 Misfolding Variants. Int J Mol Sci 2024; 25:4521. [PMID: 38674104 PMCID: PMC11050442 DOI: 10.3390/ijms25084521] [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: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
ABCA4-related retinopathy is the most common inherited Mendelian eye disorder worldwide, caused by biallelic variants in the ATP-binding cassette transporter ABCA4. To date, over 2200 ABCA4 variants have been identified, including missense, nonsense, indels, splice site and deep intronic defects. Notably, more than 60% are missense variants that can lead to protein misfolding, mistrafficking and degradation. Currently no approved therapies target ABCA4. In this study, we demonstrate that ABCA4 misfolding variants are temperature-sensitive and reduced temperature growth (30 °C) improves their traffic to the plasma membrane, suggesting the folding of these variants could be rescuable. Consequently, an in vitro platform was developed for the rapid and robust detection of ABCA4 traffic to the plasma membrane in transiently transfected cells. The system was used to assess selected candidate small molecules that were reported to improve the folding or traffic of other ABC transporters. Two candidates, 4-PBA and AICAR, were identified and validated for their ability to enhance both wild-type ABCA4 and variant trafficking to the cell surface in cell culture. We envision that this platform could serve as a primary screen for more sophisticated in vitro testing, enabling the discovery of breakthrough agents to rescue ABCA4 protein defects and mitigate ABCA4-related retinopathy.
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Affiliation(s)
- Davide Piccolo
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
| | - Christina Zarouchlioti
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
| | - James Bellingham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
| | - Rosellina Guarascio
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
| | - Kalliopi Ziaka
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
| | - Robert S. Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Michael E. Cheetham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; (D.P.); (C.Z.); (R.G.); (K.Z.)
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34
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Wang W. Protein-Based Tools for Studying Neuromodulation. ACS Chem Biol 2024; 19:788-797. [PMID: 38581649 PMCID: PMC11129172 DOI: 10.1021/acschembio.4c00037] [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: 04/08/2024]
Abstract
Neuromodulators play crucial roles in regulating neuronal activity and affecting various aspects of brain functions, including learning, memory, cognitive functions, emotional states, and pain modulation. In this Account, we describe our group's efforts in designing sensors and tools for studying neuromodulation. Our lab focuses on developing new classes of integrators that can detect neuromodulators across the whole brain while leaving a mark for further imaging analysis at high spatial resolution. Our lab also designed chemical- and light-dependent protein switches for controlling peptide activity to potentially modulate the endogenous receptors of the neuromodulatory system in order to study the causal effects of selective neuronal pathways.
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Affiliation(s)
- Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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35
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Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building Synthetic Biosensors Using Red Blood Cell Proteins. ACS Synth Biol 2024; 13:1273-1289. [PMID: 38536408 DOI: 10.1021/acssynbio.3c00754] [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: 04/09/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Toward addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC-protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including noninvasive monitoring of physiological signals for a range of diagnostic applications.
