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Otsuka Y, Sasaki K, Suyotha W, Furusawa H, Miyazawa K, Konno H, Yano S. Construction of a fusion protein consisting of α-1,3-glucan-binding domains and tetrameric red fluorescent protein, which is involved in the aggregation of α-1,3-glucan and inhibition of fungal biofilm formation. J Biosci Bioeng 2022; 133:524-532. [PMID: 35314116 DOI: 10.1016/j.jbiosc.2022.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022]
Abstract
Agl-KA, an α-1,3-glucan-hydrolyzing enzyme from Bacillus circulans KA-304, has three α-1,3-glucan-binding domains DS1, CB6, and DS2 (DCD). While their individual binding activities toward insoluble α-1,3-glucan and fungal cell-wall are weak, the three domains in combination bind strongly to the α-1,3-glucan and the cell-wall. In this study, we constructed DCD-tetraRFP by fusing DCD with DsRed-Express2, a tetrameric red fluorescent protein. DCD-tetraRFP forms a tetramer in an aqueous solution and contains twelve substrate-binding domains in one complex. We also constructed DCD-monoGFP by fusing DCD with AcGFP1, a monomeric green fluorescent protein. The molecular weight of DCD-tetraRFP and DCD-monoGFP were compared. The results of gel filtration chromatography and dynamic light scattering indicated that DCD-tetraRFP was larger than DCD-monoGFP, suggesting that DCD-tetraRFP had a tetrameric structure. In addition, DCD-tetraRFP bound to insoluble α-1,3-glucan strongly, and the amount of DCD-tetraRFP binding to 0.01% α-1,3-glucan was about twice of DCD-monoGFP. The Kd values of DCD-tetraRFP (measurements per subunit) and DCD-monoGFP were 0.16 and 0.84 μM, respectively. Adding DCD-tetraRFP to a suspension of α-1,3-glucan caused glucan aggregation; however, adding DCD-monoGFP did not. These data suggested that DCD-tetraRFP had four DCDs sterically arranged in different directions so that DCD-tetraRFP cross-linked with the substrate, causing aggregation. Lastly, the aggregates of DCD-tetraRFP and α-1,3-glucan captured Aspergillus oryzae conidia and decreased their biofilm formation by 80% in a 24-well dish.
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Affiliation(s)
- Yuitsu Otsuka
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Kai Sasaki
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Wasana Suyotha
- Department of Industrial Biotechnology, Faculty of Agro-industry, Prince of Songkla University, Hat Yai 90112, Thailand
| | - Hiroyuki Furusawa
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Ken Miyazawa
- Laboratory of Filamentous Mycoses, Department of Fungal Infection, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hiroyuki Konno
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shigekazu Yano
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan.
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2
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Effect of amount of hydrated water and mobility of hydrated poly(
2‐methoxyethyl
acrylate) on denaturation of adsorbed fibrinogen. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Yazawa K, Furusawa H. Entropy-Driven Mechanisms between Disulfide-Bond Formation Protein A (DsbA) and B (DsbB) in Escherichia coli. ACS OMEGA 2019; 4:8341-8349. [PMID: 31459922 PMCID: PMC6648927 DOI: 10.1021/acsomega.9b00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/30/2019] [Indexed: 06/10/2023]
Abstract
A disulfide-bond formation system for nascent proteins in the Escherichia coli periplasm contains efficient electron transfer systems for the catalysis of oxidation. This electrochemical system has interesting implications in vivo. Disulfide bonds are formed by disulfide-bond formation protein A (DsbA), which contains two reactive cysteines. DsbA is reoxidized by a membrane protein, disulfide-bond formation protein B (DsbB), which has four catalytic cysteines. The oxidation of DsbA by DsbB seems energetically unfavorable on the basis of the redox potential. The oxidizing power of ubiquinone (UQ), which endogenously binds with DsbB, is believed to promote this reaction. However, using UQ-deficient DsbB, it was found that the oxidation of DsbA by DsbB proceeds independently of UQ. Thus, the reaction mechanism of DsbA oxidation by DsbB is under debate. In this study, we used the quartz crystal microbalance technique, which detects the intermediate complex between DsbA and DsbB during DsbA oxidation as a change in mass, to obtain kinetic parameters of DsbA oxidation under both the oxidized and reduced states of UQ at acidic and basic pH. In addition, we utilized sodium dodecyl sulfate polyacrylamide gel electrophoresis mobility shift assay technique to determine the pK a of the cysteine thiol groups in DsbA and DsbB. We found that DsbA oxidation proceeded independently of UQ and was greatly affected in kinetics by the shuffling of electrons among the four cysteine residues in DsbB, regardless of pH. These results suggest that DsbA oxidation is driven in an entropy-dependent manner, in which the electron-delocalized intermediate complex is stabilized by preventing a reverse reaction. These findings could contribute to the design of bio-inspired electrochemical systems for industrial applications.
