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Matthews CJ, Patrick WM. An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range. Protein Sci 2023; 32:e4743. [PMID: 37515423 PMCID: PMC10451018 DOI: 10.1002/pro.4743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
l-Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme-based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off-the-shelf malate-oxidizing enzymes have been used in previous devices. These typically have linear ranges poorly suited for the l-malate concentrations found in fruit processing and winemaking, making it necessary to use precisely diluted samples. Here, we describe a pipeline of database-mining, gene synthesis, recombinant expression, and spectrophotometric assays to characterize previously untested enzymes for their suitability in biosensors. The pipeline yielded a bespoke biocatalyst-the Ascaris suum malic enzyme carrying mutation R181Q [AsME(R181Q)]. Our first prototype with AsME(R181Q) had an ultra-wide linear range of 50-200 mM l-malate, corresponding to concentrations found in undiluted fruit juices (including grape). Changing the dication from Mg2+ to Mn2+ increased sensitivity five-fold and adding citrate (100 mM) increased it another six-fold, albeit decreasing the linear range to 1-10 mM. To our knowledge, this is the first time an l-malate biosensor with a tuneable combination of sensitivity and linear range has been described. The sensor response was also tested in the presence of various molecules abundant in juices and wines, with ascorbate shown to be a potent interferent. Interference was mitigated by the addition of ascorbate oxidase, allowing for differential measurements on an undiluted, untreated wine sample that corresponded well with commercial l-malate testing kits. Overall, this work demonstrates the power of an enzyme-centric approach for designing electrochemical biosensors with improved operational parameters and novel functionality.
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Affiliation(s)
- Christopher J. Matthews
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Wayne M. Patrick
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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2
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Mardikoraem M, Woldring D. Machine Learning-driven Protein Library Design: A Path Toward Smarter Libraries. Methods Mol Biol 2022; 2491:87-104. [PMID: 35482186 DOI: 10.1007/978-1-0716-2285-8_5] [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: 06/14/2023]
Abstract
Proteins are small yet valuable biomolecules that play a versatile role in therapeutics and diagnostics. The intricate sequence-structure-function paradigm in the realm of proteins opens the possibility for directly mapping amino acid sequence to function. However, the rugged nature of the protein fitness landscape and an astronomical number of possible mutations even for small proteins make navigating this system a daunting task. Moreover, the scarcity of functional proteins and the ease with which deleterious mutations are introduced, due to complex epistatic relationships, compound the existing challenges. This highlights the need for auxiliary tools in current techniques such as rational design and directed evolution. To that end, the state-of-the-art machine learning can offer time and cost efficiency in finding high fitness proteins, circumventing unnecessary wet-lab experiments. In the context of improving library design, machine learning provides valuable insights via its unique features such as high adaptation to complex systems, multi-tasking, and parallelism, and the ability to capture hidden trends in input data. Finally, both the advancements in computational resources and the rapidly increasing number of sequences in protein databases will allow more promising and detailed insights delivered from machine learning to protein library design. In this chapter, fundamental concepts and a method for machine learning-driven library design leveraging deep sequencing datasets will be discussed. We elaborate on (1) basic knowledge about machine learning algorithms, (2) the benefit of machine learning in library design, and (3) methodology for implementing machine learning in library design.
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Affiliation(s)
- Mehrsa Mardikoraem
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.
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3
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The 40-Year Mystery of Insect Odorant-Binding Proteins. Biomolecules 2021; 11:biom11040509. [PMID: 33808208 PMCID: PMC8067015 DOI: 10.3390/biom11040509] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022] Open
Abstract
The survival of insects depends on their ability to detect molecules present in their environment. Odorant-binding proteins (OBPs) form a family of proteins involved in chemoreception. While OBPs were initially found in olfactory appendages, recently these proteins were discovered in other chemosensory and non-chemosensory organs. OBPs can bind, solubilize and transport hydrophobic stimuli to chemoreceptors across the aqueous sensilla lymph. In addition to this broadly accepted "transporter role", OBPs can also buffer sudden changes in odorant levels and are involved in hygro-reception. The physiological roles of OBPs expressed in other body tissues, such as mouthparts, pheromone glands, reproductive organs, digestive tract and venom glands, remain to be investigated. This review provides an updated panorama on the varied structural aspects, binding properties, tissue expression and functional roles of insect OBPs.
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4
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Enzyme-based amperometric biosensors for malic acid - A review. Anal Chim Acta 2021; 1156:338218. [PMID: 33781460 DOI: 10.1016/j.aca.2021.338218] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Malic acid is a key flavour component of many fruits and vegetables. There is significant interest in technologies for monitoring its concentration, particularly in winemaking. In this review we systematically and comprehensively chart progress in the development of enzyme-based amperometric biosensors for malic acid. We summarise the components and analytical parameters of malic acid sensors that have been reported over the past four decades, discussing their merits and pitfalls in terms of accuracy, sensitivity, linear range, response time and stability. We discuss how advances in electrode materials, electron mediators and the use of coupled enzymes have improved sensitivity and minimised interference, but also uncover a trade-off between sensitivity and linear range. A particular focus of our review is the three types of malate oxidoreductase enzyme that have been used in malic acid biosensors. We describe their different properties and conclude that identifying and/or engineering superior alternatives will be a key future direction for improving the commercial utility of malic acid biosensors.
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5
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Dixon TA, Williams TC, Pretorius IS. Sensing the future of bio-informational engineering. Nat Commun 2021; 12:388. [PMID: 33452260 PMCID: PMC7810845 DOI: 10.1038/s41467-020-20764-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
The practices of synthetic biology are being integrated into 'multiscale' designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of 'bio-informational' engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.
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Affiliation(s)
- Thomas A Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
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6
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Ko W, Kumar R, Kim S, Lee HS. Construction of Bacterial Cells with an Active Transport System for Unnatural Amino Acids. ACS Synth Biol 2019; 8:1195-1203. [PMID: 30971082 DOI: 10.1021/acssynbio.9b00076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Engineered organisms with an expanded genetic code have attracted much attention in chemical and synthetic biology research. In this work, engineered bacterial organisms with enhanced unnatural amino acid (UAA) uptake abilities were developed by screening periplasmic binding protein (PBP) mutants for recognition of UAAs. A FRET-based assay was used to identify a mutant PBP (LBP-AEL) with excellent binding affinity ( Kd ≈ 500 nM) to multiple UAAs from 37 mutants. Bacterial cells expressing LBP-AEL showed up to 5-fold enhanced uptake of UAAs, which was determined by genetic incorporation of UAAs into a green fluorescent protein and measuring UAA concentration in cell lysates. To the best of our knowledge, this work is the first report of engineering cellular uptake of UAAs and could provide an impetus for designing advanced unnatural organisms with an expanded genetic code, which function with the efficiency comparable to that of natural organisms. The system would be useful to increase mutant protein yield from lower concentrations of UAAs for industrial and large-scale applications. In addition, the techniques used in this report such as the sensor design and the measurement of UAA concentration in cell lysates could be useful for other biochemical applications.
