1
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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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2
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Yang Z, Chan DC. Development of a signal-integrating reporter to monitor mitochondria-ER contacts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580376. [PMID: 38405790 PMCID: PMC10888864 DOI: 10.1101/2024.02.14.580376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitochondria-ER contact sites (MERCS) serve as hotspots for important cellular processes, including calcium homeostasis, phospholipid homeostasis, mitochondria dynamics, and mitochondrial quality control. MERCS reporters based on complementation of GFP fragments have been designed to visualize MERCS in real-time, but we find that they do not accurately respond to changes in MERCS content. Here, we utilize split LacZ complementing fragments to develop the first MERCS reporter system (termed SpLacZ-MERCS) that continuously integrates the MERCS information within a cell and generates a fluorescent output. Our system exhibits good organelle targeting, no artifactual tethering, and effective, dynamic tracking of the MERCS level in single cells. The SpLacZ-MERCS reporter was validated by drug treatments and genetic perturbations known to affect mitochondria-ER contacts. The signal-integrating nature of SpLacZ-MERCS may enable systematic identification of genes and drugs that regulate mitochondria-ER interactions. Our successful application of the split LacZ complementation strategy to study MERCS may be extended to study other forms of inter-organellar crosstalk.
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3
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Ma X, Mandausch FJ, Wu Y, Sahoo VK, Ma W, Leoni G, Hostiuc M, Wintgens JP, Qiu J, Kannaiyan N, Rossner MJ, Wehr MC. Comprehensive split TEV based protein-protein interaction screening reveals TAOK2 as a key modulator of Hippo signalling to limit growth. Cell Signal 2024; 113:110917. [PMID: 37813295 DOI: 10.1016/j.cellsig.2023.110917] [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: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
The conserved Hippo signalling pathway plays a crucial role in tumour formation by limiting tissue growth and proliferation. At the core of this pathway are tumour suppressor kinases STK3/4 and LATS1/2, which limit the activity of the oncogene YAP1, the primary downstream effector. Here, we employed a split TEV-based protein-protein interaction screen to assess the physical interactions among 28 key Hippo pathway components and potential upstream modulators. This screen led us to the discovery of TAOK2 as pivotal modulator of Hippo signalling, as it binds to the pathway's core kinases, STK3/4 and LATS1/2, and leads to their phosphorylation. Specifically, our findings revealed that TAOK2 binds to and phosphorylates LATS1, resulting in the reduction of YAP1 phosphorylation and subsequent transcription of oncogenes. Consequently, this decrease led to a decrease in cell proliferation and migration. Interestingly, a correlation was observed between reduced TAOK2 expression and decreased patient survival time in certain types of human cancers, including lung and kidney cancer as well as glioma. Moreover, in cellular models corresponding to these cancer types the downregulation of TAOK2 by CRISPR inhibition led to reduced phosphorylation of LATS1 and increased proliferation rates, supporting TAOK2's role as tumour suppressor gene. By contrast, overexpression of TAOK2 in these cellular models lead to increased phospho-LATS1 but reduced cell proliferation. As TAOK2 is a druggable kinase, targeting TAOK2 could serve as an attractive pharmacological approach to modulate cell growth and potentially offer strategies for combating cancer.
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Affiliation(s)
- Xiao Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Fiona J Mandausch
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Wenbo Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Giovanna Leoni
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Madalina Hostiuc
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jan P Wintgens
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jiajun Qiu
- Department of Otolaryngology Head & Neck Surgery, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | | | - Moritz J Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany; Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University of 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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4
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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5
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Xu Z, Zhang X, Pal C, Rozners E, Callahan BP. Enzyme Fragment Complementation Driven by Nucleic Acid Hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572427. [PMID: 38187717 PMCID: PMC10769296 DOI: 10.1101/2023.12.19.572427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A modified protein fragment complementation assay has been designed and validated as a gain-of-signal biosensor for nucleic acid:nucleic acid interactions. The assay uses fragments of NanoBiT, the split luciferase reporter enzyme, that are esterified at their C-termini to steramers, sterol-modified oligodeoxynucleotides. The Drosophila hedgehog autoprocessing domain, DHhC, served as a self-cleaving catalyst for these bioconjugations. In the presence of ssDNA or RNA with segments complementary to the steramers and adjacent to one another, the two NanoBiT fragments productively associate, reconstituting NanoBiT enzyme activity. NanoBiT luminescence in samples containing nM ssDNA or RNA template exceeded background by 30-fold and as high as 120-fold depending on assay conditions. A unique feature of this detection system is the absence of a self-labeling domain in the NanoBiT bioconjugates. Eliminating that extraneous bulk broadens the detection range from short oligos to full-length mRNA.
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Affiliation(s)
- Zihan Xu
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Xiaoyu Zhang
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Chandan Pal
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Brian P. Callahan
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
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6
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Estep JA, Sun LO, Riccomagno MM. A luciferase fragment complementation assay to detect focal adhesion kinase (FAK) signaling events. Heliyon 2023; 9:e15282. [PMID: 37089315 PMCID: PMC10119766 DOI: 10.1016/j.heliyon.2023.e15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Integrin Adhesion Complexes (IACs) serve as links between the cytoskeleton and extracellular environment, acting as mechanosensing and signaling hubs. As such, IACs participate in many aspects of cellular motility, tissue morphogenesis, anchorage-dependent growth and cell survival. Focal Adhesion Kinase (FAK) has emerged as a critical organizer of IAC signaling events due to its early recruitment and diverse substrates, and thus has become a genetic and therapeutic target. Here we present the design and characterization of simple, reversible, and scalable Bimolecular Complementation sensors to monitor FAK phosphorylation in living cells. These probes provide novel means to quantify IAC signaling, expanding on the currently available toolkit for interrogating FAK phosphorylation during diverse cellular processes.
