1
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Kane BJ, Okuda‐Shimazaki J, Andrews MM, Kerrigan JA, Murphy KV, Sode K. Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β-hydroxybutyrate binding proteins. Protein Sci 2024; 33:e5025. [PMID: 38864689 PMCID: PMC11167705 DOI: 10.1002/pro.5025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 06/13/2024]
Abstract
Polyhydroxyalkanoates are a class of biodegradable, thermoplastic polymers which represent a major carbon source for various bacteria. Proteins which mediate the translocation of polyhydroxyalkanoate breakdown products, such as β-hydroxybutyrate (BHB)-a ketone body which in humans serves as an important biomarker, have not been well characterized. In our investigation to screen a solute-binding protein (SBP) which can act as a suitable recognition element for BHB, we uncovered insights at the intersection of bacterial metabolism and diagnostics. Herein, we identify SBPs associated with putative ATP-binding cassette transporters that specifically recognize BHB, with the potential to serve as recognition elements for continuous quantification of this analyte. Through bioinformatic analysis, we identified candidate SBPs from known metabolizers of polyhydroxybutyrate-including proteins from Cupriavidus necator, Ensifer meliloti, Paucimonas lemoignei, and Thermus thermophilus. After recombinant expression in Escherichia coli, we demonstrated with intrinsic tryptophan fluorescence spectroscopy that four candidate proteins interacted with BHB, ranging from nanomolar to micromolar affinity. Tt.2, an intrinsically thermostable protein from Thermus thermophilus, was observed to have the tightest binding and specificity for BHB, which was confirmed by isothermal calorimetry. Structural analyses facilitated by AlphaFold2, along with molecular docking and dynamics simulations, were used to hypothesize key residues in the binding pocket and to model the conformational dynamics of substrate unbinding. Overall, this study provides strong evidence identifying the cognate ligands of SBPs which we hypothesize to be involved in prokaryotic cellular translocation of polyhydroxyalkanoate breakdown products, while highlighting these proteins' promising biotechnological application.
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Affiliation(s)
- Bryant J. Kane
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Junko Okuda‐Shimazaki
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Madelyn M. Andrews
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Joseph A. Kerrigan
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Kyle V. Murphy
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Koji Sode
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
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2
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Jiang T, Zeng BF, Zhang B, Tang L. Single-molecular protein-based bioelectronics via electronic transport: fundamentals, devices and applications. Chem Soc Rev 2023; 52:5968-6002. [PMID: 37498342 DOI: 10.1039/d2cs00519k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Biao-Feng Zeng
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Bintian Zhang
- Shenzhen Key Laboratory of Precision Measurement and Early Warning Technology for Urban Environmental Health Risks, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.
- Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou 310027, China
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3
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Staii C. Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy. Molecules 2023; 28:4632. [PMID: 37375186 DOI: 10.3390/molecules28124632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM-force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function.
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Affiliation(s)
- Cristian Staii
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA
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4
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Murugappan K, Sundaramoorthy U, Damry AM, Nisbet DR, Jackson CJ, Tricoli A. Electrodetection of Small Molecules by Conformation-Mediated Signal Enhancement. JACS AU 2022; 2:2481-2490. [PMID: 36465535 PMCID: PMC9709943 DOI: 10.1021/jacsau.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 06/17/2023]
Abstract
Electrochemical biosensors allow the rapid, selective, and sensitive transduction of critical biological parameters into measurable signals. However, current electrochemical biosensors often fail to selectively and sensitively detect small molecules because of their small size and low molecular complexity. We have developed an electrochemical biosensing platform that harnesses the analyte-dependent conformational change of highly selective solute-binding proteins to amplify the redox signal generated by analyte binding. Using this platform, we constructed and characterized two biosensors that can sense leucine and glycine, respectively. We show that these biosensors can selectively and sensitively detect their targets over a wide range of concentrations-up to 7 orders of magnitude-and that the selectivity of these sensors can be readily altered by switching the bioreceptor's binding domain. Our work represents a new paradigm for the design of a family of modular electrochemical biosensors, where access to electrode surfaces can be controlled by protein conformational changes.