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Affiliation(s)
- Wooseok Ko
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Rahul Kumar
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
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7
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Ko W, Kim S, Lee HS. Engineering a periplasmic binding protein for amino acid sensors with improved binding properties. Org Biomol Chem 2018; 15:8761-8769. [PMID: 28994436 DOI: 10.1039/c7ob02165h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Periplasmic binding proteins (PBPs) are members of a widely distributed protein superfamily found in bacteria and archaea, and are involved in the cellular uptake of solutes. In this report, a leucine-binding PBP was engineered to detect l-Leu based on a fluorescence resonance energy transfer (FRET) change upon ligand binding. A fluorescent unnatural amino acid, l-(7-hydroxycoumarin-4-yl)ethylglycine (CouA), was genetically incorporated into the protein as a FRET donor, and a yellow fluorescent protein (YFP) was fused with its N-terminus as a FRET acceptor. When CouA was incorporated into position 178, the sensor protein showed a 2.5-fold increase in the FRET ratio. Protein engineering significantly improved its substrate specificity, showing minimal changes in the FRET ratio with the other 19 natural amino acids and d-Leu. Further modification increased the sensitivity of the sensor protein (14-fold) towards l-Leu, and it recognized l-Met as well with moderate binding affinity. Selected mutant sensors were used to measure concentrations of l-Leu in a biological sample (fetal bovine serum) and to determine the optical purity of Leu and Met. This FRET-based sensor design strategy allowed us to easily manipulate the natural receptor to improve its binding affinity and specificity and to recognize other natural molecules, which are not recognized by the wild-type receptor. The design strategy can be applied to other natural receptors, enabling engineering receptors that sense biochemically interesting molecules.
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Affiliation(s)
- Wooseok Ko
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea.
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8
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Abstract
Catalysts have long played an essential role in organic synthesis and thus hold potential as tools for chemical protein modification. However, there are only a few examples of catalyst-mediated protein labeling under biological conditions because of the difficulty of designing molecular catalysts that work in aqueous environments with high target selectivity and reaction efficiency. To overcome this situation, we have previously developed a new catalyst-based method, termed affinity-guided DMAP (4-dimethylaminopyridine) (AGD) chemistry, for site-specific protein labeling in a target-selective manner using an acyl transfer reaction. More recently, we discovered that the labeling rate and efficiency can be greatly enhanced by using "multivalent" DMAP groups. Here, we describe the principle of the multivalent AGD chemistry and the protocol for chemical labeling of FK506-binding protein 12 (FKBP12) in test tubes. In this method, the FKBP12 labeling is completed within 30 min and occurs site specifically at the vicinity of the ligand-binding pocket of the protein.
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Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Room 330, Bldg, A4, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
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9
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Siontorou CG, Batzias FA. A methodological combined framework for roadmapping biosensor research: a fault tree analysis approach within a strategic technology evaluation frame. Crit Rev Biotechnol 2013; 34:31-55. [PMID: 23919240 DOI: 10.3109/07388551.2013.790339] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Biosensor technology began in the 1960s to revolutionize instrumentation and measurement. Despite the glucose sensor market success that revolutionized medical diagnostics, and artificial pancreas promise currently the approval stage, the industry is reluctant to capitalize on other relevant university-produced knowledge and innovation. On the other hand, the scientific literature is extensive and persisting, while the number of university-hosted biosensor groups is growing. Considering the limited marketability of biosensors compared to the available research output, the biosensor field has been used by the present authors as a suitable paradigm for developing a methodological combined framework for "roadmapping" university research output in this discipline. This framework adopts the basic principles of the Analytic Hierarchy Process (AHP), replacing the lower level of technology alternatives with internal barriers (drawbacks, limitations, disadvantages), modeled through fault tree analysis (FTA) relying on fuzzy reasoning to count for uncertainty. The proposed methodology is validated retrospectively using ion selective field effect transistor (ISFET) - based biosensors as a case example, and then implemented prospectively membrane biosensors, putting an emphasis on the manufacturability issues. The analysis performed the trajectory of membrane platforms differently than the available market roadmaps that, considering the vast industrial experience in tailoring and handling crystallic forms, suggest the technology path of biomimetic and synthetic materials. The results presented herein indicate that future trajectories lie along with nanotechnology, and especially nanofabrication and nano-bioinformatics, and focused, more on the science-path, that is, on controlling the natural process of self-assembly and the thermodynamics of bioelement-lipid interaction. This retained the nature-derived sensitivity of the biosensor platform, pointing out the differences between the scope of academic research and the market viewpoint.
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Affiliation(s)
- Christina G Siontorou
- Department of Industrial Management and Technology, University of Piraeus , Karaoli and Dimitriou, Piraeus , Greece
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10
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Tamura T, Kioi Y, Miki T, Tsukiji S, Hamachi I. Fluorophore Labeling of Native FKBP12 by Ligand-Directed Tosyl Chemistry Allows Detection of Its Molecular Interactions in Vitro and in Living Cells. J Am Chem Soc 2013; 135:6782-5. [DOI: 10.1021/ja401956b] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Yoshiyuki Kioi
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Takayuki Miki
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Shinya Tsukiji
- Top Runner Incubation Center for
Academia-Industry Fusion, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Itaru Hamachi
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
- Core Research for
Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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11
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Wu K, Zhou Y, Li T, Sun J, Xing X, Song Q. Cadmium Tellurium Quantum Dots in Sol-Gel-Derived Silica Spheres Coated with Calix[6]Arene as an Optical Probe for Dalapon. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.703740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Ausili A, Pennacchio A, Staiano M, Dattelbaum JD, Fessas D, Schiraldi A, D'Auria S. Amino acid transport in thermophiles: characterization of an arginine-binding protein from Thermotoga maritima. 3. Conformational dynamics and stability. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 118:66-73. [PMID: 23232322 DOI: 10.1016/j.jphotobiol.2012.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
Arginine-binding protein from Thermotoga maritima (TmArgBP) is a 27.7 kDa protein possessing the typical two domain structure of the periplasmic binding protein family. The protein is characterized by high specificity and affinity for binding a single molecule of l-arginine. In this work, the effect of temperature and/or guanidine hydrochloride on structure and stability of the protein in the absence and in the presence of l-arginine has been investigated by differential scanning calorimetry, far-UV circular dichroism and intrinsic tryptophan phosphorescence and fluorescence. The results revealed that TmArgBP undergoes an irreversible one-step thermal unfolding process in a cooperative mode. The TmArgBP melting temperature was recorded at 115 °C. The presence of l-arginine did not change the protein secondary structure content as well as the intrinsic phosphorescence and fluorescence protein properties, even if it increases the structural stability of the protein. The obtained results are discussed in combination with a detailed inspection of the three-dimensional structure of the protein.