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Affiliation(s)
- Jason A. Estep
- Cell, Molecular and Developmental Biology Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Lu O. Sun
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin M. Riccomagno
- Cell, Molecular and Developmental Biology Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
- Neuroscience Program, Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
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7
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Vora DS, Kalakoti Y, Sundar D. Computational Methods and Deep Learning for Elucidating Protein Interaction Networks. Methods Mol Biol 2023; 2553:285-323. [PMID: 36227550 DOI: 10.1007/978-1-0716-2617-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein interactions play a critical role in all biological processes, but experimental identification of protein interactions is a time- and resource-intensive process. The advances in next-generation sequencing and multi-omics technologies have greatly benefited large-scale predictions of protein interactions using machine learning methods. A wide range of tools have been developed to predict protein-protein, protein-nucleic acid, and protein-drug interactions. Here, we discuss the applications, methods, and challenges faced when employing the various prediction methods. We also briefly describe ways to overcome the challenges and prospective future developments in the field of protein interaction biology.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Yogesh Kalakoti
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
- School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
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8
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Zhou G, Wan WW, Wang W. Modular Peroxidase-Based Reporters for Detecting Protease Activity and Protein Interactions with Temporal Gating. J Am Chem Soc 2022; 144:22933-22940. [PMID: 36511757 PMCID: PMC10026560 DOI: 10.1021/jacs.2c08280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Enzymatic reporters have been widely applied to study various biological processes because they can amplify signal through enzymatic reactions and provide good sensitivity. However, there is still a need for modular motifs for designing a series of enzymatic reporters. Here, we report a modular peroxidase-based motif, named CLAPon, that features acid-base coil-caged enhanced ascorbate peroxidase (APEX). We demonstrate the modularity of CLAPon by designing a series of reporters for detecting protease activity and protein-protein interactions (PPIs). CLAPon for protease activity showed a 390-fold fluorescent signal increase upon tobacco etch virus protease cleavage. CLAPon for PPI detection (PPI-CLAPon) has two variants, PPI-CLAPon1.0 and 1.1. PPI-CLAPon1.0 showed a signal-to-noise ratio (SNR) of up to 107 for high-affinity PPI pairs and enabled imaging with sub-cellular spatial resolution. However, the more sensitive PPI-CLAPon1.1 is required for detecting low-affinity PPI pairs. PPI-CLAPon1.0 was further engineered to a reporter with light-dependent temporal gating, called LiPPI-CLAPon1.0, which can detect a 3-min calcium-dependent PPI with an SNR of 17. LiPPI-CLAPon enables PPI detection within a specific time window with rapid APEX activation and diverse readout. Lastly, PPI-CLAPon1.0 was designed to have chemical gating, providing more versatility to complement the LiPPI-CLAPon. These CLAPon-based reporter designs can be broadly applied to study various signaling processes that involve protease activity and PPIs and provide a versatile platform to design various genetically encoded reporters.
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Affiliation(s)
- Guanwei Zhou
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Wei Wan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Corresponding Author: Wenjing Wang,
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9
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Park KS, Son RG, Kim SH, Abdelhamid MA, Pack SP. Soluble preparation and characterization of tripartite split GFP for In Vitro reconstitution applications. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Skeeters SS, Camp T, Fan H, Zhang K. The expanding role of split protein complementation in opsin-free optogenetics. Curr Opin Pharmacol 2022; 65:102236. [PMID: 35609383 PMCID: PMC9308681 DOI: 10.1016/j.coph.2022.102236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
A comprehensive understanding of signaling mechanisms helps interpret fundamental biological processes and restore cell behavior from pathological conditions. Signaling outcome depends not only on the activity of each signaling component but also on their dynamic interaction in time and space, which remains challenging to probe by biochemical and cell-based assays. Opsin-based optogenetics has transformed neural science research with its spatiotemporal modulation of the activity of excitable cells. Motivated by this advantage, opsin-free optogenetics extends the power of light to a larger spectrum of signaling molecules. This review summarizes commonly used opsin-free optogenetic strategies, presents a historical overview of split protein complementation, and highlights the adaptation of split protein recombination as optogenetic sensors and actuators.
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11
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Viruses 2021; 13:2485. [PMID: 34960755 PMCID: PMC8707919 DOI: 10.3390/v13122485] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. Here, we compared B.1.617 variants for neutralization resistance by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. B.1.617.1, B.1.617.2, and AY.1 pseudoviruses showed a modest 1.5- to 4.4-fold reduction in neutralization by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for C.37, P.1, R.1, and B.1.526 pseudoviruses, but 7- and 16-fold reductions for vaccine-elicited and convalescent sera, respectively, were seen for B.1.351 pseudoviruses. Among twenty-three therapeutic antibodies tested, four antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses and six antibodies showed either complete or partial loss of neutralization against B.1.617.1 and AY.1 pseudoviruses. Our results indicate that the current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants. Finally, the P681R substitution confers efficient cleavage of B.1.617 variants' spike proteins and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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Affiliation(s)
- Sabari Nath Neerukonda
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Russell Vassell
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Richard Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Lisa Bentley
- Office of the Assistance Secretary for Preparedness and Response, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Ann E. Eakin
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD 20892, USA;
| | - Karl J. Erlandson
- Influenza and Emerging Infectious Diseases Division, Biomedical Advanced Research and Development Authority, U.S. Department of Health and Human Services, Washington, DC 20201, USA;
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.E.); (L.C.K.)
| | - Carol D. Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA; (S.N.N.); (R.V.); (S.L.); (R.W.)
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12
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.05.467523. [PMID: 34790980 PMCID: PMC8597883 DOI: 10.1101/2021.11.05.467523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antibodies and current vaccines. Here we compared B.1.617 variants, and their single and double RBD substitutions for resistance to neutralization by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. Pseudoviruses with the B.1.617.1, B.1.617.2, and AY.1 spike showed a modest 1.5 to 4.4-fold reduction in neutralization titer by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for pseudoviruses with C.37, P.1, R.1, and B.1.526 spikes, but seven- and sixteen-fold reduction for vaccine-elicited and convalescent sera, respectively, was seen for pseudoviruses with the B.1.351 spike. Four of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses due to the L452R substitution, whereas six of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.1 pseudoviruses due to either the E484Q or L452R substitution. Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution. The modest resistance of B.1.617 variants to vaccine-elicited sera suggest that current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants, but the therapeutic antibodies need to be carefully selected based on their resistance profiles. Finally, the spike proteins of B.1.617 variants are more efficiently cleaved due to the P681R substitution, and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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13
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Sánchez-Navarro M. Advances in peptide-mediated cytosolic delivery of proteins. Adv Drug Deliv Rev 2021; 171:187-198. [PMID: 33561452 DOI: 10.1016/j.addr.2021.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023]
Abstract
The number of protein-based drugs is exponentially increasing. However, development of protein therapeutics against intracellular targets is hampered by the lack of efficient cytosolic delivery strategies. In recent years, the use of cell-penetrating peptides has been proposed as a strategy to promote protein internalization. In this article, we provide the reader with a succinct update on the strategies exploited to enable peptide-mediated cytosolic delivery of proteins. First, we analyse the various methods available for delivery. We then describe the most popular and the in vitro assays designed to assess the intracellular distribution of protein cargo.
