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Winter DL, Wairara AR, Bennett JL, Donald WA, Glover DJ. Protein Interaction Kinetics Delimit the Performance of Phosphorylation-Driven Protein Switches. ACS Synth Biol 2024; 13:1781-1797. [PMID: 38830815 DOI: 10.1021/acssynbio.4c00101] [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: 06/05/2024]
Abstract
Post-translational modifications (PTMs) such as phosphorylation and dephosphorylation can rapidly alter protein surface chemistry and structural conformation, which can switch protein-protein interactions (PPIs) within signaling networks. Recently, de novo-designed phosphorylation-responsive protein switches have been created that harness kinase- and phosphatase-mediated phosphorylation to modulate PPIs. PTM-driven protein switches are promising tools for investigating PTM dynamics in living cells, developing biocompatible nanodevices, and engineering signaling pathways to program cell behavior. However, little is known about the physical and kinetic constraints of PTM-driven protein switches, which limits their practical application. In this study, we present a framework to evaluate two-component PTM-driven protein switches based on four performance metrics: effective concentration, dynamic range, response time, and reversibility. Our computational models reveal an intricate relationship between the binding kinetics, phosphorylation kinetics, and switch concentration that governs the sensitivity and reversibility of PTM-driven protein switches. Building upon the insights of the interaction modeling, we built and evaluated novel phosphorylation-driven protein switches consisting of phosphorylation-sensitive coiled coils as sensor domains fused to fluorescent proteins as actuator domains. By modulating the phosphorylation state of the switches with a specific protein kinase and phosphatase, we demonstrate fast, reversible transitions between "on" and "off" states. The response of the switches linearly correlated to the kinase concentration, demonstrating its potential as a biosensor for kinase measurements in real time. As intended, the switches responded to specific kinase activity with an increase in the fluorescence signal and our model could be used to distinguish between two mechanisms of switch activation: dimerization or a structural rearrangement. The protein switch kinetics model developed here should enable PTM-driven switches to be designed with ideal performance for specific applications.
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Affiliation(s)
- Daniel L Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Adelgisa R Wairara
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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2
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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3
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Dhakar SS, Galera-Prat A, Lehtiö L. High-throughput screening assay for PARP-HPF1 interaction inhibitors to affect DNA damage repair. Sci Rep 2024; 14:3875. [PMID: 38365924 PMCID: PMC10873324 DOI: 10.1038/s41598-024-54123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
ADP-ribosyltransferases PARP1 and PARP2 play a major role in DNA repair mechanism by detecting the DNA damage and inducing poly-ADP-ribosylation dependent chromatin relaxation and recruitment of repair proteins. Catalytic PARP inhibitors are used as anticancer drugs especially in the case of tumors arising from sensitizing mutations. Recently, a study showed that Histone PARylation Factor (HPF1) forms a joint active site with PARP1/2. The interaction of HPF1 with PARP1/2 alters the modification site from Aspartate/Glutamate to Serine, which has been shown to be a key ADP-ribosylation event in the context of DNA damage. Therefore, disruption of PARP1/2-HPF1 interaction could be an alternative strategy for drug development to block the PARP1/2 activity. In this study, we describe a FRET based high-throughput screening assay to screen inhibitor libraries against PARP-HPF1 interaction. We optimized the conditions for FRET signal and verified the interaction by competing the FRET pair in multiple ways. The assay is robust and easy to automate. Validatory screening showed the robust performance of the assay, and we discovered two compounds Dimethylacrylshikonin and Alkannin, with µM inhibition potency against PARP1/2-HPF1 interaction. The assay will facilitate the discovery of inhibitors against HPF1-PARP1/2 complex and to develop potentially new effective anticancer agents.
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Affiliation(s)
- Saurabh S Dhakar
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
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Madahar V, Dang R, Zhang Q, Liu C, Rodgers VGJ, Liao J. Human Post-Translational SUMOylation Modification of SARS-CoV-2 Nucleocapsid Protein Enhances Its Interaction Affinity with Itself and Plays a Critical Role in Its Nuclear Translocation. Viruses 2023; 15:1600. [PMID: 37515286 PMCID: PMC10384427 DOI: 10.3390/v15071600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Viruses, such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect hosts and take advantage of host cellular machinery for genome replication and new virion production. Identifying and elucidating host pathways for viral infection is critical for understanding the development of the viral life cycle and novel therapeutics. The SARS-CoV-2 N protein is critical for viral RNA (vRNA) genome packaging in new virion formation. Using our quantitative Förster energy transfer/Mass spectrometry (qFRET/MS) coupled method and immunofluorescence imaging, we identified three SUMOylation sites of the SARS-CoV-2 N protein. We found that (1) Small Ubiquitin-like modifier (SUMO) modification in Nucleocapsid (N) protein interaction affinity increased, leading to enhanced oligomerization of the N protein; (2) one of the identified SUMOylation sites, K65, is critical for its nuclear translocation. These results suggest that the host human SUMOylation pathway may be critical for N protein functions in viral replication and pathology in vivo. Thus, blocking essential host pathways could provide a novel strategy for future anti-viral therapeutics development, such as for SARS-CoV-2 and other viruses.
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Affiliation(s)
- Vipul Madahar
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Runrui Dang
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Quanqing Zhang
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Department of Botany, College of Natural & Agricultural Sciences, University of California at Riverside, Riverside, CA 92521, USA
| | - Chuchu Liu
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Victor G J Rodgers
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
| | - Jiayu Liao
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
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López-Tena M, Farrera-Soler L, Barluenga S, Winssinger N. Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection). JACS AU 2023; 3:449-458. [PMID: 36873687 PMCID: PMC9975836 DOI: 10.1021/jacsau.2c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.
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Winter DL, Lebhar H, McCluskey JB, Glover DJ. A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates. J Nanobiotechnology 2023; 21:66. [PMID: 36829140 PMCID: PMC9960191 DOI: 10.1186/s12951-023-01817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps. RESULTS We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures. CONCLUSIONS We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.