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Affiliation(s)
- A Ausili
- Laboratory for Molecular Sensing, IBP-CNR, Naples 80131, Italy.
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13
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Kawamoto K, Uchiyama S. New Fluorogenic Benzothiadiazole and Benzoselenadiazole Reagents to Yield Environment-sensitive Fluorophores via a Reaction with Amines. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kyoko Kawamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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14
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Uchiyama S, Kimura K, Gota C, Okabe K, Kawamoto K, Inada N, Yoshihara T, Tobita S. Environment-Sensitive Fluorophores with Benzothiadiazole and Benzoselenadiazole Structures as Candidate Components of a Fluorescent Polymeric Thermometer. Chemistry 2012; 18:9552-63. [DOI: 10.1002/chem.201200597] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 12/17/2022]
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15
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Cerminara M, Desai TM, Sadqi M, Muñoz V. Downhill Protein Folding Modules as Scaffolds for Broad-Range Ultrafast Biosensors. J Am Chem Soc 2012; 134:8010-3. [DOI: 10.1021/ja301092z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele Cerminara
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Tanay M. Desai
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Mourad Sadqi
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Victor Muñoz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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16
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Li T, Zhou Y, Sun J, Tang D, Guo S, Ding X. Ultrasensitive detection of mercury(II) ion using CdTe quantum dots in sol-gel-derived silica spheres coated with calix[6]arene as fluorescent probes. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0655-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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18
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Takaoka Y, Sun Y, Tsukiji S, Hamachi I. Mechanisms of chemical protein19F-labeling and NMR-based biosensor construction in vitro and in cells using self-assembling ligand-directed tosylate compounds. Chem Sci 2011. [DOI: 10.1039/c0sc00513d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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A peptide-based fluorescent ratiometric sensor for quantitative detection of proteins. Anal Biochem 2010; 401:188-95. [PMID: 20188691 DOI: 10.1016/j.ab.2010.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 11/21/2022]
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20
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Environmentally sensitive fluorescent sensors based on synthetic peptides. SENSORS 2010; 10:3126-44. [PMID: 22319290 PMCID: PMC3274215 DOI: 10.3390/s100403126] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/27/2010] [Accepted: 03/24/2010] [Indexed: 01/02/2023]
Abstract
Biosensors allow the direct detection of molecular analytes, by associating a biological receptor with a transducer able to convert the analyte-receptor recognition event into a measurable signal. We review recent work aimed at developing synthetic fluorescent molecular sensors for a variety of analytes, based on peptidic receptors labeled with environmentally sensitive fluorophores. Fluorescent indicators based on synthetic peptides are highly interesting alternatives to protein-based sensors, since they can be synthesized chemically, are stable, and can be easily modified in a site-specific manner for fluorophore coupling and for immobilization on solid supports.
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21
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Design strategies of fluorescent biosensors based on biological macromolecular receptors. SENSORS 2010; 10:1355-76. [PMID: 22205872 PMCID: PMC3244018 DOI: 10.3390/s100201355] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 11/17/2022]
Abstract
Fluorescent biosensors to detect the bona fide events of biologically important molecules in living cells are increasingly demanded in the field of molecular cell biology. Recent advances in the development of fluorescent biosensors have made an outstanding contribution to elucidating not only the roles of individual biomolecules, but also the dynamic intracellular relationships between these molecules. However, rational design strategies of fluorescent biosensors are not as mature as they look. An insatiable request for the establishment of a more universal and versatile strategy continues to provide an attractive alternative, so-called modular strategy, which permits facile preparation of biosensors with tailored characteristics by a simple combination of a receptor and a signal transducer. This review describes an overview of the progress in design strategies of fluorescent biosensors, such as auto-fluorescent protein-based biosensors, protein-based biosensors covalently modified with synthetic fluorophores, and signaling aptamers, and highlights the insight into how a given receptor is converted to a fluorescent biosensor. Furthermore, we will demonstrate a significance of the modular strategy for the sensor design.
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22
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Han C, Li H. Host-molecule-coated quantum dots as fluorescent sensors. Anal Bioanal Chem 2009; 397:1437-44. [DOI: 10.1007/s00216-009-3361-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 11/26/2009] [Accepted: 11/29/2009] [Indexed: 12/20/2022]
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23
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Khoury GA, Fazelinia H, Chin JW, Pantazes RJ, Cirino PC, Maranas CD. Computational design of Candida boidinii xylose reductase for altered cofactor specificity. Protein Sci 2009; 18:2125-38. [PMID: 19693930 DOI: 10.1002/pro.227] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from NADPH to NADH. By compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or BLOSUM62 scores of the residues populating the cofactor binding site. Instead, we find that the use of a detailed cofactor binding energy approximation is needed to adequately capture the relative affinity towards different cofactors. The implicit solvation models Generalized Born with molecular volume integration and Generalized Born with simple switching were integrated in the iterative protein redesign and optimization (IPRO) framework to drive the redesign of Candida boidinii xylose reductase (CbXR) to function using the non-native cofactor NADH. We identified 10 variants, out of the 8,000 possible combinations of mutations, that improve the computationally assessed binding affinity for NADH by introducing mutations in the CbXR binding pocket. Experimental testing revealed that seven out of ten possessed significant xylose reductase activity utilizing NADH, with the best experimental design (CbXR-GGD) being 27-fold more active on NADH. The NADPH-dependent activity for eight out of ten predicted designs was either completely abolished or significantly diminished by at least 90%, yielding a greater than 10(4)-fold change in specificity to NADH (CbXR-REG). The remaining two variants (CbXR-RTT and CBXR-EQR) had dual cofactor specificity for both nicotinamide cofactors.
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Affiliation(s)
- George A Khoury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, 16802, USA
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Yun YH, Eteshola E, Bhattacharya A, Dong Z, Shim JS, Conforti L, Kim D, Schulz MJ, Ahn CH, Watts N. Tiny medicine: nanomaterial-based biosensors. SENSORS (BASEL, SWITZERLAND) 2009; 9:9275-99. [PMID: 22291565 PMCID: PMC3260642 DOI: 10.3390/s91109275] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 11/03/2009] [Accepted: 11/09/2009] [Indexed: 12/15/2022]
Abstract
Tiny medicine refers to the development of small easy to use devices that can help in the early diagnosis and treatment of disease. Early diagnosis is the key to successfully treating many diseases. Nanomaterial-based biosensors utilize the unique properties of biological and physical nanomaterials to recognize a target molecule and effect transduction of an electronic signal. In general, the advantages of nanomaterial-based biosensors are fast response, small size, high sensitivity, and portability compared to existing large electrodes and sensors. Systems integration is the core technology that enables tiny medicine. Integration of nanomaterials, microfluidics, automatic samplers, and transduction devices on a single chip provides many advantages for point of care devices such as biosensors. Biosensors are also being used as new analytical tools to study medicine. Thus this paper reviews how nanomaterials can be used to build biosensors and how these biosensors can help now and in the future to detect disease and monitor therapies.