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14
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Muscle Enriched Lamin Interacting Protein ( Mlip) Binds Chromatin and Is Required for Myoblast Differentiation. Cells 2021; 10:cells10030615. [PMID: 33802236 PMCID: PMC7998221 DOI: 10.3390/cells10030615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Muscle-enriched A-type lamin-interacting protein (Mlip) is a recently discovered Amniota gene that encodes proteins of unknown biological function. Here we report Mlip’s direct interaction with chromatin, and it may function as a transcriptional co-factor. Chromatin immunoprecipitations with microarray analysis demonstrated a propensity for Mlip to associate with genomic regions in close proximity to genes that control tissue-specific differentiation. Gel mobility shift assays confirmed that Mlip protein complexes with genomic DNA. Blocking Mlip expression in C2C12 myoblasts down-regulates myogenic regulatory factors (MyoD and MyoG) and subsequently significantly inhibits myogenic differentiation and the formation of myotubes. Collectively our data demonstrate that Mlip is required for C2C12 myoblast differentiation into myotubes. Mlip may exert this role as a transcriptional regulator of a myogenic program that is unique to amniotes.
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15
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Calabretta MM, Lopreside A, Montali L, Cevenini L, Roda A, Michelini E. A Genetically Encoded Bioluminescence Intracellular Nanosensor for Androgen Receptor Activation Monitoring in 3D Cell Models. SENSORS 2021; 21:s21030893. [PMID: 33572727 PMCID: PMC7865915 DOI: 10.3390/s21030893] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022]
Abstract
In recent years, there has been an increasing demand for predictive and sensitive in vitro tools for drug discovery. Split complementation assays have the potential to enlarge the arsenal of in vitro tools for compound screening, with most of them relying on well-established reporter gene assays. In particular, ligand-induced complementation of split luciferases is emerging as a suitable approach for monitoring protein–protein interactions. We hereby report an intracellular nanosensor for the screening of compounds with androgenic activity based on a split NanoLuc reporter. We also confirm the suitability of using 3D spheroids of Human Embryonic Kidney (HEK-293) cells for upgrading the 2D cell-based assay. A limit of detection of 4 pM and a half maximal effective concentration (EC50) of 1.7 ± 0.3 nM were obtained for testosterone with HEK293 spheroids. This genetically encoded nanosensor also represents a new tool for real time imaging of the activation state of the androgen receptor, thus being suitable for analysing molecules with androgenic activity, including new drugs or endocrine disrupting molecules.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40126 Bologna, Italy
| | - Antonia Lopreside
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40126 Bologna, Italy
| | - Laura Montali
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40126 Bologna, Italy
| | - Luca Cevenini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
| | - Aldo Roda
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
| | - Elisa Michelini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (M.M.C.); (A.L.); (L.M.); (L.C.); (A.R.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40126 Bologna, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
- Health Sciences and Technologies-Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy
- Correspondence:
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16
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Massoud TF, Paulmurugan R. Molecular Imaging of Protein–Protein Interactions and Protein Folding. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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17
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Kroning KE, Wang W. Temporally gated molecular tools for tracking protein-protein interactions in live cells. Methods Enzymol 2020; 640:205-223. [PMID: 32560799 DOI: 10.1016/bs.mie.2020.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Protein-protein interactions (PPIs) are essential in most biological processes. Even though many methods were designed to detect PPIs, detecting PPIs in a large volume of cells with a temporal resolution remains challenging. Recent development of light gated transcriptional reporters, such as SPARK and iTANGO, enabled detection of PPI in a large population of cells with a temporal resolution on the order of minutes. In this chapter, we discussed in detail the application of SPARK to detect PPIs between the activated β-2 adrenergic receptor (B2AR) and both Gα mimic and β-arrestin2. Because SPARK is a multi-component system, the protein expression level is critical for its optimal performance. We also discussed the detailed protocols for using SPARK with either transfection or lentiviral infection in HEK296T/17 cells.
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Affiliation(s)
- Kayla E Kroning
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Wenjing Wang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States.
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18
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Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
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Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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19
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Wang T, Yang N, Liang C, Xu H, An Y, Xiao S, Zheng M, Liu L, Wang G, Nie L. Detecting Protein-Protein Interaction Based on Protein Fragment Complementation Assay. Curr Protein Pept Sci 2020; 21:598-610. [PMID: 32053071 DOI: 10.2174/1389203721666200213102829] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 11/22/2022]
Abstract
Proteins are the most critical executive molecules by responding to the instructions stored in the genetic materials in any form of life. More frequently, proteins do their jobs by acting as a roleplayer that interacts with other protein(s), which is more evident when the function of a protein is examined in the real context of a cell. Identifying the interactions between (or amongst) proteins is very crucial for the biochemistry investigation of an individual protein and for the attempts aiming to draw a holo-picture for the interacting members at the scale of proteomics (or protein-protein interactions mapping). Here, we introduced the currently available reporting systems that can be used to probe the interaction between candidate protein pairs based on the fragment complementation of some particular proteins. Emphasis was put on the principles and details of experimental design. These systems are dihydrofolate reductase (DHFR), β-lactamase, tobacco etch virus (TEV) protease, luciferase, β- galactosidase, GAL4, horseradish peroxidase (HRP), focal adhesion kinase (FAK), green fluorescent protein (GFP), and ubiquitin.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Ningning Yang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Hongjv Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Yafei An
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Sha Xiao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Mengyuan Zheng
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Lu Liu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Gaozhan Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Lei Nie
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
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20
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21
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Jones K, Kentala K, Beck MW, An W, Lippert AR, Lewis JC, Dickinson BC. Development of a Split Esterase for Protein-Protein Interaction-Dependent Small-Molecule Activation. ACS CENTRAL SCIENCE 2019; 5:1768-1776. [PMID: 31807678 PMCID: PMC6891849 DOI: 10.1021/acscentsci.9b00567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 05/21/2023]
Abstract
Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small-molecule-based imaging agents are widely used in biological studies, and small-molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small-molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show that the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate that the esterase-based reporter system is compatible with other commonly used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small-molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show that the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Kaitlin Kentala
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Michael W. Beck
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Weiwei An
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Alexander R. Lippert
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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22
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Akama K, Iwanaga N, Yamawaki K, Okuda M, Jain K, Ueno H, Soga N, Minagawa Y, Noji H. Wash- and Amplification-Free Digital Immunoassay Based on Single-Particle Motion Analysis. ACS NANO 2019; 13:13116-13126. [PMID: 31675215 DOI: 10.1021/acsnano.9b05917] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Digital enzyme-linked immunosorbent assay (ELISA) is a powerful analytical method for highly sensitive protein biomarker detection. The current protocol of digital ELISA requires multiple washing steps and signal amplification using an enzyme, which could be the potential drawback in in vitro diagnosis. In this study, we propose a digital immunoassay method, which we call "Digital HoNon-ELISA" (digital homogeneous non-enzymatic immunosorbent assay) for highly sensitive detection without washing and signal amplification. Target antigen molecules react with antibody-coated magnetic nanoparticles, which are then magnetically pulled into femtoliter-sized reactors. The antigens on the particles are captured by antibodies anchored on the bottom surface of the reactor via molecular tethers. Magnetic force enhances the efficiency of particle encapsulation in the reactors. Subsequent physical compartmentalization of the particles enhances the binding efficiency of antigen-carrying particles to the antibodies. The tethered particles show characteristic Brownian motion within a limited space by the molecular tethering, which is distinct from free diffusion or nonspecific binding of antigen-free particles. The number of tethered particles directly correlates with the concentration of the target antigen. Digital HoNon-ELISA was used with a prostate-specific antigen to achieve a detection of 0.093 pg/mL, which is over 9.0-fold the sensitivity of commercialized highly sensitive ELISA (0.84 pg/mL) and comparable to digital ELISA (0.055 pg/mL). This digital immunoassay strategy has sensitivity similar to digital ELISA with simplicity similar to homogeneous assay. Such similarity allows for potential application in rapid and simple digital diagnostic tests without the need for washing and enzymatic amplification.