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Affiliation(s)
- Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Te Ling
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Kelly A Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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36
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024:10.1038/s41596-024-00979-z. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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37
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Pan Z, Zhuo L, Wan TY, Chen RY, Li YZ. DnaK duplication and specialization in bacteria correlates with increased proteome complexity. mSystems 2024; 9:e0115423. [PMID: 38530057 PMCID: PMC11019930 DOI: 10.1128/msystems.01154-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/10/2024] [Indexed: 03/27/2024] Open
Abstract
The chaperone 70 kDa heat shock protein (Hsp70) is important for cells from bacteria to humans to maintain proteostasis, and all eukaryotes and several prokaryotes encode Hsp70 paralogs. Although the mechanisms of Hsp70 function have been clearly illuminated, the function and evolution of Hsp70 paralogs is not well studied. DnaK is a highly conserved bacterial Hsp70 family. Here, we show that dnaK is present in 98.9% of bacterial genomes, and 6.4% of them possess two or more DnaK paralogs. We found that the duplication of dnaK is positively correlated with an increase in proteomic complexity (proteome size, number of domains). We identified the interactomes of the two DnaK paralogs of Myxococcus xanthus DK1622 (MxDnaKs), which revealed that they are mostly nonoverlapping, although both prefer α and β domain proteins. Consistent with the entire M. xanthus proteome, MxDnaK substrates have both significantly more multi-domain proteins and a higher isoelectric point than that of Escherichia coli, which encodes a single DnaK homolog. MxDnaK1 is transcriptionally upregulated in response to heat shock and prefers to bind cytosolic proteins, while MxDnaK2 is downregulated by heat shock and is more associated with membrane proteins. Using domain swapping, we show that the nucleotide-binding domain and the substrate-binding β domain are responsible for the significant differences in DnaK interactomes, and the nucleotide binding domain also determines the dimerization of MxDnaK2, but not MxDnaK1. Our work suggests that bacterial DnaK has been duplicated in order to deal with a more complex proteome, and that this allows evolution of distinct domains to deal with different subsets of target proteins.IMPORTANCEAll eukaryotic and ~40% of prokaryotic species encode multiple 70 kDa heat shock protein (Hsp70) homologs with similar but diversified functions. Here, we show that duplication of canonical Hsp70 (DnaK in prokaryotes) correlates with increasing proteomic complexity and evolution of particular regions of the protein. Using the Myxococcus xanthus DnaK duplicates as a case, we found that their substrate spectrums are mostly nonoverlapping, and are both consistent to that of Escherichia coli DnaK in structural and molecular characteristics, but show differential enrichment of membrane proteins. Domain/region swapping demonstrated that the nucleotide-binding domain and the β substrate-binding domain (SBDβ), but not the SBDα or disordered C-terminal tail region, are responsible for this functional divergence. This work provides the first direct evidence for regional evolution of DnaK paralogs.
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Affiliation(s)
- Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- Suzhou Research Institute, Shandong University, Suzhou, China
| | - Tian-yu Wan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Rui-yun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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38
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Peruzzi JA, Steinkühler J, Vu TQ, Gunnels TF, Hu VT, Lu P, Baker D, Kamat NP. Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes. Nat Commun 2024; 15:3162. [PMID: 38605024 PMCID: PMC11009411 DOI: 10.1038/s41467-024-47163-1] [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: 12/19/2022] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We use this principle to sort proteins both between and within membranes, thereby achieving one-pot assembly of vesicles with distinct functions and controlled split-protein assembly, respectively. Our results shed light on protein organization in biological membranes and provide a framework to design self-organizing membrane-based materials with applications such as artificial cells, biosensors, and therapeutic nanoparticles.
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Affiliation(s)
- Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Jan Steinkühler
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Timothy Q Vu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Vivian T Hu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Neha P Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
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39
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Shulgina Y, Trinidad MI, Langeberg CJ, Nisonoff H, Chithrananda S, Skopintsev P, Nissley AJ, Patel J, Boger RS, Shi H, Yoon PH, Doherty EE, Pande T, Iyer AM, Doudna JA, Cate JHD. RNA language models predict mutations that improve RNA function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588317. [PMID: 38617247 PMCID: PMC11014562 DOI: 10.1101/2024.04.05.588317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. While advances in deep learning enable the prediction of accurate protein structural models, RNA structure prediction is not possible at present due to a lack of abundant high-quality reference data. Furthermore, available sequence data are generally not associated with organismal phenotypes that could inform RNA function. We created GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences derived from GTDB genomes to experimental and predicted optimal growth temperatures of GTDB reference organisms. This enables construction of deep and diverse RNA sequence alignments to be used for machine learning. Using GARNET, we define the minimal requirements for a sequence- and structure-aware RNA generative model. We also develop a GPT-like language model for RNA in which triplet tokenization provides optimal encoding. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identified mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.