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Affiliation(s)
- Kenjiro Yazawa
- Division
of Biological and Medical Fibers, Interdisciplinary Cluster for Cutting
Edge Research, Institute for Fiber Engineering, Shinshu University, 3-15-1 Tokida, Ueda City, Nagano 386-8567, Japan
- Department
of Biomolecular Engineering, Tokyo Institute
of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroyuki Furusawa
- Innovative
Flex Course for Frontier Organic Material Systems (iFront), Graduate
School of Science and Engineering, Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Department
of Biomolecular Engineering, Tokyo Institute
of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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4
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Genick CC, Wright SK. Biophysics: for HTS hit validation, chemical lead optimization, and beyond. Expert Opin Drug Discov 2017; 12:897-907. [DOI: 10.1080/17460441.2017.1349096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christine C. Genick
- Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Protein Sciences, Basel, Switzerland
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
| | - S. Kirk Wright
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
- Protein Sciences, Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA, USA
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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6
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - George Papadakis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
- Department
of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion, Greece
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Furusawa H, Sekine T, Ozeki T. Hydration and Viscoelastic Properties of High- and Low-Density Polymer Brushes Using a Quartz-Crystal Microbalance Based on Admittance Analysis (QCM-A). Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Furusawa
- Innovative Flex Course for Frontier Organic Material
Systems (iFront), Graduate School of Science and Engineering, Yamagata University,
4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tomomi Sekine
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tomomitsu Ozeki
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Furusawa H, Tsuyuki Y, Takahashi S, Okahata Y. In situ monitoring of structural changes during formation of 30S translation initiation complex by energy dissipation measurement using 27-MHz quartz-crystal microbalance. Anal Chem 2014; 86:5406-15. [PMID: 24794712 DOI: 10.1021/ac500487b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosome is a bionanomachine that facilitates an orderly translation process during protein synthesis in living cells. Real-time monitoring of conformational changes in ribosomal subunits in aqueous solution is important to understand the regulatory mechanism of protein synthesis, because conformational changes in ribosome in E. coli have been predicted to operate the switch from translation initiation to an elongation process during translation. We performed an energy dissipation measurement by using a quartz-crystal microbalance-admittance (QCM-A) technique for in situ monitoring of conformational changes in pre-30S translation initiation complex in response to the binding of fMet-tRNA(fMet) in aqueous solution. The addition of fMet-tRNA(fMet) caused changes in the physical property (increased dehydration and elasticity) in 30S ribosomal subunit in the presence of mRNA and IF2/guanosine 5'-triphosphate (GTP) on the QCM plate. Furthermore, two sequential changes triggered by the addition of fMet-tRNA(fMet) were observed in 30S ribosomal subunit bound to mRNA in the presence of IF2/GTP and IF3. These observations suggest that the structural changes in 30S ribosomal subunit caused by the binding of fMet-tRNA(fMet) with IF2/GTP in the presence of IF3 could act as a switch to regulate the orderly processing in the construction of translation initiation complex, because the structural distinction can be a guidepost in the process for the relevant biomolecules.
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Affiliation(s)
- Hiroyuki Furusawa
- Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University , 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
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Yazawa K, Furusawa H, Okahata Y. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system. J Biol Chem 2013; 288:35969-81. [PMID: 24145032 PMCID: PMC3861646 DOI: 10.1074/jbc.m113.519876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/18/2013] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone.