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Affiliation(s)
- Daniel L. Winter
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hélène Lebhar
- grid.1005.40000 0004 4902 0432Recombinant Products Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Joshua B. McCluskey
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dominic J. Glover
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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Wang J, Xie H, Dong Q, Liu J, Su J, An Y, Zeng B, Sun B, Liu J. The effect of arginine on inhibiting amyloid fibril derived from β-casein and the binding studies with multi-spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 282:121681. [PMID: 35917615 DOI: 10.1016/j.saa.2022.121681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
In general, β-casein is a stable molecular chaperone. However, the fact that amyloid fibrils derived from β-casein has been reported in some cases, which were usually associated with some malignant breast diseases. As an important amino acid, arginine not only exhibits the significance in casein synthesis in mammary gland, but also has great potentiality in inhibiting the amyloid fibril formation. Therefore, the influence of arginine on the amyloid fibrils formed by β-casein and further molecular mechanism were studied firstly with multi-spectroscopic techniques in the present work. The results of Thioflavin T determination, particle size analysis, transmission electron microscope observation showed that arginine not only inhibited the aggregation of β-casein at the growth stage, but also depolymerized the mature amyloid fibrils at the saturation stage. The further fluorescence experiment results demonstrated that the complex was formed between β-casein and arginine. Besides, there was one binding site and 0.48 nm binding distance. The thermodynamic parameters like ΔG0, ΔS0, ΔH0 were all negative, showing their binding reaction was spontaneous, and hydrogen bond and van der Waals force were the possibly chief intermolecular forces. Furthermore, the synchronous fluorescence spectra showing that the conformation of β-casein was affected and its tyrosine residues were gradually buried inside the protein. Our research would provide new insights into the treatments for the breast amyloidosis.
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Affiliation(s)
- Jia Wang
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Hongliu Xie
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Qinghai Dong
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Jiayin Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Jun Su
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Yang An
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Baohua Zeng
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, PR China
| | - Bingxue Sun
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China
| | - Jihua Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, Changchun, PR China.
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Sowa ST, Bosetti C, Galera-Prat A, Johnson MS, Lehtiö L. An Evolutionary Perspective on the Origin, Conservation and Binding Partner Acquisition of Tankyrases. Biomolecules 2022; 12:1688. [PMID: 36421702 PMCID: PMC9688111 DOI: 10.3390/biom12111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 01/04/2024] Open
Abstract
Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species may exist. In this work, we confirm the widespread distribution of tankyrases throughout the branches of multicellular animal life and identify the single-celled choanoflagellates as earliest origin of tankyrases. We further show that the sequences and structural aspects of TNKSs are well-conserved even between distantly related species. We also experimentally characterized an anciently diverged tankyrase homolog from the sponge Amphimedon queenslandica and show that the basic functional aspects, such as poly-ADP-ribosylation activity and interaction with the canonical tankyrase binding peptide motif, are conserved. Conversely, the presence of tankyrase binding motifs in orthologs of confirmed interaction partners varies greatly between species, indicating that tankyrases may have different sets of interaction partners depending on the animal lineage. Overall, our analysis suggests a remarkable degree of conservation for tankyrases, and that their regulatory functions in cells have likely changed considerably throughout evolution.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Chiara Bosetti
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering and InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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Human SUMOylation Pathway Is Critical for Influenza B Virus. Viruses 2022; 14:v14020314. [PMID: 35215907 PMCID: PMC8876058 DOI: 10.3390/v14020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
The identification and elucidation of host pathways for viral infection are critical for understanding the viral infection processes and novel therapeutics development. Here, for the first time, we discover that the human SUMOylation pathway is essential for the IBV viral life cycle. First, IBV viruses were completely inhibited by a novel SUMOylation specific inhibitor, STE025, discovered from our FRET-based high-throughput screening, and the inhibition was very potent, with IC50~ 0.1 µM in an IBV-induced cell death rescue assay; Second, we determined that the IBV M1 protein was SUMOylated, which was mediated by the SUMOylation E2 conjugation enzyme and the E3 ligase enzyme at very high affinities, of 0.20 µM and 0.22 µM, respectively; Third, the mutation of the IBV M1 SUMOylation site, K21R, completely abolished the viral particle generation, strongly suggesting the requirement of SUMOylation for the IBV life cycle. These results suggest that the blockage of the host human SUMOylation pathway is very effective for IBV inhibition. We therefore propose that the host SUMOylation pathway is a critical host factor for the IBV virus life cycle. The identification and inhibition of critical host factor(s) provide a novel strategy for future anti-viral therapeutics development, such as IBV and other viruses.
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Sowa ST, Galera-Prat A, Wazir S, Alanen HI, Maksimainen MM, Lehtiö L. A molecular toolbox for ADP-ribosyl binding proteins. CELL REPORTS METHODS 2021; 1:100121. [PMID: 34786571 PMCID: PMC8580838 DOI: 10.1016/j.crmeth.2021.100121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022]
Abstract
Proteins interacting with ADP-ribosyl groups are often involved in disease-related pathways or viral infections, making them attractive drug targets. We present a robust and accessible assay applicable to both hydrolyzing or non-hydrolyzing binders of mono- and poly-ADP-ribosyl groups. This technology relies on a C-terminal tag based on a Gi protein alpha subunit peptide (GAP), which allows for site-specific introduction of cysteine-linked mono- and poly-ADP-ribosyl groups or analogs. By fusing the GAP-tag and ADP-ribosyl binders to fluorescent proteins, we generate robust FRET partners and confirm the interaction with 22 known ADP-ribosyl binders. The applicability for high-throughput screening of inhibitors is demonstrated with the SARS-CoV-2 nsp3 macrodomain, for which we identify suramin as a moderate-affinity yet non-specific inhibitor. High-affinity ADP-ribosyl binders fused to nanoluciferase complement this technology, enabling simple blot-based detection of ADP-ribosylated proteins. All these tools can be produced in Escherichia coli and will help in ADP-ribosylation research and drug discovery.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Sarah Wazir
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Heli I. Alanen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mirko M. Maksimainen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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11
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Liu Y, Zhang F, Jiang L, Perry JJP, Zhao Z, Liao J. Product inhibition kinetics determinations - Substrate interaction affinity and enzymatic kinetics using one quantitative FRET assay. Int J Biol Macromol 2021; 193:1481-1487. [PMID: 34780893 DOI: 10.1016/j.ijbiomac.2021.10.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/27/2021] [Indexed: 02/05/2023]
Abstract
Product inhibition is a common phenomenon during enzyme-catalyzed reactions. Almost all product molecules of an enzyme reaction should have some structural similarities to the substrate, and can thus still have affinities to the active site of the enzyme as product inhibitor. Currently, the characterizations of product inhibition are generally carried out by different methods to determine product binding affinity to the enzyme and the enzyme kinetics parameters, and then these parameters are combined to determine product inhibition. However, due to different sensitivity and variations, kinetics parameters determined from different methods are often not compatible, resulting in not accurate measurement. Here, we report a novel method that determines the two different classes of kinetics parameters, IC50 and Ki(or KD), Kcat and KM, using one single assay method-quantitative FRET(qFRET) assay for characterizing the product inhibition of pre-SUMO1's maturation by its protease SENP1. One method to determine all kinetics parameters provides, for the first time, not only a convenient method to determine all kinetics parameters, but more importantly, a novel approach to combine different measurements with mutually compatible results and errors.