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Affiliation(s)
- Yekaterina Shulgina
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Conner J Langeberg
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Hunter Nisonoff
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Seyone Chithrananda
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Amos J Nissley
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Jaymin Patel
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ron S Boger
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Tara Pande
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Aditya M Iyer
- Department of Physics, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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40
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Cullum SA, Platt S, Dale N, Isaac OC, Wragg ES, Soave M, Veprintsev DB, Woolard J, Kilpatrick LE, Hill SJ. Mechano-sensitivity of β2-adrenoceptors enhances constitutive activation of cAMP generation that is inhibited by inverse agonists. Commun Biol 2024; 7:417. [PMID: 38580813 PMCID: PMC10997663 DOI: 10.1038/s42003-024-06128-2] [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: 09/27/2023] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
The concept of agonist-independent signalling that can be attenuated by inverse agonists is a fundamental element of the cubic ternary complex model of G protein-coupled receptor (GPCR) activation. This model shows how a GPCR can exist in two conformational states in the absence of ligands; an inactive R state and an active R* state that differ in their affinities for agonists, inverse agonists, and G-protein alpha subunits. The proportion of R* receptors that exist in the absence of agonists determines the level of constitutive receptor activity. In this study we demonstrate that mechanical stimulation can induce β2-adrenoceptor agonist-independent Gs-mediated cAMP signalling that is sensitive to inhibition by inverse agonists such as ICI-118551 and propranolol. The size of the mechano-sensitive response is dependent on the cell surface receptor expression level in HEK293G cells, is still observed in a ligand-binding deficient D113A mutant β2-adrenoceptor and can be attenuated by site-directed mutagenesis of the extracellular N-glycosylation sites on the N-terminus and second extracellular loop of the β2-adrenoceptor. Similar mechano-sensitive agonist-independent responses are observed in HEK293G cells overexpressing the A2A-adenosine receptor. These data provide new insights into how agonist-independent constitutive receptor activity can be enhanced by mechanical stimulation and regulated by inverse agonists.
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Affiliation(s)
- Sean A Cullum
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Simon Platt
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Natasha Dale
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Oliver C Isaac
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Edward S Wragg
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Laura E Kilpatrick
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors, University of Nottingham, Nottingham, NG7 2UH, UK.
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41
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Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 PMCID: PMC10986514 DOI: 10.1128/spectrum.04199-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
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Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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42
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol 2024; 31:667-677. [PMID: 38326651 DOI: 10.1038/s41594-024-01223-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 plays a central role in development by suppressing Hedgehog signaling. The fundamental basis of how GPR161 is activated remains unclear. Here, we determined a cryogenic-electron microscopy structure of active human GPR161 bound to heterotrimeric Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, a sterol that binds adjacent to transmembrane helices 6 and 7 stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress Gs-mediated signaling. These mutants retain the ability to suppress GLI2 transcription factor accumulation in primary cilia, a key function of ciliary GPR161. By contrast, a protein kinase A-binding site in the GPR161 C terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Douglas F Covey
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ron O Dror
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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43
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Hirai Y, Kawaguchi Y, Kasahara C, Hirose H, Futaki S. Liquid Droplet-Mediated Formulation of Lipid Nanoparticles Encapsulating Immunoglobulin G for Cytosolic Delivery. Mol Pharm 2024; 21:1653-1661. [PMID: 38290425 DOI: 10.1021/acs.molpharmaceut.3c00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Antibodies are promising biopharmaceuticals that offer new therapeutic options for diseases. Since antibodies are membrane impermeable, approaches that allow immunoglobulin Gs (IgGs) to access intracellular therapeutic targets would open new horizons in antibody therapies. Lipid nanoparticles (LNPs) are among the classes of vectors that deliver biopharmaceuticals into cells. Using liquid droplets formed by IgG and polyglutamate, we report here a unique approach to forming LNPs containing IgG via liquid droplets formed in the presence of polyglutamic acid (polyE). The addition of polyE promoted the formation of smaller LNPs with cationic lipids than in its absence, and the formed LNPs were much more efficient in cytosolic IgG delivery and targeting of cellular proteins. This approach also allows for the encapsulation of intact IgG without the need for chemical or sequence modification. The intracellularly delivered IgG retained its target binding ability, as demonstrated by labeling of nuclear pore complex and HRas-GFP and inhibition of antiapoptotic cell death by phosphorylated Akt protein in live cells.