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Affiliation(s)
- Krishnan Murugappan
- Nanotechnology
Research Laboratory, Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT2601, Australia
- CSIRO,
Mineral Resources, Private
Bag 10, Clayton South, VIC3169, Australia
| | | | - Adam M. Damry
- Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
- Department
of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ONK1N 6N5, Canada
| | - David R. Nisbet
- Laboratory
of Advanced Biomaterials, Research School of Chemistry and the John
Curtin School of Medical Research, The Australian
National University, Canberra, ACT2601, Australia
- The Graeme
Clark Institute, The University of Melbourne, Melbourne, VIC3010, Australia
- Department
of Biomedical Engineering, Faculty of Engineering and Information
Technology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, The Australian National University, Canberra, ACT2601, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, The Australian National
University, Canberra, ACT2601, Australia
| | - Antonio Tricoli
- Nanotechnology
Research Laboratory, Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT2601, Australia
- Nanotechnology
Research Laboratory, Faculty of Engineering, University of Sydney, Sydney, NSW2006, Australia
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5
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Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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6
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N'Guetta PEY, Fink MM, Rizk SS. Engineering a fluorescence biosensor for the herbicide glyphosate. Protein Eng Des Sel 2020; 33:gzaa021. [PMID: 32930799 DOI: 10.1093/protein/gzaa021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
Glyphosate, the active ingredient in RoundUp, is the most widely used herbicide on the globe, and has recently been linked to an increased risk in non-Hodgkin's lymphoma in exposed individuals. Therefore, detection and monitoring of glyphosate levels in water and soil is important for public safety. Here, we describe a biosensor for glyphosate based on an engineered Escherichia coli phosphonate-binding protein (PhnD). Mutations in the binding pocket were introduced to convert PhnD into a glyphosate-binding protein. A fluorescence group attached near the hinge of the protein was added to monitor binding of glyphosate and to determine its concentration in unknown samples. The resulting engineered biosensor can detect glyphosate in tap water and in soil samples treated with the herbicide at submicromolar concentrations, well below the limit for drinking water in the USA. Incorporating this biosensor in a device would allow rapid and continuous monitoring of glyphosate in water and soil samples.
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Affiliation(s)
| | - Maggie M Fink
- Department of Chemistry and Biochemistry, Indiana University, South Bend, IN 46615, USA
| | - Shahir S Rizk
- Department of Chemistry and Biochemistry, Indiana University, South Bend, IN 46615, USA
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7
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Kurnik M, Pang EZ, Plaxco KW. An Electrochemical Biosensor Architecture Based on Protein Folding Supports Direct Real‐Time Measurements in Whole Blood. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Martin Kurnik
- Department of Chemistry and Biochemistry University of California Santa Barbara Santa Barbara CA 93106 USA
- Center for Bioengineering University of California Santa Barbara Santa Barbara CA 93106 USA
| | - Eric Z. Pang
- Department of Chemistry and Biochemistry University of California Santa Barbara Santa Barbara CA 93106 USA
- Center for Bioengineering University of California Santa Barbara Santa Barbara CA 93106 USA
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry University of California Santa Barbara Santa Barbara CA 93106 USA
- Center for Bioengineering University of California Santa Barbara Santa Barbara CA 93106 USA
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8
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Kurnik M, Pang EZ, Plaxco KW. An Electrochemical Biosensor Architecture Based on Protein Folding Supports Direct Real-Time Measurements in Whole Blood. Angew Chem Int Ed Engl 2020; 59:18442-18445. [PMID: 32668060 DOI: 10.1002/anie.202007256] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/10/2020] [Indexed: 12/21/2022]
Abstract
The ability to monitor drug and biomarker concentrations in the body with high frequency and in real time would revolutionize our understanding of biology and our capacity to personalize medicine. The few in vivo molecular sensors that currently exist, however, all rely on the specific chemical or enzymatic reactivity of their targets and thus are not generalizable. In response, we demonstrate here an electrochemical sensing architecture based on binding-induced protein folding that is 1) independent of the reactivity of its targets, 2) reagentless, real-time, and with a resolution of seconds, and 3) selective enough to deploy in undiluted bodily fluids. As a proof of principle, we use the SH3 domain from human Fyn kinase to build a sensor that discriminates between the protein's peptide targets and responds rapidly and quantitatively even when challenged in whole blood. The resulting sensor architecture could drastically expand the chemical space accessible to continuous, real-time biosensors.