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Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Fan Zhang
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China; Physical Examination Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Jiang
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - J Jefferson P Perry
- City of Hope Biomedical Research Center, 1218 S. Fifth Avenue, Office 2268 Monrovia, CA 91016, USA
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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12
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Liao J, Madahar V, Dang R, Jiang L. Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution. Molecules 2021; 26:molecules26216339. [PMID: 34770748 PMCID: PMC8588070 DOI: 10.3390/molecules26216339] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play pivotal roles in life, and the protein interaction affinity confers specific protein interaction events in physiology or pathology. Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research to detect molecular interactions in vitro and in vivo. The FRET assay provides very high sensitivity and efficiency. Several attempts have been made to develop the FRET assay into a quantitative measurement for protein-protein interaction affinity in the past. However, the progress has been slow due to complicated procedures or because of challenges in differentiating the FRET signal from other direct emission signals from donor and receptor. This review focuses on recent developments of the quantitative FRET analysis and its application in the determination of protein-protein interaction affinity (KD), either through FRET acceptor emission or donor quenching methods. This paper mainly reviews novel theatrical developments and experimental procedures rather than specific experimental results. The FRET-based approach for protein interaction affinity determination provides several advantages, including high sensitivity, high accuracy, low cost, and high-throughput assay. The FRET-based methodology holds excellent potential for those difficult-to-be expressed proteins and for protein interactions in living cells.
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Affiliation(s)
- Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
- Biomedical Science, School of Medicine, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: ; Tel.: +1-951-827-6240; Fax: +1-951-827-6416
| | - Vipul Madahar
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Runrui Dang
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Ling Jiang
- Department of Biochemistry and Molecular Biology, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin 150040, China;
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Jung J, Bong JH, Sung JS, Lee SJ, Lee M, Kang MJ, Jose J, Pyun JC. Fluorescein and Rhodamine B-Binding Domains from Autodisplayed Fv-Antibody Library. Bioconjug Chem 2021; 32:2213-2223. [PMID: 34617729 DOI: 10.1021/acs.bioconjchem.1c00376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, the binding domains for fluorescent dyes were presented that could be used as synthetic peptides or fusion proteins. Fv-antibodies against two fluorescent dyes (fluorescein and rhodamine B) were screened from the Fv-antibody library, which was prepared on the outer membrane of Escherichia coli using the autodisplay technology. Two clones with binding activities to each fluorescent dye were screened separately from the library using flow cytometry. The binding activity of the screened Fv-antibodies on the outer membrane was analyzed using fluorescent imaging with the corresponding fluorescent dyes. The CDR3 regions of the screened Fv-antibodies (11 amino acid residues) were synthesized into peptides, and each peptide was analyzed for its binding activity to each fluorescent dye using fluorescence resonance energy transfer (FRET) experiments. These CDR3 regions were demonstrated to have a binding activity to each fluorescent dye when the regions were co-expressed as a fusion protein with Z-domain.
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Affiliation(s)
- Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Jeong Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Soo Jeong Lee
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Misu Lee
- Division of Life Sciences, College of Life Science and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Min-Jung Kang
- Medicine Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, PharmaCampus, Westphalian Wilhelms-University Münster, Corrensstr. 48, Münster 48149, Germany
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Korea
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14
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Hariharan C, Tao Y, Jiang L, Wen X, Liao J. Assay technologies for apoptosis and autophagy. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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15
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Wen D, Li X, Geng X, Hirai M, Ajito S, Takahashi K, Ozaki M, Hojo MK, Uebi T, Iwasa T. Characterization of Localization, Ligand Binding, and pH-Dependent Conformational Changes of Two Chemosensory Proteins Expressed in the Antennae of the Japanese Carpenter Ant, Camponotus Japonicus. Zoolog Sci 2020; 37:371-381. [PMID: 32729716 DOI: 10.2108/zs190138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/12/2020] [Indexed: 11/17/2022]
Abstract
Camponotus japonicus uses basiconic antennal sensilla (s. basiconica) to sense a colony-specific blend of species-specific cuticular hydrocarbons (CHCs). The inner portion of the s. basiconica is filled with sensillar lymph and chemosensory proteins (CSPs) presumed to transport CHCs to olfactory neuron receptors. Although 12 CSPs have been found in C. japonicus antennae, we focused on CjapCSP1 and CjapCSP13. The molecular basis of CSP1 function was explored by observation of its structure in solution at pH 4.0 and 7.0 through circular dichroism (CD) and X-ray solution scattering. Although the secondary structure did not vary with pH change, the radius of gyration (Rg) was larger by 5.3% (0.74 Å increase) at pH 4.0 than at pH 7.0. The dissociation constant (Kd) for CjapCSP1 measured with a fluorescent probe, 1-N-phenylnaphthylamine, was larger at pH 4.0 than at pH 7.0, suggesting that acidic pH triggers ligand dissociation. In contrast to CjapCSP1, the Rg of CjapCSP13 was slightly smaller at pH 4.0 than at pH 7.0. Western blotting and immunohistochemistry with protein-specific antisera revealed that both CjapCSP1 and CjapCSP13 are detected in the antennae, but differ in their specific internal localization. Binding to four compounds, including the ant CHC (z)-9-tricosene, was examined. Although both CjapCSP1 and CjapCSP13 bound to (z)-9-tricosene, CjapCSP13 bound with higher affinity than CjapCSP1 and showed different binding properties. CjapCSP1 and CjapCSP13 are synthesized by the same cells of the antenna, but function differently in CHC distribution due to differences in their localization and binding characteristics.