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Affiliation(s)
- Yusuke Hirai
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yoshimasa Kawaguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Chisato Kasahara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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44
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MIMURA Y, HIONO T, HUYNH LT, OGINO S, KOBAYASHI M, ISODA N, SAKODA Y. Establishment of a superinfection exclusion method for pestivirus titration using a recombinant reporter pestiviruses. J Vet Med Sci 2024; 86:389-395. [PMID: 38355118 PMCID: PMC11061576 DOI: 10.1292/jvms.24-0005] [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: 01/04/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Pestiviruses are classified into two biotypes based on their cytopathogenicity. As the majority of pestivirus field isolates are noncytopathogenic, their titration requires alternative methods rather than direct observation of cytopathogenic effects, such as immunostaining using specific antibodies or interference with cytopathogenic strains. However, these methods require microscopic observation to assess virus growth, which is time- and labor-intensive, especially when handling several samples. In this study, we developed a novel luciferase-based pestivirus titration method using the superinfection exclusion phenomenon with recombinant reporter pestiviruses that possessed an 11-amino-acid subunit derived from NanoLuc luciferase (HiBiT). In this method, swine kidney cells were inoculated with classical swine fever virus (CSFV) and superinfected with the reporter CSFV vGPE-/HiBiT 5 days postinoculation. Virus titer was determined based on virus growth measured in luminescence using the culture fluid 3 days after superinfection; the resultant virus titer was comparable to that obtained by immunoperoxidase staining. Furthermore, this method has proven to be applicable for the titration of border disease virus (BDV) by superinfection with both the homologous reporter BDV and heterologous reporter CSFV, suggesting that this novel virus titration method is a simple technique for automated virus detection based on the luciferase system.
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Affiliation(s)
- Yume MIMURA
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takahiro HIONO
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Hokkaido,
Japan
- International Collaboration Unit, International Institute
for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Hokkaido University Institute for Vaccine Research and
Development (HU-IVReD), Hokkaido University, Hokkaido, Japan
| | - Loc Tan HUYNH
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- Faculty of Veterinary Medicine, College of Agriculture, Can
Tho University, Can Tho, Vietnam
| | - Saho OGINO
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Maya KOBAYASHI
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Norikazu ISODA
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Hokkaido,
Japan
- International Collaboration Unit, International Institute
for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Hokkaido University Institute for Vaccine Research and
Development (HU-IVReD), Hokkaido University, Hokkaido, Japan
| | - Yoshihiro SAKODA
- Laboratory of Microbiology, Department of Disease Control,
Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Hokkaido,
Japan
- International Collaboration Unit, International Institute
for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Hokkaido University Institute for Vaccine Research and
Development (HU-IVReD), Hokkaido University, Hokkaido, Japan
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45
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Grady CJ, Castellanos Franco EA, Schossau J, Ashbaugh RC, Pelled G, Gilad AA. A putative design for the electromagnetic activation of split proteins for molecular and cellular manipulation. Front Bioeng Biotechnol 2024; 12:1355915. [PMID: 38605993 PMCID: PMC11007078 DOI: 10.3389/fbioe.2024.1355915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
The ability to manipulate cellular function using an external stimulus is a powerful strategy for studying complex biological phenomena. One approach to modulate the function of the cellular environment is split proteins. In this method, a biologically active protein or an enzyme is fragmented so that it reassembles only upon a specific stimulus. Although many tools are available to induce these systems, nature has provided other mechanisms to expand the split protein toolbox. Here, we show a novel method for reconstituting split proteins using magnetic stimulation. We found that the electromagnetic perceptive gene (EPG) changes conformation due to magnetic field stimulation. By fusing split fragments of a certain protein to both termini of the EPG, the fragments can be reassembled into a functional protein under magnetic stimulation due to conformational change. We show this effect with three separate split proteins: NanoLuc, APEX2, and herpes simplex virus type-1 thymidine kinase. Our results show, for the first time, that reconstitution of split proteins can be achieved only with magnetic fields. We anticipate that this study will be a starting point for future magnetically inducible split protein designs for cellular perturbation and manipulation. With this technology, we can help expand the toolbox of the split protein platform and allow better elucidation of complex biological systems.