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Affiliation(s)
- Kenjiro Yazawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Furusawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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10
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Fluorescence modulation sensing of positively and negatively charged proteins on lipid bilayers. Biointerphases 2013; 8:1. [PMID: 24706114 DOI: 10.1186/1559-4106-8-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detecting ligand-receptor binding on cell membrane surfaces is required to understand their function and behavior. Detection platforms can also provide an avenue for the development of medical devices and sensor biotechnology. The use of fluorescence techniques for such purposes is highly desirable as they provide high sensitivity. Herein, we describe a technique that utilizes the sensitivity of fluorescence without directly tagging the analyte of interest to monitor ligand-receptor interactions on supported lipid bilayers. The fluorescence signal is modulated according to the charge state of the target analyte. The binding event elicits protonation or deprotonation of pH-responsive reporter dyes embedded in the lipid bilayer. METHODS Supported lipid membranes containing ortho-conjugated rhodamine B-POPE (1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine), which fluoresces in its protonated but not in its deprotonated form, were utilized as sensor platforms for biotin-avidin and biotin-streptavidin binding events. The membranes contained 5 mol% biotin-PE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl) (sodium salt) as a capture ligand. Supported lipid bilayers were formed in the channels of microfluidic devices and the fluorescence intensity of the dye was monitored as protein was introduced. RESULTS The binding of avidin, which is positively charged at pH 7.2, made the bilayer surface charge more positive, which in turn deprotonated the ortho-rhodamine B dye, reducing its fluorescence. The binding of streptavidin, which is negatively charged at pH 7.2, had the opposite effect. Reducing the ionic strength of the analyte solution by removing 150 mM NaCl from the 10 mM phosphate buffered saline (PBS) solution raised the apparent pKa of the ortho-rhodamine B titration point by about 1 pH unit. This could be exploited in conjunction with bulk solution pH changes to turn the rhodamine B-POPE dye into a sensor for streptavidin involving a decrease, rather than an increase, in the fluorescence response, at pH values below streptavidin's pI value. CONCLUSIONS This study demonstrates the ability to monitor ligand-receptor interactions on supported lipid bilayers through the protonation or deprotonation of reporter dyes for both negatively and positively charged analytes over a range of pH and ionic strength conditions. Specifically, the sensitivity and pH-operating range of this technique can be optimized by modulating the sensing conditions which are employed.
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11
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OGI H. Wireless-electrodeless quartz-crystal-microbalance biosensors for studying interactions among biomolecules: a review. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2013; 89:401-17. [PMID: 24213205 PMCID: PMC3865356 DOI: 10.2183/pjab.89.401] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/02/2013] [Indexed: 05/24/2023]
Abstract
The mass sensitivity of quartz-crystal microbalance (QCM) was drastically improved by removing electrodes and wires attached on the quartz surfaces. Instead of wire connections, intended vibrations of quartz oscillators were excited and detected by antennas through electromagnetic waves. This noncontacting measurement is the key for ultrahigh-sensitive detection of proteins in liquids as well as quantitative measurements. This review shows the principle of wireless QCMs, their applications to studying interactions among biomolecules and aggregation reactions of amyloid β peptides, and the next-generation MEMS QCM, the resonance acoustic microbalance with naked embedded quartz (RAMNE-Q).