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Affiliation(s)
- Durige Wen
- Division of Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan
| | - Xing Li
- Division of Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan
| | - Xiong Geng
- Division of Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan
| | - Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, Maebashi 371-8510, Japan
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, Maebashi 371-8510, Japan
| | - Kosuke Takahashi
- Graduate School of Science and Technology, Gunma University, Maebashi 371-8510, Japan
| | - Mamiko Ozaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Masaru K Hojo
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Tatsuya Uebi
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Tatsuo Iwasa
- Division of Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan.,Academic Support Center, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan,
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16
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Sowa ST, Vela-Rodríguez C, Galera-Prat A, Cázares-Olivera M, Prunskaite-Hyyryläinen R, Ignatev A, Lehtiö L. A FRET-based high-throughput screening platform for the discovery of chemical probes targeting the scaffolding functions of human tankyrases. Sci Rep 2020; 10:12357. [PMID: 32704068 PMCID: PMC7378079 DOI: 10.1038/s41598-020-69229-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022] Open
Abstract
Tankyrases catalyse poly-ADP-ribosylation of their binding partners and the modification serves as a signal for the subsequent proteasomal degradation of these proteins. Tankyrases thereby regulate the turnover of many proteins involved in multiple and diverse cellular processes, such as mitotic spindle formation, telomere homeostasis and Wnt/β-catenin signalling. In recent years, tankyrases have become attractive targets for the development of inhibitors as potential therapeutics against cancer and fibrosis. Further, it has become clear that tankyrases are not only enzymes, but also act as scaffolding proteins forming large cellular signalling complexes. While many potent and selective tankyrase inhibitors of the poly-ADP-ribosylation function exist, the inhibition of tankyrase scaffolding functions remains scarcely explored. In this work we present a robust, simple and cost-effective high-throughput screening platform based on FRET for the discovery of small molecule probes targeting the protein–protein interactions of tankyrases. Validatory screening with the platform led to the identification of two compounds with modest binding affinity to the tankyrase 2 ARC4 domain, demonstrating the applicability of this approach. The platform will facilitate identification of small molecules binding to tankyrase ARC or SAM domains and help to advance a structure-guided development of improved chemical probes targeting tankyrase oligomerization and substrate protein interactions.
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Affiliation(s)
- Sven T Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Carlos Vela-Rodríguez
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mariana Cázares-Olivera
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Alexander Ignatev
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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17
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Hochreiter B, Kunze M, Moser B, Schmid JA. Advanced FRET normalization allows quantitative analysis of protein interactions including stoichiometries and relative affinities in living cells. Sci Rep 2019; 9:8233. [PMID: 31160659 PMCID: PMC6547726 DOI: 10.1038/s41598-019-44650-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
FRET (Fluorescence Resonance Energy Transfer) measurements are commonly applied to proof protein-protein interactions. However, standard methods of live cell FRET microscopy and signal normalization only allow a principle assessment of mutual binding and are unable to deduce quantitative information of the interaction. We present an evaluation and normalization procedure for 3-filter FRET measurements, which reflects the process of complex formation by plotting FRET-saturation curves. The advantage of this approach relative to traditional signal normalizations is demonstrated by mathematical simulations. Thereby, we also identify the contribution of critical parameters such as the total amount of donor and acceptor molecules and their molar ratio. When combined with a fitting procedure, this normalization facilitates the extraction of key properties of protein complexes such as the interaction stoichiometry or the apparent affinity of the binding partners. Finally, the feasibility of our method is verified by investigating three exemplary protein complexes. Altogether, our approach offers a novel method for a quantitative analysis of protein interactions by 3-filter FRET microscopy, as well as flow cytometry. To facilitate the application of this method, we created macros and routines for the programs ImageJ, R and MS-Excel, which we make publicly available.
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Affiliation(s)
- Bernhard Hochreiter
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Markus Kunze
- Medical University Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Vienna, Austria
| | - Bernhard Moser
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Johannes A Schmid
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria.
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18
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Butler VJ, Cortopassi WA, Gururaj S, Wang AL, Pierce OM, Jacobson MP, Kao AW. Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro. Biochemistry 2019; 58:2670-2674. [PMID: 31099551 DOI: 10.1021/acs.biochem.9b00275] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Progranulin (PGRN) is an evolutionarily conserved glycoprotein associated with several disease states, including neurodegeneration, cancer, and autoimmune disorders. This protein has recently been implicated in the regulation of lysosome function, whereby PGRN may bind to and promote the maturation and activity of the aspartyl protease cathepsin D (proCTSD, inactive precursor; matCTSD, mature, enzymatically active form). As the full-length PGRN protein can be cleaved into smaller peptides, called granulins, we assessed the function of these granulin peptides in binding to proCTSD and stimulating matCTSD enzyme activity in vitro. Here, we report that full-length PGRN and multi-granulin domain peptides bound to proCTSD with low to submicromolar binding affinities. This binding promoted proCTSD destabilization, the magnitude of which was greater for multi-granulin domain peptides than for full-length PGRN. Such destabilization correlated with enhanced matCTSD activity at acidic pH. The presence and function of multi-granulin domain peptides have typically been overlooked in previous studies. This work provides the first in vitro quantification of their binding and activity on proCTSD. Our study highlights the significance of multi-granulin domain peptides in the regulation of proCTSD maturation and enzymatic activity and suggests that attention to PGRN processing will be essential for the future understanding of the molecular mechanisms leading to neurodegenerative disease states with loss-of-function mutations in PGRN.