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Affiliation(s)
- Connor J. Grady
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | | | - Jory Schossau
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Ryan C. Ashbaugh
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, United States
| | - Galit Pelled
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - Assaf A. Gilad
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
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46
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Wang M, Yao X, Tong X, Qi D, Ye X. Lnc-RPS6P3 Inhibits Influenza A Virus Replication and Attenuates the Inhibitory Effect of NS1 on Innate Immune Response. Microorganisms 2024; 12:654. [PMID: 38674599 PMCID: PMC11052439 DOI: 10.3390/microorganisms12040654] [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: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Host factors play important roles in influenza A virus (IAV) replication. In order to identify novel host factors involved in IAV replication, we compared the differentially expressed genes in A549 cells after IAV infection. We found that lncRNA lnc-RPS6P3 was up-regulated upon viral infection and poly(I:C) and IFN-β treatment, indicating it was an interferon-stimulated gene. Functional analysis demonstrated that overexpression of lnc-RPS6P3 inhibited IAV replication while knockdown of lnc-RPS6P3 promoted viral infection in A549 cells. Lnc-RPS6P3 inhibited both transcription and replication of IAV. Further study showed that lnc-RPS6P3 interacted with viral NP and interfered with NP self-oligomerization and, consequently, inhibited vRNP activity. In addition, lnc-RPS6P3 interacted with viral NS1 and reduced the interaction of NS1 and RIG-I; it also attenuated the inhibitory effect of NS1 on IFN-β stimulation. In conclusion, we revealed that lnc-RPS6P3 is an interferon-stimulated gene that inhibits IAV replication and attenuates the inhibitory effect of NS1 on innate immune response.
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Affiliation(s)
- Mingge Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xinli Yao
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomei Tong
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Dandan Qi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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47
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Shizukuishi S, Ogawa M, Kuroda E, Hamaguchi S, Sakuma C, Kakuta S, Tanida I, Uchiyama Y, Akeda Y, Ryo A, Ohnishi M. Pneumococcal sialidase promotes bacterial survival by fine-tuning of pneumolysin-mediated membrane disruption. Cell Rep 2024; 43:113962. [PMID: 38483905 DOI: 10.1016/j.celrep.2024.113962] [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: 10/02/2023] [Revised: 01/24/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Pneumolysin (Ply) is an indispensable cholesterol-dependent cytolysin for pneumococcal infection. Although Ply-induced disruption of pneumococci-containing endosomal vesicles is a prerequisite for the evasion of endolysosomal bacterial clearance, its potent activity can be a double-edged sword, having a detrimental effect on bacterial survivability by inducing severe endosomal disruption, bactericidal autophagy, and scaffold epithelial cell death. Thus, Ply activity must be maintained at optimal levels. We develop a highly sensitive assay to monitor endosomal disruption using NanoBiT-Nanobody, which shows that the pneumococcal sialidase NanA can fine-tune Ply activity by trimming sialic acid from cell-membrane-bound glycans. In addition, oseltamivir, an influenza A virus sialidase inhibitor, promotes Ply-induced endosomal disruption and cytotoxicity by inhibiting NanA activity in vitro and greater tissue damage and bacterial clearance in vivo. Our findings provide a foundation for innovative therapeutic strategies for severe pneumococcal infections by exploiting the duality of Ply activity.