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Affiliation(s)
- Kenji Akama
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Niina Iwanaga
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Koya Yamawaki
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Masaki Okuda
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Krupali Jain
- Central Research Laboratories , Sysmex Corporation , 4-4-4 Takatsukadai , Nishi-ku, Kobe 651-2271 , Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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23
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Lin T, Scott BL, Hoppe AD, Chakravarty S. FRETting about the affinity of bimolecular protein-protein interactions. Protein Sci 2019; 27:1850-1856. [PMID: 30052312 DOI: 10.1002/pro.3482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a powerful tool to study macromolecular interactions such as protein-protein interactions (PPIs). Fluorescent protein (FP) fusions enable FRET-based PPI analysis of signaling pathways and molecular structure in living cells. Despite FRET's importance in PPI studies, FRET has seen limited use in quantifying the affinities of PPIs in living cells. Here, we have explored the relationship between FRET efficiency and PPI affinity over a wide range when expressed from a single plasmid system in Escherichia coli. Using live-cell microscopy and a set of 20 pairs of small interacting proteins, belonging to different structural folds and interaction affinities, we demonstrate that FRET efficiency can reliably measure the dissociation constant (KD ) over a range of mM to nM. A 10-fold increase in the interaction affinity results in 0.05 unit increase in FRET efficiency, providing sufficient resolution to quantify large affinity differences (> 10-fold) using live-cell FRET. This approach provides a rapid and simple strategy for assessment of PPI affinities over a wide range and will have utility for high-throughput analysis of protein interactions.
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Affiliation(s)
- Tao Lin
- Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, 57007
| | - Brandon L Scott
- Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, 57007
| | - Adam D Hoppe
- Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, 57007.,BioSNTR, Brookings, South Dakota, 57007
| | - Suvobrata Chakravarty
- Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, 57007.,BioSNTR, Brookings, South Dakota, 57007
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24
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Abstract
Receptor tyrosine kinases (RTKs) play important roles in cell growth, motility, differentiation, and survival. These single-pass membrane proteins are grouped into subfamilies based on the similarity of their extracellular domains. They are generally thought to be activated by ligand binding, which promotes homodimerization and then autophosphorylation in trans. However, RTK interactions are more complicated, as RTKs can interact in the absence of ligand and heterodimerize within and across subfamilies. Here, we review the known cross-subfamily RTK heterointeractions and their possible biological implications, as well as the methodologies which have been used to study them. Moreover, we demonstrate how thermodynamic models can be used to study RTKs and to explain many of the complicated biological effects which have been described in the literature. Finally, we discuss the concept of the RTK interactome: a putative, extensive network of interactions between the RTKs. This RTK interactome can produce unique signaling outputs; can amplify, inhibit, and modify signaling; and can allow for signaling backups. The existence of the RTK interactome could provide an explanation for the irreproducibility of experimental data from different studies and for the failure of some RTK inhibitors to produce the desired therapeutic effects. We argue that a deeper knowledge of RTK interactome thermodynamics can lead to a better understanding of fundamental RTK signaling processes in health and disease. We further argue that there is a need for quantitative, thermodynamic studies that probe the strengths of the interactions between RTKs and their ligands and between different RTKs.
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Affiliation(s)
- Michael D. Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
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25
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Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A. Directed Evolution of Split APEX2 Peroxidase. ACS Chem Biol 2019; 14:619-635. [PMID: 30848125 PMCID: PMC6548188 DOI: 10.1021/acschembio.8b00919] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.
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Affiliation(s)
- Yisu Han
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Tess Caroline Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D. Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Daniela Boassa
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - David Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Mark H. Ellisman
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - Alice Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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26
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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27
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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28
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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Gao XJ, Chong LS, Kim MS, Elowitz MB. Programmable protein circuits in living cells. Science 2018; 361:1252-1258. [PMID: 30237357 DOI: 10.1126/science.aat5062] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
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Affiliation(s)
- Xiaojing J Gao
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucy S Chong
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Kim
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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30
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Weiffert T, Linse S. Protein stabilization with retained function of monellin using a split GFP system. Sci Rep 2018; 8:12763. [PMID: 30143736 PMCID: PMC6109104 DOI: 10.1038/s41598-018-31177-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/10/2018] [Indexed: 11/09/2022] Open
Abstract
Sweet proteins are an unexploited resource in the search for non-carbohydrate sweeteners mainly due to their low stability towards heating. Variants of the sweet protein monellin, with increased stability, were derived by an in vivo screening method based on the thermodynamic linkage between fragment complementation and protein stability. This approach depends on the correlation between mutational effects on the affinity between protein fragments and the stability of the intact protein. By linking the two fragments of monellin to the split GFP (green fluorescent protein) system, reconstitution of GFP was promoted and moderately fluorescent colonies were obtained. Two separate random libraries were produced for the monellin chains and the mutant clones were ranked based on fluorescence intensity. Mutants with increased affinity between the fragments, and subsequently increased stability, caused increased fluorescence intensity of split GFP. Single chain monellin variants of the top-ranked mutants for each chain, S76Y in the A-chain and W3C + R39G in the B-chain and all combinations thereof, were expressed and the increase in stability was verified by temperature denaturation studies using circular dichroism spectroscopy. Functionality studies showed that mutant S76Y has retained sweetness and has potential use within the food industry.
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Affiliation(s)
- Tanja Weiffert
- Department of Biochemistry and Structural Biology, Chemical Centre, Lund University, SE221 00, Lund, Sweden.