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Affiliation(s)
- Yeo-Heung Yun
- Nanoworld and Smart Materials and Devices Laboratory, College of Engineering, University of Cincinnati, OH, 45221, USA; E-Mail:
| | - Edward Eteshola
- Davis Heart & Lung Research Inst, Biomedical Engineering Dept. The Ohio State University, OH, 43210, USA; E-Mail:
| | - Amit Bhattacharya
- Environmental Health, College of Medicine, University of Cincinnati, OH, 45267, USA; E-Mail:
| | - Zhongyun Dong
- Internal Medicine, College of Medicine, University of Cincinnati, OH, 45221, USA; E-Mail: (Z.D.); (L.C.)
| | - Joon-Sub Shim
- BioMEMS Lab, College of Engineering, University of Cincinnati, OH, 45221, USA; E-Mail:
| | - Laura Conforti
- Internal Medicine, College of Medicine, University of Cincinnati, OH, 45221, USA; E-Mail: (Z.D.); (L.C.)
| | - Dogyoon Kim
- College of Dentistry, The Ohio State University, OH, 43210, USA; E-Mail:
| | - Mark J. Schulz
- Nanoworld and Smart Materials and Devices Laboratory, College of Engineering, University of Cincinnati, OH, 45221, USA; E-Mail:
| | - Chong H. Ahn
- BioMEMS Lab, College of Engineering, University of Cincinnati, OH, 45221, USA; E-Mail:
| | - Nelson Watts
- University of Cincinnati, Bone Health and Osteoporosis Center, College of Medicine, OH, 45221, USA; E-Mail:
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Tsukiji S, Wang H, Miyagawa M, Tamura T, Takaoka Y, Hamachi I. Quenched ligand-directed tosylate reagents for one-step construction of turn-on fluorescent biosensors. J Am Chem Soc 2009; 131:9046-54. [PMID: 19499918 DOI: 10.1021/ja902486c] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Semisynthetic fluorescent biosensors consisting of a protein framework and a synthetic fluorophore are powerful analytical tools for specific detection of biologically relevant molecules. We report herein a novel method that allows for the construction of turn-on fluorescent semisynthetic biosensors in a one-step manner. The strategy is based on the ligand-directed tosyl (LDT) chemistry, a new type of affinity-guided protein labeling scheme which can site-specifically introduce synthetic probes to the surface of proteins with concomitant release of the affinity ligands. Novel quenched ligand-directed tosylate (Q-LDT) reagents were designed by connecting an organic dye to a conjugate of a protein ligand and a fluorescence quencher through a tosyl linker. The Q-LDT-mediated labeling directly converts a natural protein to a fluorescently labeled protein that remains noncovalently complexed with the cleaved ligand-tethered quencher. The fluorescence of this labeled protein is initially quenched and only in the presence of specific analytes is the fluorescence enhanced (turned on) due to the expulsion of the ligand-quencher fragment. Using a single labeling step, this approach was successfully applied to carbonic anhydrase II (CAII) and a Src homology 2 (SH2) domain to generate turn-on fluorescent biosensors toward CAII inhibitors and phosphotyrosine peptides, respectively. Detailed investigations revealed that the obtained biosensors exhibit their natural ligand selectivity. The high target-specificity of the LDT chemistry also allowed us to prepare the SH2 domain-based biosensor not only in a purified form but also in a bacterial cell lysate. These results demonstrate the utility of the Q-LDT-based approach to expand the applications of semisynthetic biosensors.
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Affiliation(s)
- Shinya Tsukiji
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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Katritzky AR, Yoshioka M, Narindoshvili T, Chung A, Johnson JV. Fluorescent labeling of peptides on solid phase. Org Biomol Chem 2008; 6:4582-6. [DOI: 10.1039/b811693h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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DAI Z, ZHANG J, DONG Q, GUO N, XU S, SUN B, BU Y. Adaption of Au Nanoparticles and CdTe Quantum Dots in DNA Detection. Chin J Chem Eng 2007. [DOI: 10.1016/s1004-9541(08)60004-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Amiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Sci 2007; 16:2350-9. [PMID: 17905834 PMCID: PMC2211708 DOI: 10.1110/ps.073119507] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 08/13/2007] [Accepted: 08/14/2007] [Indexed: 10/22/2022]
Abstract
Periplasmic expression screening is a selection technique used to enrich high-affinity proteins in Escherichia coli. We report using this screening method to rapidly select a mutated D-glucose/D-galactose-binding protein (GGBP) having low affinity to glucose. Wild-type GGBP has an equilibrium dissociation constant of 0.2 microM and mediates the transport of glucose within the periplasm of E. coli. The protein undergoes a large conformational change on binding glucose and, when labeled with an environmentally sensitive fluorophore, GGBP can relay glucose concentrations, making it of potential interest as a biosensor for diabetics. This use necessitates altering the glucose affinity of GGBP, bringing it into the physiologically relevant range for monitoring glucose in humans (1.7-33 mM). To accomplish this a focused library was constructed using structure-based site-saturation mutagenesis to randomize amino acids in the binding pocket of GGBP at or near direct H-bonding sites and screening the library within the bacterial periplasm. After selection, equilibrium dissociation constants were confirmed by glucose titration and fluorescence monitoring of purified mutants labeled site-specifically at E149C with the fluorophore IANBD (N,N'-dimethyl-N-(iodoacetyl)-N'-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylene-diamine). The screening identified a single mutation A213R that lowers GGBP glucose affinity 5000-fold to 1 mM. Computational modeling suggested the large decrease in affinity was accomplished by the arginine side chain perturbing H-bonding and increasing the entropic barrier to the closed conformation. Overall, these experiments demonstrate the ability of structure-based site-saturation mutagenesis and periplasmic expression screening to discover low-affinity GGBP mutants having potential utility for measuring glucose in humans.
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Affiliation(s)
- Terry J Amiss
- BD Technologies, Research Triangle Park, NC 27709, USA.
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Thomas J, Sherman DB, Amiss TJ, Andaluz SA, Pitner JB. Synthesis and Biosensor Performance of a Near-IR Thiol-Reactive Fluorophore Based on Benzothiazolium Squaraine. Bioconjug Chem 2007; 18:1841-6. [PMID: 17848078 DOI: 10.1021/bc700146r] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Environmentally sensitive near-IR (NIR) dyes are useful fluorophores for various biosensor applications when tissue absorption, scattering, and autofluorescence are a leading concern. Biosensors operating in the NIR region (generally wavelengths >650 nm) would avoid interference from biological media and thereby facilitate relatively interference free sensing. Squaraine dyes are potential candidates to serve as reporter molecules due to their spectral properties in the NIR region, but none is commercially available for site-specific coupling to proteins through native or engineered thiols on cysteine. In this context, we have synthesized a thiol-reactive squaraine that displays fluorescence emission above 650 nm and have coupled the dye site-specifically to various mutants of glucose/galactose binding protein that contained an engineered cysteine for attachment. Mutant E149C/A213R/L238S ISQ GGBP gave a fluorescence change of +50% and a binding constant of 12 mM, which is in the human physiological range for glucose.