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Affiliation(s)
- Victoria J Butler
- Department of Neurology , University of California , San Francisco , California 94143 , United States
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94143 , United States
| | - Sushmitha Gururaj
- Department of Neurology , University of California , San Francisco , California 94143 , United States
| | - Austin L Wang
- Department of Neurology , University of California , San Francisco , California 94143 , United States
| | - Olivia M Pierce
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94143 , United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94143 , United States
| | - Aimee W Kao
- Department of Neurology , University of California , San Francisco , California 94143 , United States
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19
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Söveges B, Imre T, Póti ÁL, Sok P, Kele Z, Alexa A, Kele P, Németh K. Tracking down protein-protein interactions via a FRET-system using site-specific thiol-labeling. Org Biomol Chem 2018; 16:5756-5763. [PMID: 29947400 DOI: 10.1039/c8ob00742j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster resonance energy transfer is among the most popular tools to follow protein-protein interactions. Although limited to certain cases, site-specific fluorescent labeling of proteins via natural functions by means of chemical manipulations can redeem laborious protein engineering techniques. Herein we report on the synthesis of a heterobifunctional tag and its use in site-specific protein labeling studies aiming at exploring protein-protein interactions. The oxadiazole-methylsulfonyl functionality serves as a thiol specific warhead that enables easy and selective installation of fluorescent labels through a bioorthogonal motif. Mitogen activated protein kinase (MAPK14) and its substrate mitogen activated protein kinase activated kinase (MAPKAP2) or its docking motif, a 22 amino acid-long peptide fragment, were labeled with a donor and an acceptor, respectively. Evolution of strong FRET signals upon protein-protein interactions supported the specific communication between the partners. Using an efficient FRET pair allowed the estimation of dissociation constants for protein-protein and peptide-protein interactions (145 nM and 240 nM, respectively).
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Affiliation(s)
- B Söveges
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Organic Chemistry, Chemical Biology Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - T Imre
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Instrumentation Center, MS Metabolomics Research Group, Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| | - Á L Póti
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Enzymology, Protein Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - P Sok
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Enzymology, Protein Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Zs Kele
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Organic Chemistry, Chemical Biology Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - A Alexa
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Enzymology, Protein Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - P Kele
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Organic Chemistry, Chemical Biology Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - K Németh
- Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Organic Chemistry, Chemical Biology Research Group, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
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20
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Miller BS, Parolo C, Turbé V, Keane CE, Gray ER, McKendry RA. Quantifying Biomolecular Binding Constants using Video Paper Analytical Devices. Chemistry 2018; 24:9783-9787. [PMID: 29772094 PMCID: PMC6055620 DOI: 10.1002/chem.201802394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 01/08/2023]
Abstract
A novel ultra-low-cost biochemical analysis platform to quantify protein dissociation binding constants and kinetics using paper microfluidics is reported. This approach marries video imaging with one of humankind's oldest materials: paper, requiring no large, expensive laboratory equipment, complex microfluidics or external power. Temporal measurements of nanoparticle-antibody conjugates binding on paper is found to follow the Langmuir Adsorption Model. This is exploited to measure a series of antibody-antigen dissociation constants on paper, showing excellent agreement with a gold-standard benchtop interferometer. The concept is demonstrated with a camera and low-end smartphone, 500-fold cheaper than the reference method, and can be multiplexed to measure ten reactions in parallel. These findings will help to widen access to quantitative analytical biochemistry, for diverse applications spanning disease diagnostics, drug discovery, and environmental analysis in resource-limited settings.
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Affiliation(s)
- Benjamin S. Miller
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Claudio Parolo
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
| | - Valérian Turbé
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Candice E. Keane
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
| | - Eleanor R. Gray
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
| | - Rachel A. McKendry
- London Centre for NanotechnologyUniversity College London17–19 Gordon StreetLondonWC1H 0AHUK
- Division of MedicineUniversity College London, Cruciform BuildingGower StreetLondonWC1E 6BTUK
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21
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Margineanu A, Chan JJ, Kelly DJ, Warren SC, Flatters D, Kumar S, Katan M, Dunsby CW, French PMW. Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM). Sci Rep 2016; 6:28186. [PMID: 27339025 PMCID: PMC4919659 DOI: 10.1038/srep28186] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/19/2016] [Indexed: 11/09/2022] Open
Abstract
We present a high content multiwell plate cell-based assay approach to quantify protein interactions directly in cells using Förster resonance energy transfer (FRET) read out by automated fluorescence lifetime imaging (FLIM). Automated FLIM is implemented using wide-field time-gated detection, typically requiring only 10 s per field of view (FOV). Averaging over biological, thermal and shot noise with 100's to 1000's of FOV enables unbiased quantitative analysis with high statistical power. Plotting average donor lifetime vs. acceptor/donor intensity ratio clearly identifies protein interactions and fitting to double exponential donor decay models provides estimates of interacting population fractions that, with calibrated donor and acceptor fluorescence intensities, can yield dissociation constants. We demonstrate the application to identify binding partners of MST1 kinase and estimate interaction strength among the members of the RASSF protein family, which have important roles in apoptosis via the Hippo signalling pathway. KD values broadly agree with published biochemical measurements.