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Affiliation(s)
- Martin Kurnik
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Eric Z Pang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
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9
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Qu JH, Dillen A, Saeys W, Lammertyn J, Spasic D. Advancements in SPR biosensing technology: An overview of recent trends in smart layers design, multiplexing concepts, continuous monitoring and in vivo sensing. Anal Chim Acta 2019; 1104:10-27. [PMID: 32106939 DOI: 10.1016/j.aca.2019.12.067] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/04/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022]
Abstract
Inspired by the rapid progress and existing limitations in surface plasmon resonance (SPR) biosensing technology, we have summarized the recent trends in the fields of both chip-SPR and fiber optic (FO)-SPR biosensors during the past five years, primarily regarding smart layers design, multiplexing, continuous monitoring and in vivo sensing. Versatile surface chemistries, biomaterials and nanomaterials have been utilized thus far to generate smart layers on SPR platforms and as such achieve oriented immobilization of bioreceptors, improved fouling resistance and sensitivity enhancement, collectively aiming to improve the biosensing performance. Furthermore, often driven by the desires for time- and cost-effective quantification of multiple targets in a single measurement, efforts have been made to implement multiplex bioassays on SPR platforms. While this aspect largely remains difficult to attain, numerous alternative strategies arose for obtaining parallel analysis of multiple analytes in one single device. Additionally, one of the upcoming challenges in this field will be to succeed in using SPR platforms for continuous measurements and in vivo sensing, and as such match up other biosensing platforms where these goals have been already conquered. Overall, this review will give insight into multiple possibilities that have become available over the years for boosting the performance of SPR biosensors. However, because combining them all into one optimal sensor is practically not feasible, the final application needs to be considered while designing an SPR biosensor, as this will determine the requirements of the bioassay and will thus help in selecting the essential elements from the recent progress made in SPR sensing.
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Affiliation(s)
- Jia-Huan Qu
- KU Leuven, Department of Biosystems - Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Annelies Dillen
- KU Leuven, Department of Biosystems - Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Wouter Saeys
- KU Leuven, Department of Biosystems, MeBioS - Biophotonics, Kasteelpark Arenberg 30, Box 2456, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems - Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium.
| | - Dragana Spasic
- KU Leuven, Department of Biosystems - Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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10
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Mächtel R, Narducci A, Griffith DA, Cordes T, Orelle C. An integrated transport mechanism of the maltose ABC importer. Res Microbiol 2019; 170:321-337. [PMID: 31560984 PMCID: PMC6906923 DOI: 10.1016/j.resmic.2019.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to transport a large diversity of molecules actively across biological membranes. A combination of biochemical, biophysical, and structural studies has established the maltose transporter MalFGK2 as one of the best characterized proteins of the ABC family. MalF and MalG are the transmembrane domains, and two MalKs form a homodimer of nucleotide-binding domains. A periplasmic maltose-binding protein (MalE) delivers maltose and other maltodextrins to the transporter, and triggers its ATPase activity. Substrate import occurs in a unidirectional manner by ATP-driven conformational changes in MalK2 that allow alternating access of the substrate-binding site in MalF to each side of the membrane. In this review, we present an integrated molecular mechanism of the transport process considering all currently available information. Furthermore, we summarize remaining inconsistencies and outline possible future routes to decipher the full mechanistic details of transport by MalEFGK2 complex and that of related importer systems.
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Affiliation(s)
- Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Douglas A Griffith
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 passage du Vercors, 69367 Lyon, France.
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11
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Cormann KU, Baumgart M, Bott M. Structure-Based Design of Versatile Biosensors for Small Molecules Based on the PAS Domain of a Thermophilic Histidine Kinase. ACS Synth Biol 2018; 7:2888-2897. [PMID: 30525476 DOI: 10.1021/acssynbio.8b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of biosensors for in vitro quantification of small molecules such as metabolites or man-made chemicals is still a major challenge. Here we show that engineered variants of the sensory PAS domain of the histidine kinase CitA of the thermophilic bacterium Geobacillus thermoleovorans represent promising alternatives to established biorecognition elements. By combining binding site grafting and rational design we constructed protein variants binding l-malate, ethylmalonate, or the aromatic compound phthalate instead of the native ligand citrate. Due to more favorable entropy contributions, the wild-type protein and its engineered variants exhibited increased (nano- to micromolar) affinities and improved enantioselectivity compared to CitA homologues of mesophilic organisms. Ligand binding was directly converted into an optical signal that was preserved after immobilization of the protein. A fluorescently labeled variant was used to quantify ethylmalonate, an urinary biomarker for ethylmalonic encephalopathy, in synthetic urine, thereby demonstrating the applicability of the sensor in complex samples.