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Chemical Centre, Lund University, SE221 00, Lund, Sweden
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Fisher KH, Fragiadaki M, Pugazhendhi D, Bausek N, Arredondo MA, Thomas SJ, Brown S, Zeidler MP. A genome-wide RNAi screen identifies MASK as a positive regulator of cytokine receptor stability. J Cell Sci 2018; 131:jcs.209551. [PMID: 29848658 DOI: 10.1242/jcs.209551] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/16/2018] [Indexed: 01/01/2023] Open
Abstract
Cytokine receptors often act via the Janus kinase and signal transducer and activator of transcription (JAK/STAT) pathway to form a signalling cascade that is essential for processes such as haematopoiesis, immune responses and tissue homeostasis. In order to transduce ligand activation, cytokine receptors must dimerise. However, mechanisms regulating their dimerisation are poorly understood. In order to better understand the processes regulating cytokine receptor levels, and their activity and dimerisation, we analysed the highly conserved JAK/STAT pathway in Drosophila, which acts via a single receptor, known as Domeless. We performed a genome-wide RNAi screen in Drosophila cells, identifying MASK as a positive regulator of Domeless dimerisation and protein levels. We show that MASK is able to regulate receptor levels and JAK/STAT signalling both in vitro and in vivo We also show that its human homologue, ANKHD1, is also able to regulate JAK/STAT signalling and the levels of a subset of pathway receptors in human cells. Taken together, our results identify MASK as a novel regulator of cytokine receptor levels, and suggest functional conservation, which may have implications for human health.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Katherine H Fisher
- The Bateson Centre, Department of Biomedical Science, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
| | - Maria Fragiadaki
- The Bateson Centre, Department of Biomedical Science, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
| | - Dhamayanthi Pugazhendhi
- The Bateson Centre, Department of Biomedical Science, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
| | - Nina Bausek
- The Bateson Centre, Department of Biomedical Science, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
| | - Maria A Arredondo
- Department of Oncology & Human Metabolism, The University of Sheffield, Sheffield, S10 2RX, UK
| | - Sally J Thomas
- Department of Oncology & Human Metabolism, The University of Sheffield, Sheffield, S10 2RX, UK
| | - Stephen Brown
- The Sheffield RNAi Screening Facility, Department of Biomedical Science, The University of Sheffield, S10 2TN, UK
| | - Martin P Zeidler
- The Bateson Centre, Department of Biomedical Science, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
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Hastings JF, Han JZR, Shearer RF, Kennedy SP, Iconomou M, Saunders DN, Croucher DR. Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP). J Vis Exp 2018. [PMID: 29985350 DOI: 10.3791/57109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The assembly of protein complexes is a central mechanism underlying the regulation of many cell signaling pathways. A major focus of biomedical research is deciphering how these dynamic protein complexes act to integrate signals from multiple sources in order to direct a specific biological response, and how this becomes deregulated in many disease settings. Despite the importance of this key biochemical mechanism, there is a lack of experimental techniques that can facilitate the specific and sensitive deconvolution of these multi-molecular signaling complexes. Here this shortcoming is addressed through the combination of a protein complementation assay with a conformation-specific nanobody, which we have termed Bimolecular Complementation Affinity Purification (BiCAP). This novel technique facilitates the specific isolation and downstream proteomic characterization of any pair of interacting proteins, to the exclusion of un-complexed individual proteins and complexes formed with competing binding partners. The BiCAP technique is adaptable to a wide array of downstream experimental assays, and the high degree of specificity afforded by this technique allows more nuanced investigations into the mechanics of protein complex assembly than is currently possible using standard affinity purification techniques.
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Affiliation(s)
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research
| | - Robert F Shearer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research; Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen
| | - Sean P Kennedy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research; RCSI Molecular Medicine, Royal College of Surgeons in Ireland
| | - Mary Iconomou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research; Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics
| | | | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research; St Vincent's Hospital Clinical School, University of New South Wales; School of Medicine and Medical Science, University College Dublin;
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Conformational Stability of the Hemagglutinin of H5N1 Influenza A Viruses Influences Susceptibility to Broadly Neutralizing Stem Antibodies. J Virol 2018; 92:JVI.00247-18. [PMID: 29593038 PMCID: PMC5974491 DOI: 10.1128/jvi.00247-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/14/2018] [Indexed: 12/29/2022] Open
Abstract
Vaccines that elicit broadly neutralizing antibodies to the conserved stem of hemagglutinin (HA) are being developed as universal influenza vaccines that protect against influenza across multiple years. However, different influenza virus strains, even those in the same subtype with identical stem sequences, can vary in susceptibility to broadly neutralizing stem antibodies, and the reasons are not understood. Here we studied potential mechanisms underlying the differing sensitivities of a panel of H5N1 HA pseudoviruses to broadly neutralizing stem antibodies. We found that greater HA conformational stability, as measured by thermal inactivation and pH triggering of conformational changes, correlates with reduced neutralization sensitivity and antibody binding to HA under neutral- and low-pH conditions. Our data indicate that the conformational stability of HA is an important attribute of susceptibility to broadly neutralizing stem antibodies and is influenced by residues outside the stem antibody epitopes. IMPORTANCE The influenza virus surface glycoprotein hemagglutinin (HA) mediates virus attachment and membrane fusion between virus and host cells, allowing the viral core to enter the host cell cytoplasm for replication. Fusion occurs when HA undergoes low-pH-induced-conformational changes during endocytosis. Broadly neutralizing antibodies targeted to the conserved stem region of HA interfere with conformational changes required for fusion. Vaccines that elicit such antibodies are being developed as novel universal influenza vaccines for multiyear protection. We investigated why H5N1 HAs from different strains differ in their sensitivity to broadly neutralizing stem antibodies despite having conserved epitopes. We report that HA conformational stability due to residues outside the antibody binding site accounted for much of the variation in susceptibility to neutralization by stem antibodies. These findings highlight the importance of nonepitope residues in influencing neutralization sensitivity to stem antibodies and the complexities in developing universal vaccines targeting conserved epitopes in the HA stem.