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Affiliation(s)
- Joseph Thomas
- BD Technologies, Research Triangle Park, NC 27709, USA.
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30
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Tian Y, Cuneo MJ, Changela A, Höcker B, Beese LS, Hellinga HW. Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. Protein Sci 2007; 16:2240-50. [PMID: 17766373 PMCID: PMC2204141 DOI: 10.1110/ps.072969407] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstrom resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 +/- 1 degrees C and 144 +/- 2 degrees C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C*Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.
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Affiliation(s)
- Yaji Tian
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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31
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Basabe-Desmonts L, Reinhoudt DN, Crego-Calama M. Design of fluorescent materials for chemical sensing. Chem Soc Rev 2007; 36:993-1017. [PMID: 17534482 DOI: 10.1039/b609548h] [Citation(s) in RCA: 614] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an enormous demand for chemical sensors for many areas and disciplines. High sensitivity and ease of operation are two main issues for sensor development. Fluorescence techniques can easily fulfill these requirements and therefore fluorescent-based sensors appear as one of the most promising candidates for chemical sensing. However, the development of sensors is not trivial; material science, molecular recognition and device implementation are some of the aspects that play a role in the design of sensors. The development of fluorescent sensing materials is increasingly captivating the attention of the scientists because its implementation as a truly sensory system is straightforward. This critical review shows the use of polymers, sol-gels, mesoporous materials, surfactant aggregates, quantum dots, and glass or gold surfaces, combined with different chemical approaches for the development of fluorescent sensing materials. Representative examples have been selected and they are commented here.
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Affiliation(s)
- Lourdes Basabe-Desmonts
- Department of Supramolecular Chemistry and Technology, MESA+ Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
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32
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Staiano M, Scognamiglio V, Mamone G, Rossi M, Parracino A, Rossi M, D'Auria S. Glutamine-Binding Protein fromEscherichiaColiSpecifically Binds a Wheat Gliadin Peptide. 2. Resonance Energy Transfer Studies Suggest a New Sensing Approach for an Easy Detection of Wheat Gliadin. J Proteome Res 2006; 5:2083-6. [PMID: 16944918 DOI: 10.1021/pr060258+] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work is presented the first attempt to develop a fluorescence assay for detection of traces of gluten in food by utilizing the recombinant glutamine-binding protein (GlnBP) from E. coli. We found that GlnBP specifically binds the sequence of amino acids present both in gliadin and other prolamines classified as toxic for celiac patients. Affinity chromatography experiments together with mass spectrometry experiments demonstrated that GlnBP can bind the following amino acid sequence XXQPQPQQQQQQQQQQQQL. Sequence alignment experiments pointed out that this sequence is exclusively representative of the gliadin and the other prolamines considered toxic for celiac patients. These findings suggest the development of a competitive resonance energy transfer (RET) assay for an easy and rapid detection of this sequence in raw and cooked food.
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Affiliation(s)
- Maria Staiano
- Institute of Protein Biochemistry, C.N.R., Via Pietro Castellino, 111 80131, Naples, Italy
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33
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de Lorimier RM, Tian Y, Hellinga HW. Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins. Protein Sci 2006; 15:1936-44. [PMID: 16823040 PMCID: PMC2242582 DOI: 10.1110/ps.062261606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Development of biosensor devices typically requires incorporation of the molecular recognition element into a solid surface for interfacing with a signal detector. One approach is to immobilize the signal transducing protein directly on a solid surface. Here we compare the effects of two direct immobilization methods on ligand binding, kinetics, and signal transduction of reagentless fluorescent biosensors based on engineered periplasmic binding proteins. We used thermostable ribose and glucose binding proteins cloned from Thermoanaerobacter tengcongensis and Thermotoga maritima, respectively. To test the behavior of these proteins in semispecifically oriented layers, we covalently modified lysine residues with biotin or sulfhydryl functions, and attached the conjugates to plastic surfaces derivatized with streptavidin or maleimide, respectively. The immobilized proteins retained ligand binding and signal transduction but with adversely affected affinities and signal amplitudes for the thiolated, but not the biotinylated, proteins. We also immobilized these proteins in a more specifically oriented layer to maleimide-derivatized plates using a His(2)Cys(2) zinc finger domain fused at either their N or C termini. Proteins immobilized this way either retained, or displayed enhanced, ligand affinity and signal amplitude. In all cases tested ligand binding by immobilized proteins is reversible, as demonstrated by several iterations of ligand loading and elution. The kinetics of ligand exchange with the immobilized proteins are on the order of seconds.
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Affiliation(s)
- Robert M de Lorimier
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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34
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Rizk SS, Cuneo MJ, Hellinga HW. Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. Protein Sci 2006; 15:1745-51. [PMID: 16751609 PMCID: PMC2242554 DOI: 10.1110/ps.062135206] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Escherichia coli phnD gene is hypothesized to code for the periplasmic binding component of a phosphonate uptake system. Here we report the characterization of the phosphonate-binding properties of the phnD protein product. We find that PhnD exhibits high affinity for 2-aminoethylphosphonate (5 nM), the most commonly occurring natural phosphonate produced by lower eukaryotes, but also binds several other phosphonates with micromolar affinities. A significant number of man-made phosphonates, such as insecticides and chemical warfare agents, are chemical threats and environmental pollutants. Consequently, there is an interest in developing methods for the detection and bioremediation of phosphonates. Bacterial periplasmic-binding proteins have been utilized for developing reagentless biosensors that report analytes by coupling ligand-binding events to changes in the emission properties of a covalently conjugated environmentally-sensitive fluorophore. Several PhnD conjugates described here show large changes in fluorescence upon binding to methylphosphonate (MP), with two conjugates exhibiting up to 50% decrease in emission intensity. Since MP is the final degradation product of many nerve agents, these PhnD conjugates can function as components in a biosensor system for chemical warfare agents.