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Affiliation(s)
- Hirotsugu OGI
- Graduate School of Engineering, Osaka University, Osaka, Japan
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12
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Wiseman ME, Frank CW. Antibody adsorption and orientation on hydrophobic surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1765-74. [PMID: 22181558 DOI: 10.1021/la203095p] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The orientation of a monoclonal, anti-streptavidin human IgG1 antibody on a model hydrophobic, CH(3)-terminated surface (1-dodecanethiol self-assembled monolayer on gold) was studied by monitoring the mechanical coupling between the adsorbed layer and the surface as well as the binding of molecular probes to the antibodies. In this study, the streptavidin antigen was used as a probe for the Fab portions of the antibody, while bacteria-derived Protein G' was used as a probe for the Fc region. Bovine serum albumin (BSA) acted as a blocking protein. Monolayer coverage occurred around 468 ng/cm(2). Below 100 ng/cm(2), antibodies were found to adsorb flat-on, tightly coupled to the surface and unable to capture their antigen, whereas the Fc region was able to bind Protein G'. At half-monolayer coverage, there was a transition in the mechanism of adsorption to allow for vertically oriented antibodies, as evidenced by the binding of both Protein G' and streptavidin as well as looser mechanical coupling with the surface. Monolayer coverage was characterized by a reduced level in probe binding per antibody and an even less rigid coupling to the surface.
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Affiliation(s)
- Meredith E Wiseman
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stauffer III, Stanford, California 94305-5025, United States
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Coan KED, Swann MJ, Ottl J. Measurement and Differentiation of Ligand-Induced Calmodulin Conformations by Dual Polarization Interferometry. Anal Chem 2012; 84:1586-91. [DOI: 10.1021/ac202844e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristin E. D. Coan
- Novartis Institutes for BioMedical
Research Basel, CPC/LFP/Label-free Technologies, Novartis Pharma AG, Basel, Switzerland
| | - Marcus J. Swann
- Farfield Group Ltd., West Wing 7, Voyager, Chicago Avenue, Manchester
Airport, Manchester, M90 3DQ, United Kingdom
| | - Johannes Ottl
- Novartis Institutes for BioMedical
Research Basel, CPC/LFP/Label-free Technologies, Novartis Pharma AG, Basel, Switzerland
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Nirschl M, Ottl J, Vörös J. Conformational Changes of Calmodulin on Calcium and Peptide Binding Monitored by Film Bulk Acoustic Resonators. BIOSENSORS 2011; 1:164-76. [PMID: 25585566 PMCID: PMC4264349 DOI: 10.3390/bios1040164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/04/2011] [Accepted: 12/12/2011] [Indexed: 11/21/2022]
Abstract
Film bulk acoustic resonators (FBAR) are mass sensitive, label-free biosensors that allow monitoring of the interaction between biomolecules. In this paper we use the FBAR to measure the binding of calcium and the CaMKII peptide to calmodulin. Because the mass of the calcium is too small to be detected, the conformational change caused by the binding process is measured by monitoring the resonant frequency and the motional resistance of the FBAR. The resonant frequency is a measure for the amount of mass coupled to the sensor while the motional resistance is influenced by the viscoelastic properties of the adsorbent. The measured frequency shift during the calcium adsorptions was found to be strongly dependent on the surface concentration of the immobilized calmodulin, which indicates that the measured signal is significantly influenced by the amount of water inside the calmodulin layer. By plotting the measured motional resistance against the frequency shift, a mass adsorption can be distinguished from processes involving measurable conformational changes. With this method three serial processes were identified during the peptide binding. The results show that the FBAR is a promising technology for the label-free measurement of conformational changes.
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Affiliation(s)
- Martin Nirschl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Johannes Ottl
- Novartis Institute of Biomedical Research Basel, CPC/LFP, Novartis Pharma AG, Postfach, Basel CH 4002, Switzerland.
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich Gloriastrasse 35, 8092 Zurich, Switzerland.
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Yoshimine H, Kojima T, Furusawa H, Okahata Y. Small Mass-Change Detectable Quartz Crystal Microbalance and Its Application to Enzymatic One-Base Elongation on DNA. Anal Chem 2011; 83:8741-7. [DOI: 10.1021/ac202224d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroshi Yoshimine
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Taisuke Kojima
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Furusawa
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
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Ogi H, Yanagida T, Hirao M, Nishiyama M. Replacement-free mass-amplified sandwich assay with 180-MHz electrodeless quartz-crystal microbalance biosensor. Biosens Bioelectron 2011; 26:4819-22. [DOI: 10.1016/j.bios.2011.05.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/28/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
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Nirschl M, Reuter F, Vörös J. Review of transducer principles for label-free biomolecular interaction analysis. BIOSENSORS 2011; 1:70-92. [PMID: 25586921 PMCID: PMC4264362 DOI: 10.3390/bios1030070] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/18/2011] [Accepted: 06/29/2011] [Indexed: 01/12/2023]
Abstract
Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR) instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM) and the film bulk acoustic resonator (FBAR), calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.