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Establishing a Split Luciferase Assay for Proteinkinase G (PKG) Interaction Studies. Int J Mol Sci 2018; 19:ijms19041180. [PMID: 29649180 PMCID: PMC5979328 DOI: 10.3390/ijms19041180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/04/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023] Open
Abstract
Nitric oxide (NO/cyclic guanosine monophosphate (cGMP)-regulated cellular mechanisms are involved in a variety of (patho-) physiological processes. One of the main effector molecules in this system, proteinkinase G (PKG), serves as a molecular switch by phosphorylating different target proteins and thereby turning them on or off. To date, only a few interaction partners of PKG have been described although the identification of protein–protein interactions (PPI) is indispensable for the understanding of cellular processes and diseases. Conventionally used methods to detect PPIs exhibit several disadvantages, e.g., co-immunoprecipitations, which depend on suitable high-affinity antibodies. Therefore, we established a cell-based protein-fragment complementation assay (PCA) for the identification of PKG target proteins. Here, a reporter protein (click beetle luciferase) is split into two fragments and fused to two different possible interaction partners. If interaction occurs, the reporter protein is functionally complemented and the catalyzed reaction can then be quantitatively measured. By using this technique, we confirmed the regulator of G-Protein signaling 2 (RGS2) as an interaction partner of PKGIα (a PKG-isoform) following stimulation with 8-Br-cGMP and 8-pCPT-cGMP. Hence, our results support the conclusion that the established approach could serve as a novel tool for the rapid, easy and cost-efficient detection of novel PKG target proteins.
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35
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Moustaqil M, Bhumkar A, Gonzalez L, Raoul L, Hunter DJB, Carrive P, Sierecki E, Gambin Y. A Split-Luciferase Reporter Recognizing GFP and mCherry Tags to Facilitate Studies of Protein-Protein Interactions. Int J Mol Sci 2017; 18:E2681. [PMID: 29232933 PMCID: PMC5751283 DOI: 10.3390/ijms18122681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 12/31/2022] Open
Abstract
The use of fluorescently-tagged proteins in microscopy has become routine, and anti-GFP (Green fluorescent protein) affinity matrices are increasingly used in proteomics protocols. However, some protein-protein interactions assays, such as protein complementation assays (PCA), require recloning of each protein as a fusion with the different parts of the complementation system. Here we describe a generic system where the complementation is separated from the proteins and can be directly used with fluorescently-tagged proteins. By using nanobodies and performing tests in cell-free expression systems, we accelerated the development of multiple reporters, detecting heterodimers and homodimers or oligomers tagged with GFP or mCherry. We demonstrate that the system can detect interactions at a broad range of concentrations, from low nanomolar up to micromolar.
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Affiliation(s)
- Mehdi Moustaqil
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Akshay Bhumkar
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Laura Gonzalez
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Lisa Raoul
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Dominic J B Hunter
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
| | - Pascal Carrive
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Emma Sierecki
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
| | - Yann Gambin
- European Molecular Biology Laboratory Australia (EMBL Australia) Node in Single Molecule Science, Sydney NSW 2031, Australia.
- School of Medical Sciences, The University of New South Wales, Sydney NSW 2031, Australia.
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36
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Nealon JO, Philomina LS, McGuffin LJ. Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. Int J Mol Sci 2017; 18:E2623. [PMID: 29206185 PMCID: PMC5751226 DOI: 10.3390/ijms18122623] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/17/2022] Open
Abstract
The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development.
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Affiliation(s)
- John Oliver Nealon
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK.
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37
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Verhoef LGGC, Wade M. Visualization of Protein Interactions in Living Cells Using Bimolecular Luminescence Complementation (BiLC). ACTA ACUST UNITED AC 2017; 90:30.5.1-30.5.14. [PMID: 29091275 DOI: 10.1002/cpps.42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The number of intracellular protein-protein interactions (PPIs) far exceeds the total number of proteins encoded by the genome. Dynamic cellular PPI networks respond to external stimuli and endogenous metabolism in order to maintain homeostasis. Many PPIs are directly involved in disease pathogenesis and/or resistance to therapeutics; they therefore represent potential drug targets. A technology generally termed 'bimolecular complementation' relies on the physical splitting of a molecular reporter (such as a fluorescent or luminescent protein) and fusion of the resulting two fragments to a pair of interacting proteins. When these proteins interact, they effectively reconstitute the activity of the molecular reporter (typically leading to increased fluorescence or luminescence). This unit describes the selection and development of bimolecular luminescence complementation (BiLC) assays for reporting intracellular PPIs, and provides examples in which BiLC was used to identify small molecules that can modulate PPIs. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lisette G G C Verhoef
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Mark Wade
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
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38
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Noda N, Awais R, Sutton R, Awais M, Ozawa T. Dynamic monitoring of p53 translocation to mitochondria for the analysis of specific inhibitors using luciferase-fragment complementation. Biotechnol Bioeng 2017; 114:2818-2827. [DOI: 10.1002/bit.26407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Natsumi Noda
- Department of Chemistry, School of Science; The University of Tokyo; Bunkyo-ku Tokyo Japan
| | - Raheela Awais
- School of Life Sciences; University of Liverpool; Liverpool United Kingdom
| | - Robert Sutton
- NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, University of Liverpool; Royal Liverpool University Hospital; Liverpool United Kingdom
| | - Muhammad Awais
- NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, University of Liverpool; Royal Liverpool University Hospital; Liverpool United Kingdom
| | - Takeaki Ozawa
- Department of Chemistry, School of Science; The University of Tokyo; Bunkyo-ku Tokyo Japan
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39
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Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP. High-throughput precision measurement of subcellular localization in single cells. Cytometry A 2017; 91:180-189. [PMID: 28094900 DOI: 10.1002/cyto.a.23054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023]
Abstract
To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow cytometry to include data relating to localization of proteins to and within organelles. We used SLA to detect the nuclear import of transcription factors across cell subsets in complex samples. We further measured intranuclear re-localization of target proteins across the cell cycle and upon DNA damage induction. SLA combines multiple single-cell methods to bring about a new dimension of inquiry and analysis in complex cell populations. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Tyler J Burns
- Department of Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Andreas P Frei
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Pier F Gherardini
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Felice A Bava
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Jake E Batchelder
- Immunology and Microbial Pathogenesis, Joan and Sanford I. Weill Medical College of Cornell University, New York, New York
| | - Yuki Yoshiyasu
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Julie M Yu
- Department of Biological Sciences, University of California Berkeley, Berkeley, California
| | | | - Samuel C Kimmey
- Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Veronica D Gonzalez
- Stanford University School of Medicine, Baxter Laboratory for Stem Cell Biology, Stanford, California
| | - Wendy J Fantl
- Stanford Comprehensive Cancer Institute and Department of Obstetrics and Gynecology, Stanford University, Stanford, California
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, California
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40
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Mo X, Qi Q, Ivanov AA, Niu Q, Luo Y, Havel J, Goetze R, Bell S, Moreno CS, Cooper LAD, Johns MA, Khuri FR, Du Y, Fu H. AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay. Mol Pharmacol 2017; 91:339-347. [PMID: 28087810 DOI: 10.1124/mol.116.107623] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/09/2017] [Indexed: 01/07/2023] Open
Abstract
The c-Myc (MYC) transcription factor is a major cancer driver and a well-validated therapeutic target. However, directly targeting MYC has been challenging. Thus, identifying proteins that interact with and regulate MYC may provide alternative strategies to inhibit its oncogenic activity. In this study, we report the development of a NanoLuc-based protein-fragment complementation assay (NanoPCA) and mapping of the MYC protein interaction hub in live mammalian cells. The NanoPCA system was configured to enable detection of protein-protein interactions (PPI) at the endogenous level, as shown with PRAS40 dimerization, and detection of weak interactions, such as PINCH1-NCK2. Importantly, NanoPCA allows the study of PPI dynamics with reversible interactions. To demonstrate its utility for large-scale PPI detection in mammalian intracellular environment, we have used NanoPCA to examine MYC interaction with 83 cancer-associated proteins in live cancer cell lines. Our new MYC PPI data confirmed known MYC-interacting proteins, such as MAX, GSK3A, and SMARCA4, and revealed a panel of novel MYC interaction partners, such as RAC-α serine/threonine-protein kinase (AKT)1, liver kinase B (LKB)1, and Yes-associated protein (YAP)1. The MYC interactions with AKT1, LKB1, and YAP1 were confirmed by coimmunoprecipitation of endogenous proteins. Importantly, AKT1, LKB1, and YAP1 were able to activate MYC in a transcriptional reporter assay. Thus, these vital growth control proteins may represent promising MYC regulators, suggesting new mechanisms that couple energetic and metabolic pathways and developmental signaling to MYC-regulated cellular programs.