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Affiliation(s)
- Sayaka Shizukuishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Michinaga Ogawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Eisuke Kuroda
- Department of Transformative Infection Control Development Studies, Osaka University Graduate School of Medicine, Osaka, Japan; Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Shigeto Hamaguchi
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan; Department of Transformative Analysis for Human Specimen, Osaka University Graduate School of Medicine, Osaka, Japan; Division of Infection Control and Prevention, Osaka University Hospital, Osaka, Japan
| | - Chisato Sakuma
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Tokyo, Japan; Department of Cellular and Molecular Neuropathology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Isei Tanida
- Department of Cellular and Molecular Neuropathology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan; Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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48
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Ham D, Inoue A, Xu J, Du Y, Chung KY. Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Commun Biol 2024; 7:362. [PMID: 38521872 PMCID: PMC10960872 DOI: 10.1038/s42003-024-06056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Shenzhen Futian Biomedical Innovation R&D Center, the Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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49
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van Aalen EA, Lurvink JJJ, Vermeulen L, van Gerven B, Ni Y, Arts R, Merkx M. Turning Antibodies into Ratiometric Bioluminescent Sensors for Competition-Based Homogeneous Immunoassays. ACS Sens 2024; 9:1401-1409. [PMID: 38380622 PMCID: PMC10964239 DOI: 10.1021/acssensors.3c02478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
Here we present LUCOS (Luminescent Competition Sensor), a modular and broadly applicable bioluminescent diagnostic platform enabling the detection of both small molecules and protein biomarkers. The construction of LUCOS sensors entails the covalent and site-specific coupling of a bioluminescent sensor component to an analyte-specific antibody via protein G-mediated photoconjugation. Target detection is accomplished through intramolecular competition with a tethered analyte competitor for antibody binding. We established two variants of LUCOS: an inherent ratiometric LUCOSR variant and an intensiometric LUCOSI version, which can be used for ratiometric detection upon the addition of a split calibrator luciferase. To demonstrate the versatility of the LUCOS platform, sensors were developed for the detection of the small molecule cortisol and the protein biomarker NT-proBNP. Sensors for both targets displayed analyte-dependent changes in the emission ratio and enabled detection in the micromolar concentration range (KD,app = 16-92 μM). Furthermore, we showed that the response range of the LUCOS sensor can be adjusted by attenuating the affinity of the tethered NT-proBNP competitor, which enabled detection in the nanomolar concentration range (KD,app = 317 ± 26 nM). Overall, the LUCOS platform offers a highly versatile and easy method to convert commercially available monoclonal antibodies into bioluminescent biosensors that provide a homogeneous alternative for the competitive immunoassay.
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Affiliation(s)
- Eva A. van Aalen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Joep J. J. Lurvink
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Leandra Vermeulen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Benice van Gerven
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Yan Ni
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Remco Arts
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
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50
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Peach CJ, Tonello R, Gomez K, Calderon-Rivera A, Bruni R, Bansia H, Maile L, Manu AM, Hahn H, Thomsen ARB, Schmidt BL, Davidson S, des Georges A, Khanna R, Bunnett NW. Neuropilin-1 is a co-receptor for NGF and TrkA-evoked pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570398. [PMID: 38106002 PMCID: PMC10723411 DOI: 10.1101/2023.12.06.570398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Nerve growth factor (NGF) monoclonal antibodies (mAb) are one of the few patient-validated non-opioid treatments for chronic pain, despite failing to gain FDA approval due to worsened joint damage in some osteoarthritis patients. Herein, we demonstrate that neuropilin-1 (NRP1) is a nociceptor-enriched co-receptor for NGF that is necessary for tropomyosin-related kinase A (TrkA) signaling of pain. NGF binds NRP1 with nanomolar affinity. NRP1 and G Alpha Interacting Protein C-terminus 1 (GIPC1), a NRP1/TrkA adaptor, are coexpressed with TrkA in human and mouse nociceptors. NRP1 small molecule inhibitors and blocking mAb prevent NGF-stimulated action potential firing and activation of Na+ and Ca2+ channels in human and mouse nociceptors and abrogate NGF-evoked and inflammatory nociception in mice. NRP1 knockdown blunts NGF-stimulated TrkA phosphorylation, kinase signaling and transcription, whereas NRP1 overexpression enhances NGF and TrkA signaling. As well as interacting with NGF, NRP1 forms a heteromeric complex with TrkA. NRP1 thereby chaperones TrkA from the biosynthetic pathway to the plasma membrane and then to signaling endosomes, which enhances NGF-induced TrkA dimerization, endocytosis and signaling. Knockdown of GIPC1, a PDZ-binding protein that scaffolds NRP1 and TrkA to myosin VI, abrogates NGF-evoked excitation of nociceptors and pain-like behavior in mice. We identify NRP1 as a previously unrecognized co-receptor necessary for NGF/TrkA pain signaling by direct NGF binding and by chaperoning TrkA to the plasma membrane and signaling endosomes via the adaptor protein GIPC1. Antagonism of NRP1 and GIPC1 in nociceptors offers a long-awaited alternative to systemic sequestration of NGF with mAbs for the treatment of pain.
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