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Affiliation(s)
- Martin Nirschl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Switzerland.
| | - Florian Reuter
- Siemens Technology Accelerator GmbH, Otto-Hahn-Ring 6, 81739 Munich, Germany.
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Switzerland.
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18
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Becker B, Cooper MA. A survey of the 2006-2009 quartz crystal microbalance biosensor literature. J Mol Recognit 2011; 24:754-87. [DOI: 10.1002/jmr.1117] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Shur O, Wu J, Cropek DM, Banta S. Monitoring the conformational changes of an intrinsically disordered peptide using a quartz crystal microbalance. Protein Sci 2011; 20:925-30. [PMID: 21416544 DOI: 10.1002/pro.625] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 11/05/2022]
Abstract
Intrinsically disordered peptides (IDPs) have recently garnered much interest because of their role in biological processes such as molecular recognition and their ability to undergo stimulus-responsive conformational changes. The block V repeat-in-toxin motif of the Bordetella pertussis adenylate cyclase is an example of an IDP that undergoes a transition from a disordered state to an ordered beta roll conformation in the presence of calcium ions. In solution, a C-terminal capping domain is necessary for this transition to occur. To further explore the conformational behavior and folding requirements of this IDP, we have cysteine modified three previously characterized constructs, allowing for attachment to the gold surface of a quartz crystal microbalance (QCM). We demonstrate that, while immobilized, the C-terminally capped peptide exhibits similar calcium-binding properties to what have been observed in solution. In addition, immobilization on the solid surface appears to enable calcium-responsiveness in the uncapped peptides, in contrast to the behavior observed in solution. This work demonstrates the power of QCM as a tool to study the conformational changes of IDPs immobilized on surfaces and has implications for a range of potential applications where IDPs may be engineered and used including protein purification, biosensors, and other bionanotechnology applications.
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Affiliation(s)
- Oren Shur
- Department of Chemical Engineering, Columbia University, New York, New York, USA
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20
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Hall WP, Modica J, Anker J, Lin Y, Mrksich M, Van Duyne RP. A conformation- and ion-sensitive plasmonic biosensor. NANO LETTERS 2011; 11:1098-105. [PMID: 21280643 PMCID: PMC3122133 DOI: 10.1021/nl103994w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The versatile optical and biological properties of a localized surface plasmon resonance (LSPR) sensor that responds to protein conformational changes are illustrated. The sensor detects conformational changes in a surface-bound construct of the calcium-sensitive protein calmodulin. Increases in calcium concentration induce a 0.96 nm red shift in the spectral position of the LSPR extinction maximum (λ(max)). Addition of a calcium chelating agent forces the protein to return to its original conformation and is detected as a reversal of the λ(max) shift. As opposed to previous work, this work demonstrates that these conformational changes produce a detectable shift in λ(max) even in the absence of a protein label, with a signal:noise ratio near 500. In addition, the protein conformational changes reversibly switch both the wavelength and intensity of the resonance peak, representing an example of a bimodal plasmonic component that simultaneously relays two distinct forms of optical information. This highly versatile plasmonic device acts as a biological sensor, enabling the detection of calcium ions with a biologically relevant limit of detection of 23 μM, as well as the detection of calmodulin-specific protein ligands.