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Affiliation(s)
- Kai U. Cormann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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12
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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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13
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Yang F, Zuo X, Fan C, Zhang XE. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwx134] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Affiliation(s)
- Fan Yang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, CAS Excellence Center for Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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14
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Roose BW, Zemerov SD, Dmochowski IJ. Nanomolar small-molecule detection using a genetically encoded 129Xe NMR contrast agent. Chem Sci 2017; 8:7631-7636. [PMID: 29568427 PMCID: PMC5849143 DOI: 10.1039/c7sc03601a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/20/2017] [Indexed: 01/05/2023] Open
Abstract
Genetically encoded magnetic resonance imaging (MRI) contrast agents enable non-invasive detection of specific biomarkers in vivo.
Genetically encoded magnetic resonance imaging (MRI) contrast agents enable non-invasive detection of specific biomarkers in vivo. Here, we employed the hyper-CEST 129Xe NMR technique to quantify maltose (32 nM to 1 mM) through its modulation of conformational change and xenon exchange in maltose binding protein (MBP). Remarkably, no hyper-CEST signal was observed for MBP in the absence of maltose, making MBP an ultrasensitive “smart” contrast agent. The resonance frequency of 129Xe bound to MBP was greatly downfield-shifted (Δδ = 95 ppm) from the 129Xe(aq) peak, which facilitated detection in E. coli as well as multiplexing with TEM-1 β-lactamase. Finally, a Val to Ala mutation at the MBP–Xe binding site yielded 34% more contrast than WT, with 129Xe resonance frequency shifted 59 ppm upfield from WT. We conclude that engineered MBPs constitute a new class of genetically encoded, analyte-sensitive molecular imaging agents detectable by 129Xe NMR/MRI.
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Affiliation(s)
- B W Roose
- Department of Chemistry , University of Pennsylvania , 231 South 34th St. , Philadelphia , PA 19104-6323 , USA .
| | - S D Zemerov
- Department of Chemistry , University of Pennsylvania , 231 South 34th St. , Philadelphia , PA 19104-6323 , USA .
| | - I J Dmochowski
- Department of Chemistry , University of Pennsylvania , 231 South 34th St. , Philadelphia , PA 19104-6323 , USA .
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15
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Younger AKD, Dalvie NC, Rottinghaus AG, Leonard JN. Engineering Modular Biosensors to Confer Metabolite-Responsive Regulation of Transcription. ACS Synth Biol 2017; 6:311-325. [PMID: 27744683 DOI: 10.1021/acssynbio.6b00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efforts to engineer microbial factories have benefitted from mining biological diversity and high throughput synthesis of novel enzymatic pathways, yet screening and optimizing metabolic pathways remain rate-limiting steps. Metabolite-responsive biosensors may help to address these persistent challenges by enabling the monitoring of metabolite levels in individual cells and metabolite-responsive feedback control. We are currently limited to naturally evolved biosensors, which are insufficient for monitoring many metabolites of interest. Thus, a method for engineering novel biosensors would be powerful, yet we lack a generalizable approach that enables the construction of a wide range of biosensors. As a step toward this goal, we here explore several strategies for converting a metabolite-binding protein into a metabolite-responsive transcriptional regulator. By pairing a modular protein design approach with a library of synthetic promoters and applying robust statistical analyses, we identified strategies for engineering biosensor-regulated bacterial promoters and for achieving design-driven improvements of biosensor performance. We demonstrated the feasibility of this strategy by fusing a programmable DNA binding motif (zinc finger module) with a model ligand binding protein (maltose binding protein), to generate a novel biosensor conferring maltose-regulated gene expression. This systematic investigation provides insights that may guide the development of additional novel biosensors for diverse synthetic biology applications.
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Affiliation(s)
- Andrew K. D. Younger
- Interdisciplinary
Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil C. Dalvie
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Austin G. Rottinghaus
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert
H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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16
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Hall EA, Chen S, Chun J, Du Y, Zhao Z. A molecular biology approach to protein coupling at a biosensor interface. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Parlak O, Turner AP. Switchable bioelectronics. Biosens Bioelectron 2016; 76:251-65. [DOI: 10.1016/j.bios.2015.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 12/26/2022]
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18
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Vagin MY, Trashin SA, Beloglazkina EK, Majouga AG. Direct reagentless detection of the affinity binding of recombinant His-tagged firefly luciferase with a nickel-modified gold electrode. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Peters RF, Gutierrez-Rivera L, Dew SK, Stepanova M. Surface enhanced Raman spectroscopy detection of biomolecules using EBL fabricated nanostructured substrates. J Vis Exp 2015:52712. [PMID: 25867853 PMCID: PMC4401373 DOI: 10.3791/52712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.