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Affiliation(s)
- Anca Margineanu
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Jia Jia Chan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Douglas J. Kelly
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Sean C. Warren
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Delphine Flatters
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques in silico, Inserm UMR-S 973, 35 rue Helene Brion, 75013 Paris, France
| | - Sunil Kumar
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Matilda Katan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Christopher W. Dunsby
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Paul M. W. French
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
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22
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Booth EA, Thorner J. A FRET-based method for monitoring septin polymerization and binding of septin-associated proteins. Methods Cell Biol 2016; 136:35-56. [PMID: 27473902 DOI: 10.1016/bs.mcb.2016.03.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Much about septin function has been inferred from in vivo studies using mainly genetic methods, and much of what we know about septin organization has been obtained through examination of static structures in vitro primarily by electron microscopy. Deeper mechanistic insight requires real-time analysis of the dynamics of the assembly of septin-based structures and how other proteins associate with them. We describe here a Förster resonance energy transfer (FRET)-based approach for measuring in vitro the rate and extent of filament formation from septin complexes, binding of other proteins to septin structures, and the apparent affinities of these interactions. FRET is particularly well suited for interrogating protein-protein interactions, especially on a rapid timescale; the spectral change provides an unambiguous indication of whether two elements within the system under study are associating and serves as a molecular-level "ruler" because it is very sensitive to the separation between the donor and acceptor fluorophores over biologically relevant distances (≤10nm). The necessary procedures involve generation of appropriate cysteine-less and single cysteine-containing septin variants, expression and purification of the heterooctameric complexes containing them, efficient labeling of the purified complexes with desired fluorophores, fluorimetric measurement of FRET, and appropriate safeguards and controls in data acquisition and analysis. Our methods can be used to interrogate the effects of buffer conditions, small molecules, and septin-binding proteins on septin filament assembly or stability; determine the effect of alternative septin subunits, mutational alterations, or posttranslational modifications on assembly; and, delineate the location of septin-binding proteins.
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Affiliation(s)
- E A Booth
- University of California, Berkeley, CA, United States
| | - J Thorner
- University of California, Berkeley, CA, United States
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23
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Geometrical assembly of ultrastable protein templates for nanomaterials. Nat Commun 2016; 7:11771. [PMID: 27249579 PMCID: PMC4895442 DOI: 10.1038/ncomms11771] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 04/28/2016] [Indexed: 11/15/2022] Open
Abstract
The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein–protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions. Protein nanotechnology for the fabrication of protein-based nanoscale devices is gaining momentum but assembling well-defined three-dimensional shapes is still challenging. Here, the authors use an existing prefoldin assembled system to design a template for the construction of geometrically constrained structures.
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24
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Blaževitš O, Mideksa YG, Šolman M, Ligabue A, Ariotti N, Nakhaeizadeh H, Fansa EK, Papageorgiou AC, Wittinghofer A, Ahmadian MR, Abankwa D. Galectin-1 dimers can scaffold Raf-effectors to increase H-ras nanoclustering. Sci Rep 2016; 6:24165. [PMID: 27087647 PMCID: PMC4834570 DOI: 10.1038/srep24165] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Galectin-1 (Gal-1) dimers crosslink carbohydrates on cell surface receptors. Carbohydrate-derived inhibitors have been developed for cancer treatment. Intracellularly, Gal-1 was suggested to interact with the farnesylated C-terminus of Ras thus specifically stabilizing GTP-H-ras nanoscale signalling hubs in the membrane, termed nanoclusters. The latter activity may present an alternative mechanism for how overexpressed Gal-1 stimulates tumourigenesis. Here we revise the current model for the interaction of Gal-1 with H-ras. We show that it indirectly forms a complex with GTP-H-ras via a high-affinity interaction with the Ras binding domain (RBD) of Ras effectors. A computationally generated model of the Gal-1/C-Raf-RBD complex is validated by mutational analysis. Both cellular FRET as well as proximity ligation assay experiments confirm interaction of Gal-1 with Raf proteins in mammalian cells. Consistently, interference with H-rasG12V-effector interactions basically abolishes H-ras nanoclustering. In addition, an intact dimer interface of Gal-1 is required for it to positively regulate H-rasG12V nanoclustering, but negatively K-rasG12V nanoclustering. Our findings suggest stacked dimers of H-ras, Raf and Gal-1 as building blocks of GTP-H-ras-nanocluster at high Gal-1 levels. Based on our results the Gal-1/effector interface represents a potential drug target site in diseases with aberrant Ras signalling.
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Affiliation(s)
- Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Yonatan G. Mideksa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eyad K. Fansa
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | | | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
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25
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Andreotti G, Monti MC, Citro V, Cubellis MV. Heterodimerization of Two Pathological Mutants Enhances the Activity of Human Phosphomannomutase2. PLoS One 2015; 10:e0139882. [PMID: 26488408 PMCID: PMC4619449 DOI: 10.1371/journal.pone.0139882] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/18/2015] [Indexed: 12/04/2022] Open
Abstract
The most frequent disorder of glycosylation is due to mutations in the gene encoding phosphomannomutase2 (PMM2-CDG). For this disease, which is autosomal and recessive, there is no cure at present. Most patients are composite heterozygous and carry one allele encoding an inactive mutant, R141H, and one encoding a hypomorphic mutant. Phosphomannomutase2 is a dimer. We reproduced composite heterozygosity in vitro by mixing R141H either with the wild type protein or the most common hypomorphic mutant F119L and compared the quaternary structure, the activity and the stability of the heterodimeric enzymes. We demonstrated that the activity of R141H/F119L heterodimers in vitro, which reproduces the protein found in patients, has the same activity of wild type/R141H, which reproduces the protein found in healthy carriers. On the other hand the stability of R141H/F119L appears to be reduced both in vitro and in vivo. These findings suggest that a therapy designed to enhance protein stability such as those based on pharmacological chaperones or modulation of proteostasis could be beneficial for PMM2-CDG patients carrying R141H/F119L genotype as well as for other genotypes where protein stability rather than specific activity is affected by mutations.