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Affiliation(s)
- W Paige Hall
- Department of Chemistry, Northwestern University, 2145 North Sheridan Road, Evanston, Illinois 60208, United States
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21
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Su Z, Chen L, Liu Y, He X, Zhou Y, Xie Q, Yao S. 35MHz quartz crystal microbalance and surface plasmon resonance studies on the binding of angiotensin converting enzyme with lisinopril. Biosens Bioelectron 2011; 26:3240-5. [DOI: 10.1016/j.bios.2010.12.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/12/2010] [Accepted: 12/21/2010] [Indexed: 11/25/2022]
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22
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Ultrathin-film oscillator biosensors excited by ultrafast light pulses. Biosens Bioelectron 2010; 26:1273-7. [PMID: 20656469 DOI: 10.1016/j.bios.2010.06.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 06/27/2010] [Accepted: 06/30/2010] [Indexed: 11/24/2022]
Abstract
Novel thin-film oscillator biosensors are developed using picosecond ultrasound method. 100-nm silicon-nitride thin films and 16-nm Pt thin films are used, and ultrashort light pulses are focused on their surfaces to excite the through-thickness resonance vibrations, which are detected by the delayed probe-light pulses using the optoelastic effect. Their fundamental resonance frequencies are 45 and 132 GHz, corresponding to theoretical mass sensitivities of 5.0×10(-5) and 2.2×10(-5) pg/cm(2)/Hz, respectively. These thin-film biosensors are used for detecting human immunoglobulin G (hIgG) with Staphylococcus aureus protein A nonspecifically immobilized on the film surfaces. Injection of a 5 nM analyte caused 2% decrease in the resonance frequency.
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23
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Lee HS, Contarino M, Umashankara M, Schön A, Freire E, Smith AB, Chaiken IM, Penn LS. Use of the quartz crystal microbalance to monitor ligand-induced conformational rearrangements in HIV-1 envelope protein gp120. Anal Bioanal Chem 2009; 396:1143-52. [PMID: 20016882 DOI: 10.1007/s00216-009-3313-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 11/10/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022]
Abstract
We evaluated the potential of a quartz crystal microbalance with dissipation monitoring (QCM-D) to provide a sensitive, label-free method for detecting the conformational rearrangement of glycoprotein gp120 upon binding to different ligands. This glycoprotein is normally found on the envelope of the HIV-1 virus and is involved in viral entry into host cells. It was immobilized on the surface of the sensing element of the QCM-D and was exposed to individual solutions of several different small-molecule inhibitors as well as to a solution of a soluble form of the host cell receptor to which gp120 binds. Instrument responses to ligand-triggered changes were in qualitative agreement with conformational changes as suggested by other biophysical methods.
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Affiliation(s)
- Hyun-Su Lee
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
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24
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Ogi H, Naga H, Fukunishi Y, Hirao M, Nishiyama M. 170-MHz Electrodeless Quartz Crystal Microbalance Biosensor: Capability and Limitation of Higher Frequency Measurement. Anal Chem 2009; 81:8068-73. [DOI: 10.1021/ac901267b] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hirotsugu Ogi
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan, and Central Workshop, Osaka University, Machikaneyama 1-2, Toyonaka, Osaka 560-0043, Japan
| | - Hironao Naga
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan, and Central Workshop, Osaka University, Machikaneyama 1-2, Toyonaka, Osaka 560-0043, Japan
| | - Yuji Fukunishi
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan, and Central Workshop, Osaka University, Machikaneyama 1-2, Toyonaka, Osaka 560-0043, Japan
| | - Masahiko Hirao
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan, and Central Workshop, Osaka University, Machikaneyama 1-2, Toyonaka, Osaka 560-0043, Japan
| | - Masayoshi Nishiyama
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan, and Central Workshop, Osaka University, Machikaneyama 1-2, Toyonaka, Osaka 560-0043, Japan
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25
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Ogi H, Okamoto K, Nagai H, Fukunishi Y, Hirao M. Replacement-Free Electrodeless Quartz Crystal Microbalance Biosensor Using Nonspecific-Adsorption of Streptavidin on Quartz. Anal Chem 2009; 81:4015-20. [DOI: 10.1021/ac9004524] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hirotsugu Ogi
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan and PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Ken Okamoto
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan and PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Hironao Nagai
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan and PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Yuji Fukunishi
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan and PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
| | - Masahiko Hirao
- Graduate School of Engineering Science, Osaka University, Machikaneyama 1-3, Toyonaka, Osaka 560-8531, Japan and PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, Japan
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