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Affiliation(s)
- Xiulei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Qi Qi
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Andrei A Ivanov
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Qiankun Niu
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Yin Luo
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Jonathan Havel
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Russell Goetze
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Sydney Bell
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Carlos S Moreno
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Lee A D Cooper
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Margaret A Johns
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Fadlo R Khuri
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Yuhong Du
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
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41
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Characterizing Dynamic Protein-Protein Interactions Using the Genetically Encoded Split Biosensor Assay Technique Split TEV. Methods Mol Biol 2017; 1596:219-238. [PMID: 28293890 DOI: 10.1007/978-1-4939-6940-1_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dynamic protein-protein interactions (PPIs) are fundamental building blocks of cellular signaling and monitoring their regulation promotes the understanding of signaling in health and disease. Genetically encoded split protein biosensor assays, such as the split TEV method, have proved to be highly valuable when studying regulated PPIs in living cells. Split TEV is based on the functional complementation of two previously inactive TEV protease fragments fused to interacting proteins and provides a robust, sensitive and flexible readout to monitor PPIs both at the membrane and in the cytosol. Thus, split TEV can be used to analyze interactomes of receptors, membrane-associated proteins, and cytosolic proteins. In particular, split TEV is useful to assay activities of relevant drug targets, such as receptor tyrosine kinases and G protein-coupled receptors, in compound screens. As split TEV uses genetically encoded readouts, including standard reporters based on fluorescence and luminescence, the technique can also be combined with scalable molecular barcode reporter systems, allowing the integration into multiplexed high-throughput assay approaches. Split TEV can be used in standard heterologous cell lines and primary cell types, including neurons, either in a transient or stably integrated format. When using cell lines, the basic protocol takes 30-96 h to complete, depending on the complexity of the experimental question addressed.
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42
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Croucher DR, Iconomou M, Hastings JF, Kennedy SP, Han JZR, Shearer RF, McKenna J, Wan A, Lau J, Aparicio S, Saunders DN. Bimolecular complementation affinity purification (BiCAP) reveals dimer-specific protein interactions for ERBB2 dimers. Sci Signal 2016; 9:ra69. [PMID: 27405979 DOI: 10.1126/scisignal.aaf0793] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The dynamic assembly of multiprotein complexes is a central mechanism of many cell signaling pathways. This process is key to maintaining the spatiotemporal specificity required for an accurate, yet adaptive, response to rapidly changing cellular conditions. We describe a technique for the specific isolation and downstream proteomic characterization of any two interacting proteins, to the exclusion of their individual moieties and competing binding partners. We termed the approach bimolecular complementation affinity purification (BiCAP) because it combines the use of conformation-specific nanobodies with a protein-fragment complementation assay with affinity purification. Using BiCAP, we characterized the specific interactome of the epidermal growth factor receptor (EGFR) family member ERBB2 when in the form of a homodimer or when in the form of a heterodimer with either EGFR or ERBB3. We identified dimer-specific interaction patterns for key adaptor proteins and identified a number of previously unknown interacting partners. Functional analysis for one of these newly identified partners revealed a noncanonical mechanism of extracellular signal-regulated kinase (ERK) activation that is specific to the ERBB2:ERBB3 heterodimer and acts through the adaptor protein FAM59A in breast cancer cells.
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Affiliation(s)
- David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. St. Vincent's Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia. School of Medicine, University College Dublin, Belfield, Dublin D4, Ireland.
| | - Mary Iconomou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jordan F Hastings
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Sean P Kennedy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. Systems Biology Ireland, University College Dublin, Belfield, Dublin D4, Ireland
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Robert F Shearer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jessie McKenna
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Adrian Wan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Joseph Lau
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Darren N Saunders
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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43
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Büttner FH, Kumpf R, Menzel S, Reulle D, Valler MJ. Evaluation of the InteraX™ System Technology in a High-Throughput Screening Environment. ACTA ACUST UNITED AC 2016; 10:485-94. [PMID: 16093558 DOI: 10.1177/1087057104272568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The authors have developed a cell-based high-throughput screening (HTS)-compatible assay tomeasure EGFRdimerization using the InteraX TMenzyme complementation technology of Applied Biosystems. The cells contain 2 chimeric proteins with complementing deletionmutants of the beta galactosidase enzyme, each fused to the extracellular and transmembrane part of EGFR. On binding of EGF, EGF receptor dimerizes and an active beta galactosidase is built. The authors used this homogeneous 384-well assay to screen about 20,000 diverse compounds. From 2 independent primary screen runs 239 hits were identified. For run 1, amean S/Bratio of 4.26 and ameanZβ factor of 0.74were obtained, for run 2 amean S/Bratio of 3.88 and amean Zβ factor of 0.71 were obtained. After hit confirmation, repeated 4 times, 112 hits remainedwith a confirmation rate of 48.9%. Thirty of the 112 could be identified as cytotoxic. Fifty-one of the remaining 82 compounds could be shown to be inhibitors of the beta galactosidase enzymeitself. In summary, 31 compounds remained as potential EGFRdimerization or EGF stimulation inhibitors. The authors conclude that the InteraX TMsystemtechnology is HTS capable and can detect smallmolecule inhibitors capable of inhibiting protein-protein interactions.