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Affiliation(s)
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università degli Studi di Salerno, Fisciano, Italy
| | - Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
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Fu DY, Jin S, Zheng DD, Zha X, Wu Y. Peptidic inhibitors for in vitro pentamer formation of human papillomavirus capsid protein l1. ACS Med Chem Lett 2015; 6:381-5. [PMID: 25893037 DOI: 10.1021/ml500392y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/25/2015] [Indexed: 12/18/2022] Open
Abstract
A new 14 peptide, originating essentially from the helix 5 of HPV 16L1, illustrates an IC50 of 19.38 nM for the inhibition of HPV 16 L1 pentamer formation, which is highly efficient for targeting a specific protein segment. In addition, mechanism studies reveal that the length, sequence, and the folding of the peptide are critical factors for its inhibition. Particularly, the peptide shows similar inhibition against the pentamer formation of HPV 58L1, although it is designed specially for HPV 16 L1. This study opens a way for the development of high-efficiency, broad-spectrum inhibitors as a new class of anti-HPV agents, which could be extended to the treatment of other virus types.
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Affiliation(s)
- Ding-Yi Fu
- State Key Laboratory
of Supramolecular Structure and Materials, Institute of Theoretical
Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun 130012, China
| | - Shi Jin
- State Key Laboratory
of Supramolecular Structure and Materials, Institute of Theoretical
Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun 130012, China
| | - Dong-Dong Zheng
- State Key Laboratory
of Supramolecular Structure and Materials, Institute of Theoretical
Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun 130012, China
| | - Xiao Zha
- Sichuan Tumor Hospital & Institute, Chengdu 610041, China
| | - Yuqing Wu
- State Key Laboratory
of Supramolecular Structure and Materials, Institute of Theoretical
Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun 130012, China
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27
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The interaction affinity between vascular cell adhesion molecule-1 (VCAM-1) and very late antigen-4 (VLA-4) analyzed by quantitative FRET. PLoS One 2015; 10:e0121399. [PMID: 25793408 PMCID: PMC4368157 DOI: 10.1371/journal.pone.0121399] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/31/2015] [Indexed: 11/19/2022] Open
Abstract
Very late antigen-4 (VLA-4), a member of integrin superfamily, interacts with its major counter ligand vascular cell adhesion molecule-1 (VCAM-1) and plays an important role in leukocyte adhesion to vascular endothelium and immunological synapse formation. However, irregular expressions of these proteins may also lead to several autoimmune diseases and metastasis cancer. Thus, quantifying the interaction affinity of the VCAM-1/VLA-4 interaction is of fundamental importance in further understanding the nature of this interaction and drug discovery. In this study, we report an ‘in solution’ steady state organic fluorophore based quantitative fluorescence resonance energy transfer (FRET) assay to quantify this interaction in terms of the dissociation constant (Kd). We have used, in our FRET assay, the Alexa Fluor 488-VLA-4 conjugate as the donor, and Alexa Fluor 546-VCAM-1 as the acceptor. From the FRET signal analysis, Kd of this interaction was determined to be 41.82 ± 2.36 nM. To further confirm our estimation, we have employed surface plasmon resonance (SPR) technique to obtain Kd = 39.60 ± 1.78 nM, which is in good agreement with the result obtained by FRET. This is the first reported work which applies organic fluorophore based ‘in solution’ simple quantitative FRET assay to obtain the dissociation constant of the VCAM-1/VLA-4 interaction, and is also the first quantification of this interaction. Moreover, the value of Kd can serve as an indicator of abnormal protein-protein interactions; hence, this assay can potentially be further developed into a drug screening platform of VLA-4/VCAM-1 as well as other protein-ligand interactions.
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28
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Wiryawan H, Dan K, Etuale M, Shen Y, Liao J. Determination of SUMO1 and ATP affinity for the SUMO E1by quantitative FRET technology. Biotechnol Bioeng 2015; 112:652-8. [PMID: 25333792 DOI: 10.1002/bit.25480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 09/05/2014] [Accepted: 10/13/2014] [Indexed: 12/15/2022]
Abstract
SUMOylation plays important roles in many key physiological and pathological processes. The SUMOylation cascade involves a heterodimer of activating enzyme, E1 (Aos1/Uba2); a conjugating enzyme, E2 (Ubc9); and many ligase enzymes, E3. Focusing on the activation step of the SUMOylation process, we examined the interaction of E1 with its substrates. Previous studies reported the Km of E1 enzymes in ubiquitin and other ubiquitin-like pathways, but the Km of the SUMO paralogs (SUMO2 and SUMO3) is unknown. Here, by using quantitative FRET to measure the SUMO E1 enzyme kinetics of SUMO1, 2, and 3 and ATP under steady state conditions, we found that the enzyme kinetics from the quantitative FRET method are comparable to those from conventional radioactive assays. Additionally, the kinetic constants, Km , of SUMO2 (3.418 ± 0.9131 μM) and SUMO3 (2.764 ± 0.75 μM) [FW1] are approximately four to five times higher than that of SUMO1 Km (0.7458 ± 0.1105 μM). These results demonstrate the advantages of FRET technology for determining Km , including the ability to monitor reaction progress in real-time with high-throughput and high-sensitivity in an environmentally friendly manner. The processes discussed here extend the utility of quantitative FRET in characterizing protein-protein interactions and enzyme kinetics.
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Affiliation(s)
- Hilda Wiryawan
- Division of Biomedical Science, School of Medicine, University of California at Riverside, 900 University Avenue, Riverside, California, 92521
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29
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Chakraborty S, Núñez D, Hu SY, Domingo MP, Pardo J, Karmenyan A, Chiou A. FRET based quantification and screening technology platform for the interactions of leukocyte function-associated antigen-1 (LFA-1) with intercellular adhesion molecule-1 (ICAM-1). PLoS One 2014; 9:e102572. [PMID: 25032811 PMCID: PMC4102529 DOI: 10.1371/journal.pone.0102572] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/19/2014] [Indexed: 11/29/2022] Open
Abstract
The interaction between leukocyte function-associated antigen-1(LFA-1) and intercellular adhesion molecule-1 (ICAM-1) plays a pivotal role in cellular adhesion including the extravasation and inflammatory response of leukocytes, and also in the formation of immunological synapse. However, irregular expressions of LFA-1 or ICAM-1 or both may lead to autoimmune diseases, metastasis cancer, etc. Thus, the LFA-1/ICAM-1 interaction may serve as a potential therapeutic target for the treatment of these diseases. Here, we developed one simple 'in solution' steady state fluorescence resonance energy transfer (FRET) technique to obtain the dissociation constant (Kd) of the interaction between LFA-1 and ICAM-1. Moreover, we developed the assay into a screening platform to identify peptides and small molecules that inhibit the LFA-1/ICAM-1 interaction. For the FRET pair, we used Alexa Fluor 488-LFA-1 conjugate as donor and Alexa Fluor 555-human recombinant ICAM-1 (D1-D2-Fc) as acceptor. From our quantitative FRET analysis, the Kd between LFA-1 and D1-D2-Fc was determined to be 17.93±1.34 nM. Both the Kd determination and screening assay were performed in a 96-well plate platform, providing the opportunity to develop it into a high-throughput assay. This is the first reported work which applies FRET based technique to determine Kd as well as classifying inhibitors of the LFA-1/ICAM-1 interaction.