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Affiliation(s)
- Shahir S Rizk
- Duke University Medical Center, Department of Biochemistry, Durham, NC 27710, USA
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35
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Das A, Trammell SA, Hecht MH. Electrochemical and ligand binding studies of a de novo heme protein. Biophys Chem 2006; 123:102-12. [PMID: 16730114 DOI: 10.1016/j.bpc.2006.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 04/20/2006] [Indexed: 11/25/2022]
Abstract
Heme proteins can perform a variety of electrochemical functions. While natural heme proteins carry out particular functions selected by biological evolution, artificial heme proteins, in principle, can be tailored to suit specified technological applications. Here we describe initial characterization of the electrochemical properties of a de novo heme protein, S824C. Protein S824C is a four-helix bundle derived from a library of sequences that was designed by binary patterning of polar and nonpolar amino acids. Protein S824C was immobilized on a gold electrode and the formal potential of heme-protein complex was studied as a function of pH and ionic strength. The binding of exogenous N-donor ligands to heme/S824C was monitored by measuring shifts in the potential that occurred upon addition of various concentrations of imidazole or pyridine derivatives. The response of heme/S824C to these ligands was then compared to the response of isolated heme (without protein) to the same ligands. The observed shifts in potential depended on both the concentration and the structure of the added ligand. Small changes in structure of the ligand (e.g. pyridine versus 2-amino pyridine) produced significant shifts in the potential of the heme-protein. The observed shifts correlate to the differential binding of the N-donor molecules to the oxidized and reduced states of the heme. Further, it was observed that the electrochemical response of the buried heme in heme/S824C differed significantly from that of isolated heme. These studies demonstrate that the structure of the de novo protein modulates the binding of N-donor ligands to heme.
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Affiliation(s)
- Aditi Das
- Department of Chemistry, Princeton University, Princeton, NJ 08544-1009, USA
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36
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van Sint Fiet S, van Beilen JB, Witholt B. Selection of biocatalysts for chemical synthesis. Proc Natl Acad Sci U S A 2006; 103:1693-8. [PMID: 16446453 PMCID: PMC1413619 DOI: 10.1073/pnas.0504733102] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To determine whether microbial chemosensors can be used to find new or better biocatalysts, we constructed Escherichia coli hosts that recognize the product of a biocatalytic conversion through the transcriptional activator NahR and respond by expression of a lacZ or tetA reporter gene. Equipped with a benzaldehyde dehydrogenase (XylC from Pseudomonas putida), the lacZ-based host responded to the oxidation of benzaldehyde and 2-hydroxybenzaldehyde to the corresponding benzoic acids by forming blue colonies, whereas XylC- cells did not. Similarly, the tetA-based host was able to grow under selective conditions only when equipped with XylC, enabling selection of biocatalytically active cells in inactive populations at frequencies as low as 10(-6).
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Affiliation(s)
- Stephan van Sint Fiet
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
| | - Jan B. van Beilen
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
| | - Bernard Witholt
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
- *To whom correspondence should be addressed. E-mail:
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37
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Altschuh D, Oncul S, Demchenko AP. Fluorescence sensing of intermolecular interactions and development of direct molecular biosensors. J Mol Recognit 2006; 19:459-77. [PMID: 17089349 DOI: 10.1002/jmr.807] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular biosensors are devices of molecular size that are designed for sensing different analytes on the basis of biospecific recognition. They should provide two coupled functions - the recognition (specific binding) of the target and the transduction of information about the recognition event into a measurable signal. The present review highlights the achievements and prospects in design and operation of molecular biosensors for which the transduction mechanism is based on fluorescence. We focus on the general strategy of fluorescent molecular sensing, construction of sensor elements, based on natural and designed biopolymers (proteins and nucleic acids). Particular attention is given to the coupling of sensing elements with fluorescent reporter dyes and to the methods for producing efficient fluorescence responses.
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Affiliation(s)
- Danièle Altschuh
- UMR 7175 CNRS/ULP, ESBS, Parc d'Innovation, Bld S. Brant, BP 10413, 67412 Illkirch Cedex, France.
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Hu Y, Das A, Hecht MH, Scoles G. Nanografting de novo proteins onto gold surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:9103-9. [PMID: 16171339 DOI: 10.1021/la046857h] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The immobilization of novel proteins onto addressable locations on a flat surface has potential applications in a range of biotechnologies. Here we describe the nanopatterning of a de novo protein onto a gold surface. Patterning was achieved using a technique called nanografting, in which the tip of an atomic force microscope is used to disrupt a preexisting monolayer of alkanethiol molecules on a gold surface, thereby facilitating exchange with alternative thiol-linked molecules from the surrounding solution. The protein used for these studies was chosen from a designed combinatorial library of de novo sequences expressed in E. coli and was engineered to have a glycine-glycine-cysteine tag at its C-terminus, thereby enabling attachment to the gold surface through a single cysteine thiol. The average height of the grafted protein patterns was found to be somewhat higher than expected from the known NMR structure of the protein. Compression of the nanografted patches by an external force (below 10 nN) was reversible but showed some hysteresis. Interestingly, both the energy required to deform the immobilized protein patterns and the energy defined by the hysteresis loop were found to be of the same order as the energy required to unfold the monomeric protein in solution. These studies demonstrate the possibility of preparing nanometer scale protein arrays, lowering significantly the volume requirements of the protein samples necessary to fabricate protein-based biosensor arrays and thereby providing a base for increasing their sensitivity.
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Affiliation(s)
- Ying Hu
- Chemistry Department, Princeton Institute for the Science and Technology of Materials (PRISM), Princeton University, Princeton, NJ 08544, USA
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39
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Balshaw DM, Philbert M, Suk WA. Research strategies for safety evaluation of nanomaterials, Part III: nanoscale technologies for assessing risk and improving public health. Toxicol Sci 2005; 88:298-306. [PMID: 16162851 DOI: 10.1093/toxsci/kfi312] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Risk assessment in the environmental health sciences focuses on understanding the nature of environmental exposures and the potential harm posed by those exposures which in turn is determined by the perturbation of biological pathways and the individual's susceptibility to damage. While there are extensive research efforts ongoing in these areas, progress in each is currently slowed by technological limitations including comprehensive assessment of multiple exposures in real time and dynamic assessment of biological response with high temporal and quantitative resolution. This Forum article discusses recent technological innovations capitalizing on the emergent properties of nanoscale materials and their potential adaptation to improving individual exposure assessment, determination of biological response, and environmental remediation. The ultimate goal is to raise the environmental health science community's awareness of these possibilities and encourage the development of improved strategies for assessing risk and improving public health.
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Affiliation(s)
- David M Balshaw
- Center for Risk and Integrated Sciences, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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40
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Demchenko AP. The future of fluorescence sensor arrays. Trends Biotechnol 2005; 23:456-60. [PMID: 15967523 DOI: 10.1016/j.tibtech.2005.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 05/05/2005] [Accepted: 06/08/2005] [Indexed: 11/18/2022]
Abstract
The rapid progress in sensor and biosensor array technologies needs a general strategy in the design of fluorescence reporters. Such reporters should provide a high density of sensor elements, allow analysis of targets of different affinities, and be internally calibrated, reproducible and have a rapid readout. Several criteria are introduced here for the comparative evaluation of fluorescence-sensing techniques. It is shown that only the two-band wavelength ratiometric sensing with a single reporter dye exhibiting rapid reversible excited-state reaction can satisfy all these criteria and is a prospective candidate for further development.