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Affiliation(s)
- Frank H Büttner
- Department of Integrated Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany.
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44
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Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nat Biotechnol 2016; 34:774-80. [PMID: 27240195 PMCID: PMC4942342 DOI: 10.1038/nbt.3563] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 12/26/2022]
Abstract
Intercellular protein-protein interactions (PPIs) enable communication between cells in diverse biological processes, including cell proliferation, immune responses, infection, and synaptic transmission, but they are challenging to visualize because existing techniques have insufficient sensitivity and/or specificity. Here we report a split horseradish peroxidase (sHRP) as a sensitive and specific tool for the detection of intercellular PPIs. The two sHRP fragments, engineered through screening of 17 cut sites in HRP followed by directed evolution, reconstitute into an active form when driven together by an intercellular PPI, producing bright fluorescence or contrast for electron microscopy. Fusing the sHRP fragments to the proteins neurexin (NRX) and neuroligin (NLG), which bind each other across the synaptic cleft, enabled sensitive visualization of synapses between specific sets of neurons, including two classes of synapses in the mouse visual system. sHRP should be widely applicable to studying mechanisms of communication between a variety of cell types.
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Affiliation(s)
- Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
| | - Carolyn G Kwa
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California at San Diego, La Jolla, San Diego, California, USA
- Department of Neurosciences, University of California at San Diego, La Jolla, San Diego, California, USA
- Salk Institute for Biological Studies, La Jolla, San Diego, California, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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45
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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46
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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47
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Npro fusion technology: On-column complementation to improve efficiency in biopharmaceutical production. Protein Expr Purif 2016; 120:42-50. [DOI: 10.1016/j.pep.2015.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/18/2015] [Accepted: 11/24/2015] [Indexed: 11/21/2022]
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48
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Suntornnond R, An J, Tijore A, Leong KF, Chua CK, Tan LP. A Solvent-Free Surface Suspension Melt Technique for Making Biodegradable PCL Membrane Scaffolds for Tissue Engineering Applications. Molecules 2016; 21:386. [PMID: 27007364 PMCID: PMC6273409 DOI: 10.3390/molecules21030386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
In tissue engineering, there is limited availability of a simple, fast and solvent-free process for fabricating micro-porous thin membrane scaffolds. This paper presents the first report of a novel surface suspension melt technique to fabricate a micro-porous thin membrane scaffolds without using any organic solvent. Briefly, a layer of polycaprolactone (PCL) particles is directly spread on top of water in the form of a suspension. After that, with the use of heat, the powder layer is transformed into a melted layer, and following cooling, a thin membrane is obtained. Two different sizes of PCL powder particles (100 µm and 500 µm) are used. Results show that membranes made from 100 µm powders have lower thickness, smaller pore size, smoother surface, higher value of stiffness but lower ultimate tensile load compared to membranes made from 500 µm powder. C2C12 cell culture results indicate that the membrane supports cell growth and differentiation. Thus, this novel membrane generation method holds great promise for tissue engineering.
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Affiliation(s)
- Ratima Suntornnond
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Nanyang Technological University, Block N3.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Jia An
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Nanyang Technological University, Block N3.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Ajay Tijore
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Kah Fai Leong
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Nanyang Technological University, Block N3.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Chee Kai Chua
- Singapore Centre for 3D Printing, School of Mechanical and Aerospace Engineering, Nanyang Technological University, Block N3.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Lay Poh Tan
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, Singapore 639798, Singapore.
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49
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Dixon AS, Schwinn MK, Hall MP, Zimmerman K, Otto P, Lubben TH, Butler BL, Binkowski BF, Machleidt T, Kirkland TA, Wood MG, Eggers CT, Encell LP, Wood KV. NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells. ACS Chem Biol 2016; 11:400-8. [PMID: 26569370 DOI: 10.1021/acschembio.5b00753] [Citation(s) in RCA: 758] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-fragment complementation assays (PCAs) are widely used for investigating protein interactions. However, the fragments used are structurally compromised and have not been optimized nor thoroughly characterized for accurately assessing these interactions. We took advantage of the small size and bright luminescence of NanoLuc to engineer a new complementation reporter (NanoBiT). By design, the NanoBiT subunits (i.e., 1.3 kDa peptide, 18 kDa polypeptide) weakly associate so that their assembly into a luminescent complex is dictated by the interaction characteristics of the target proteins onto which they are appended. To ascertain their general suitability for measuring interaction affinities and kinetics, we determined that their intrinsic affinity (KD = 190 μM) and association constants (kon = 500 M(-1) s(-1), koff = 0.2 s(-1)) are outside of the ranges typical for protein interactions. The accuracy of NanoBiT was verified under defined biochemical conditions using the previously characterized interaction between SME-1 β-lactamase and a set of inhibitor binding proteins. In cells, NanoBiT fusions to FRB/FKBP produced luminescence consistent with the linear characteristics of NanoLuc. Response dynamics, evaluated using both protein kinase A and β-arrestin-2, were rapid, reversible, and robust to temperature (21-37 °C). Finally, NanoBiT provided a means to measure pharmacology of kinase inhibitors known to induce the interaction between BRAF and CRAF. Our results demonstrate that the intrinsic properties of NanoBiT allow accurate representation of protein interactions and that the reporter responds reliably and dynamically in cells.
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Affiliation(s)
- Andrew S. Dixon
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Mary P. Hall
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Kris Zimmerman
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | | | | | | | - Thomas A. Kirkland
- Promega Biosciences Incorporated, San Luis
Obispo, California 93401, United States
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
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50
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To TL, Zhang Q, Shu X. Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. Protein Sci 2016; 25:748-53. [PMID: 26690964 DOI: 10.1002/pro.2866] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/19/2022]
Abstract
A reversible green fluorogenic protein-fragment complementation assay was developed based on the crystal structure of UnaG, a recently discovered fluorescent protein. In living mammalian cells, the nonfluorescent fragments complemented and rapidly became fluorescent upon rapamycin-induced FKBP and Frb protein interaction, and lost fluorescence when the protein interaction was inhibited. This reversible fluorogenic reporter, named uPPI [UnaG-based protein-protein interaction (PPI) reporter], uses bilirubin (BR) as the chromophore and requires no exogenous cofactor. BR is an endogenous molecule in mammalian cells and is not fluorescent by itself. uPPI may have many potential applications in visualizing spatiotemporal dynamics of PPIs.
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Affiliation(s)
- Tsz-Leung To
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
| | - Qiang Zhang
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
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