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Affiliation(s)
| | - David Núñez
- Instituto de Carboquímica, CSIC, Zaragoza, Spain
- Immune Effector Cells Group, Aragón Health Research Institute, Biomedical Research Centre of Aragón, Zaragoza, Spain
| | - Shih-Yang Hu
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
| | - María Pilar Domingo
- Instituto de Carboquímica, CSIC, Zaragoza, Spain
- Immune Effector Cells Group, Aragón Health Research Institute, Biomedical Research Centre of Aragón, Zaragoza, Spain
| | - Julian Pardo
- Immune Effector Cells Group, Aragón Health Research Institute, Biomedical Research Centre of Aragón, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Facultad de Ciencias, University of Zaragoza, Zaragoza, Spain
- Aragón I+D Foundation, Government of Aragon, Zaragoza, Spain
- Nanoscience Institute of Aragón, Aragón I+D Foundation, University of Zaragoza, Zaragoza, Spain
| | - Artashes Karmenyan
- Biophotonics & Molecular Imaging Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Eva Ma Gálvez
- Instituto de Carboquímica, CSIC, Zaragoza, Spain
- Immune Effector Cells Group, Aragón Health Research Institute, Biomedical Research Centre of Aragón, Zaragoza, Spain
| | - Arthur Chiou
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
- Biophotonics & Molecular Imaging Research Center, National Yang-Ming University, Taipei, Taiwan
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30
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Oldach L, Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. ACTA ACUST UNITED AC 2014; 21:186-97. [PMID: 24485761 DOI: 10.1016/j.chembiol.2013.12.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
Fluorescence-based, genetically encodable biosensors are widely used tools for real-time analysis of biological processes. Over the last few decades, the number of available genetically encodable biosensors and the types of processes they can monitor have increased rapidly. Here, we aim to introduce the reader to general principles and practices in biosensor development and highlight ways in which biosensors can be used to illuminate outstanding questions of biological function. Specifically, we focus on sensors developed for monitoring kinase activity and use them to illustrate some common considerations for biosensor design. We describe several uses to which kinase and second-messenger biosensors have been put, and conclude with considerations for the use of biosensors once they are developed. Overall, as fluorescence-based biosensors continue to diversify and improve, we expect them to continue to be widely used as reliable and fruitful tools for gaining deeper insights into cellular and organismal function.
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Affiliation(s)
- Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Department of Oncology, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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31
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Malik-Chaudhry HK, Saavedra A, Liao J. A linker strategy for trans-FRET assay to determine activation intermediate of NEDDylation cascade. Biotechnol Bioeng 2014; 111:1288-95. [PMID: 24415255 DOI: 10.1002/bit.25183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022]
Abstract
Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates.
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Affiliation(s)
- Harbani Kaur Malik-Chaudhry
- Department of Bioengineering, Center for Bioengineering Research, Bourns College of Engineering, 900 University Avenue, Riverside, California, 92521
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32
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Jiang L, Saavedra AN, Way G, Alanis J, Kung R, Li J, Xiang W, Liao J. Specific substrate recognition and thioester intermediate determinations in ubiquitin and SUMO conjugation cascades revealed by a high-sensitive FRET assay. MOLECULAR BIOSYSTEMS 2014; 10:778-86. [DOI: 10.1039/c3mb70155g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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33
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Internal calibration Förster resonance energy transfer assay: a real-time approach for determining protease kinetics. SENSORS 2013; 13:4553-70. [PMID: 23567524 PMCID: PMC3673099 DOI: 10.3390/s130404553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/11/2013] [Accepted: 03/25/2013] [Indexed: 11/28/2022]
Abstract
Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research. This powerful tool can elucidate protein interactions in either a dynamic or steady state. We recently developed a series of FRET-based technologies to determine protein interaction dissociation constant and for use in high-throughput screening assays of SUMOylation. SUMO (small ubiquitin-like modifier) is conjugated to substrates through an enzymatic cascade. This important posttranslational protein modification is critical for multiple biological processes. Sentrin/SUMO-specific proteases (SENPs) act as endopeptidases to process the pre-SUMO or as isopeptidases to deconjugate SUMO from its substrate. Here, we describe a novel quantitative FRET-based protease assay for determining the kinetics of SENP1. Our strategy is based on the quantitative analysis and differentiation of fluorescent emission signals at the FRET acceptor emission wavelengths. Those fluorescent emission signals consist of three components: the FRET signal and the fluorescent emissions of donor (CyPet) and acceptor (YPet). Unlike our previous method in which donor and acceptor direct emissions were excluded by standard curves, the three fluorescent emissions were determined quantitatively during the SENP digestion process from onesample. New mathematical algorithms were developed to determine digested substrate concentrations directly from the FRET signal and donor/acceptor direct emissions. The kinetic parameters, kcat, KM, and catalytic efficiency (kcat/KM) of SENP1 catalytic domain for pre-SUMO1/2/3 were derived. Importantly, the general principles of this new quantitative methodology of FRET-based protease kinetic determinations can be applied to other proteases in a robust and systems biology approach.
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