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Affiliation(s)
- Alexander P Demchenko
- TUBITAK Research Institute for Genetic Engineering and Biotechnology, 41470 Gebze-Kocaeli, Turkey.
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Kohn JE, Plaxco KW. Engineering a signal transduction mechanism for protein-based biosensors. Proc Natl Acad Sci U S A 2005; 102:10841-5. [PMID: 16046542 PMCID: PMC1182433 DOI: 10.1073/pnas.0503055102] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 06/16/2005] [Indexed: 11/18/2022] Open
Abstract
Hybridization-induced conformational changes have been successfully used in biosensors for the transduction of DNA-binding events into readily observable optical or electronic signals. Similar signal transduction has not, however, proven of equal utility in protein-based biosensors. The discrepancy arises because, unlike ssDNA, most proteins do not undergo significant conformational changes upon ligand binding. Here, we describe a solution to this problem. We show that an arbitrarily selected, normally well folded protein can be rationally engineered such that it undergoes ligand-induced folding. The engineered protein responds rapidly (milliseconds) and selectively to its target, and it couples recognition with the largest possible conformational change: folding. These traits suggest that ligand-induced folding could serve as an ideal signal-transduction mechanism. Consistent with this claim, we demonstrate a label-free optical biosensor based on the effect that is sufficiently selective to detect its target even in complex, contaminant-ridden samples such as blood serum.
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Affiliation(s)
- Jonathan E Kohn
- Interdepartmental Program in Biomolecular Science and Engineering, Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, CA 93106, USA
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42
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Dattelbaum JD, Looger LL, Benson DE, Sali KM, Thompson RB, Hellinga HW. Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. Protein Sci 2005; 14:284-91. [PMID: 15659363 PMCID: PMC2253422 DOI: 10.1110/ps.041146005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We previously reported the construction of a family of reagentless fluorescent biosensor proteins by the structure-based design of conjugation sites for a single, environmentally sensitive small molecule dye, thus providing a mechanism for the transduction of ligand-induced conformational changes into a macroscopic fluorescence observable. Here we investigate the microscopic mechanisms that may be responsible for the macroscopic fluorescent changes in such Fluorescent Allosteric Signal Transduction (FAST) proteins. As case studies, we selected three individual cysteine mutations (F92C, D95C, and S233C) of Escherichia coli maltose binding protein (MBP) covalently labeled with a single small molecule fluorescent probe, N-((2-iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBD), each giving rise to a robust FAST protein with a distinct maltose-dependent fluorescence response. The fluorescence emission intensity, anisotropy, lifetime, and iodide-dependent fluorescence quenching were determined for each conjugate in the presence and absence of maltose. Structure-derived solvent accessible surface areas of the three FAST proteins are consistent with experimentally observed quenching data. The D95C protein exhibits the largest fluorescence change upon maltose binding. This mutant was selected for further characterization, and residues surrounding the fluorophore coupling site were mutagenized. Analysis of the resulting mutant FAST proteins suggests that specific hydrogen-bonding interactions between the fluorophore molecule and two tyrosine side-chains, Tyr171 and Tyr176, in the open state but not the closed, are responsible for the dramatic fluorescence response of this construct. Taken together these results provide insights that can be used in future design cycles to construct fluorescent biosensors that optimize signaling by engineering specific hydrogen bonds between a fluorophore and protein.
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43
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Okumoto S, Looger LL, Micheva KD, Reimer RJ, Smith SJ, Frommer WB. Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors. Proc Natl Acad Sci U S A 2005; 102:8740-5. [PMID: 15939876 PMCID: PMC1143584 DOI: 10.1073/pnas.0503274102] [Citation(s) in RCA: 284] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Indexed: 11/18/2022] Open
Abstract
Glutamate is the predominant excitatory neurotransmitter in the mammalian brain. Once released, its rapid removal from the synaptic cleft is critical for preventing excitotoxicity and spillover to neighboring synapses. Despite consensus on the role of glutamate in normal and disease physiology, technical issues limit our understanding of its metabolism in intact cells. To monitor glutamate levels inside and at the surface of living cells, genetically encoded nanosensors were developed. The fluorescent indicator protein for glutamate (FLIPE) consists of the glutamate/aspartate binding protein ybeJ from Escherichia coli fused to two variants of the green fluorescent protein. Three sensors with lower affinities for glutamate were created by mutation of residues peristeric to the ybeJ binding pocket. In the presence of ligands, FLIPEs show a concentration-dependent decrease in FRET efficiency. When expressed on the surface of rat hippocampal neurons or PC12 cells, the sensors respond to extracellular glutamate with a reversible concentration-dependent decrease in FRET efficiency. Depolarization of neurons leads to a reduction in FRET efficiency corresponding to 300 nM glutamate at the cell surface. No change in FRET was observed when cells expressing sensors in the cytosol were superfused with up to 20 mM glutamate, consistent with a minimal contribution of glutamate uptake to cytosolic glutamate levels. The results demonstrate that FLIPE sensors can be used for real-time monitoring of glutamate metabolism in living cells, in tissues, or in intact organisms, providing tools for studying metabolism or for drug discovery.
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Affiliation(s)
- Sakiko Okumoto
- Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
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44
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Pickup JC, Hussain F, Evans ND, Rolinski OJ, Birch DJS. Fluorescence-based glucose sensors. Biosens Bioelectron 2005; 20:2555-65. [PMID: 15854825 DOI: 10.1016/j.bios.2004.10.002] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 10/06/2004] [Accepted: 10/06/2004] [Indexed: 12/31/2022]
Abstract
There is an urgent need to develop technology for continuous in vivo glucose monitoring in subjects with diabetes mellitus. Problems with existing devices based on electrochemistry have encouraged alternative approaches to glucose sensing in recent years, and those based on fluorescence intensity and lifetime have special advantages, including sensitivity and the potential for non-invasive measurement when near-infrared light is used. Several receptors have been employed to detect glucose in fluorescence sensors, and these include the lectin concanavalin A (Con A), enzymes such as glucose oxidase, glucose dehydrogenase and hexokinase/glucokinase, bacterial glucose-binding protein, and boronic acid derivatives (which bind the diols of sugars). Techniques include measuring changes in fluorescence resonance energy transfer (FRET) between a fluorescent donor and an acceptor either within a protein which undergoes glucose-induced changes in conformation or because of competitive displacement; measurement of glucose-induced changes in intrinsic fluorescence of enzymes (e.g. due to tryptophan residues in hexokinase) or extrinsic fluorophores (e.g. using environmentally sensitive fluorophores to signal protein conformation). Non-invasive glucose monitoring can be accomplished by measurement of cell autofluorescence due to NAD(P)H, and fluorescent markers of mitochondrial metabolism can signal changes in extracellular glucose concentration. Here we review the principles of operation, context and current status of the various approaches to fluorescence-based glucose sensing.
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Affiliation(s)
- John C Pickup
- Department of Chemical Pathology, Guy's, King's and St Thomas's School of Medicine, Guy's Hospital, London SE1 9RT, UK.
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45
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Engfeldt T, Renberg B, Brumer H, Nygren PA, Karlström AE. Chemical Synthesis of Triple-Labelled Three-Helix Bundle Binding Proteins for Specific Fluorescent Detection of Unlabelled Protein. Chembiochem 2005; 6:1043-50. [PMID: 15880677 DOI: 10.1002/cbic.200400388] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Site-specifically triple-labelled three-helix bundle affinity proteins (affibody molecules) have been produced by total chemical synthesis. The 58 aa affinity proteins were assembled on an automated peptide synthesizer, followed by manual on-resin incorporation of three different reporter groups. An orthogonal protection strategy was developed for the site-specific introduction of 5-(2-aminethylamino)-1-naphthalenesulfonic acid (EDANS) and 6-(7-nitrobenzofurazan-4-ylamino)-hexanoic acid (NBDX), constituting a donor/acceptor pair for fluorescence resonance energy transfer (FRET), and a biotin moiety, used for surface immobilization. Circular dichroism and biosensor studies of the synthetic proteins and their recombinant counterparts revealed that the synthetic proteins were folded and retained their binding specificities. The biotin-conjugated protein could be immobilized onto a streptavidin surface without loss of activity. The synthetic, doubly fluorescent-labelled affinity proteins were shown to function as fluorescent biosensors in an assay for the specific detection of unlabelled human IgG and IgA.
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Affiliation(s)
- Torun Engfeldt
- Department of Biotechnology, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
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46
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Zhong JQ, Freyzon Y, Ehrlich DJ, Matsudaira P. Enhanced detection sensitivity using a novel solid-phase incorporated affinity fluorescent protein biosensor. ACTA ACUST UNITED AC 2005; 21:67-72. [PMID: 15113560 DOI: 10.1016/j.bioeng.2003.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 10/20/2003] [Accepted: 10/29/2003] [Indexed: 11/24/2022]
Abstract
We engineered green fluorescent protein (GFP) into affinity fluorescent proteins (aFPs) biosensors. The aFPs detect protein-protein interactions by enhanced fluorescence intensity. In a proof of principle demonstration, aFPs containing haemagglutinin (HA) tag bind specifically to the anti-HA antibody. The sensitivity and specificity is enhanced 28-fold by incorporation of aFPs into solid-phase surface.
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Affiliation(s)
- Joan Q Zhong
- Whitehead Institute for Biomedical Research, MIT, Nine Cambridge Center, Cambridge, MA 02142, USA
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47
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Doerr AJ, McLendon GL. Design, folding, and activities of metal-assembled coiled coil proteins. Inorg Chem 2005; 43:7916-25. [PMID: 15578825 DOI: 10.1021/ic0490573] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal ions serve many purposes in natural proteins, from the stabilization of tertiary structure to the direction of protein folding to crucial roles in electron transfer and catalysis. There is considerable interest in creating metal binding sites in designed proteins to understand the structural role of metal ions and to design new metalloproteins with useful functions. The de novo design of metalloproteins and the role of metals in the folding of designed proteins are reviewed here, with particular focus on the design, folding, and activities of the [M(bpy-peptide)(3)](2+) structure. This maquette is constructed by the covalent attachment of 2,2'-bipyridine to the N-termini of amphiphilic peptides, and it is assembled into a folded trimeric coiled coil by the addition of a six-coordinate transition metal ion and the resulting hydrophobic collapse of the peptides. The [M(bpy-peptide)(3)](2+) structure has been employed in diverse applications, ranging from electron transfer pathway studies to the study of optimal hydrophobic packing in a virtual library to the construction of receptors and biosensors.
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Affiliation(s)
- Allison J Doerr
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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48
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Goodchild S, Love T, Hopkins N, Mayers C. Engineering Antibodies for Biosensor Technologies. ADVANCES IN APPLIED MICROBIOLOGY 2005; 58C:185-226. [PMID: 16543034 DOI: 10.1016/s0065-2164(05)58006-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah Goodchild
- Dstl, Detection Department, Porton Down Salisbury, Wiltshire SP4 OJQ, United Kingdom
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49
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Medintz IL, Anderson GP, Lassman ME, Goldman ER, Bettencourt LA, Mauro JM. General Strategy for Biosensor Design and Construction Employing Multifunctional Surface-Tethered Components. Anal Chem 2004; 76:5620-9. [PMID: 15456279 DOI: 10.1021/ac049419o] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biosensors function by reversibly linking bioreceptor-target analyte binding with closely integrated signal generation and can either continuously monitor analyte concentrations or be returned to baseline readout values by removal of analyte. We present an approach for producing fully reversible, reagentless, self-assembling biosensors on surfaces. In the prototype biosensor, quencher-dye-labeled biotin-linked E. coli maltose binding protein (MBP) bound in a specific orientation to a NeutrAvidin-coated surface is employed as a bioreceptor. To complete sensor formation, a modular tether arm consisting of a flexible biotinylated DNA oligonucleotide, a fluorescence resonance energy-transfer (FRET) donor dye, and a distal beta-cyclodextrin (beta-CD) analyte analogue is bound in an equimolar amount to the same surface by means of DNA-directed immobilization. After self-assembly, a baseline level of FRET quenching is observed due to specific interaction between the beta-CD of the flexible tether arm and the sugar binding site of MBP, which brings the two dyes into proximity. Addition of the target analyte, the nutrient maltose, displaces the linked beta-CD-dye of the DNA-based tether arm, and a concentration-dependent change in FRET results. Biosensor sensitivity and dynamic range can be controlled by either using MBP variants having different binding constants or by binding of modulator DNA oligonucleotides that are complementary to the flexible DNA tether. The sensor can be regenerated and returned to baseline quenching levels by washing away analyte. A complex set of interactions apparently exists on the sensing surface that may contribute to sensor behavior and range. This approach may represent a general way to assemble a wide range of useful biosensors.
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Affiliation(s)
- Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA.
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50
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Dwyer MA, Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr Opin Struct Biol 2004; 14:495-504. [PMID: 15313245 DOI: 10.1016/j.sbi.2004.07.004] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The diversity of biological function, ligand binding, conformational changes and structural adaptability of the periplasmic binding protein superfamily have been exploited to engineer biosensors, allosteric control elements, biologically active receptors and enzymes using a combination of techniques, including computational design. Extensively redesigned periplasmic binding proteins have been re-introduced into bacteria to function in synthetic signal transduction pathways that respond to extracellular ligands and as biologically active enzymes.
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Affiliation(s)
- Mary A Dwyer
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
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