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Affiliation(s)
- Robert F Peters
- Department of Electrical and Computer Engineering, University of Alberta; National Institute for Nanotechnology, National Research Council of Canada
| | - Luis Gutierrez-Rivera
- Department of Electrical and Computer Engineering, University of Alberta; National Institute for Nanotechnology, National Research Council of Canada
| | - Steven K Dew
- Department of Electrical and Computer Engineering, University of Alberta; National Institute for Nanotechnology, National Research Council of Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta; National Institute for Nanotechnology, National Research Council of Canada;
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20
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Fluorescent TEM-1 β-lactamase with wild-type activity as a rapid drug sensor for in vitro drug screening. Biosci Rep 2014; 34:BSR20140057. [PMID: 25074398 PMCID: PMC4155835 DOI: 10.1042/bsr20140057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report the development of a novel fluorescent drug sensor from the bacterial drug target TEM-1 β-lactamase through the combined strategy of Val216→Cys216 mutation and fluorophore labelling for in vitro drug screening. The Val216 residue in TEM-1 is replaced with a cysteine residue, and the environment-sensitive fluorophore fluorescein-5-maleimide is specifically attached to the Cys216 residue in the V216C mutant for sensing drug binding at the active site. The labelled V216C mutant has wild-type catalytic activity and gives stronger fluorescence when β-lactam antibiotics bind to the active site. The labelled V216C mutant can differentiate between potent and impotent β-lactam antibiotics and can distinguish active-site binders from non-binders (including aggregates formed by small molecules in aqueous solution) by giving characteristic time-course fluorescence profiles. Mass spectrometric, molecular modelling and trypsin digestion results indicate that drug binding at the active site is likely to cause the fluorescein label to stay away from the active site and experience weaker fluorescence quenching by the residues around the active site, thus making the labelled V216C mutant to give stronger fluorescence in the drug-bound state. Given the ancestor's role of TEM-1 in the TEM family, the fluorescent TEM-1 drug sensor represents a good model to demonstrate the general combined strategy of Val216→Cys216 mutation and fluorophore labelling for fabricating tailor-made fluorescent drug sensors from other clinically significant TEM-type β-lactamase variants for in vitro drug screening.
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21
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Li Y, Zhang J, Huang X, Wang T. Construction and direct electrochemistry of orientation controlled laccase electrode. Biochem Biophys Res Commun 2014; 446:201-5. [PMID: 24583131 DOI: 10.1016/j.bbrc.2014.02.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
Abstract
A laccase has multiple redox centres. Chemisorption of laccases on a gold electrode through a polypeptide tag introduced at the protein surface provides an isotropic orientation of laccases on the Au surface, which allows the orientation dependent study of the direct electrochemistry of laccase. In this paper, using genetic engineering technology, two forms of recombinant laccase which has Cys-6×His tag at the N or C terminus were generated. Via the Au-S linkage, the recombinant laccase was assembled orientationally on gold electrode. A direct electron transfer and a bioelectrocatalytic activity toward oxygen reduction were observed on the two orientation controlled laccase electrodes, but their electrochemical behaviors were found to be quite different. The orientation of laccase on the gold electrode affects both the electron transfer pathway and the electron transfer efficiency of O2 reduction. The present study is helpful not only to the in-depth understanding of the direct electrochemistry of laccase, but also to the development of laccase-based biofuel cells.
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Affiliation(s)
- Ying Li
- Key Laboratory of Colloid & Interface Chemistry of the Education Ministry of China, Shandong University, Jinan 250100, PR China
| | - Jiwei Zhang
- State Key Laboratory of Microbial Technology of China, Shandong University, Jinan 250100, PR China
| | - Xirong Huang
- Key Laboratory of Colloid & Interface Chemistry of the Education Ministry of China, Shandong University, Jinan 250100, PR China; State Key Laboratory of Microbial Technology of China, Shandong University, Jinan 250100, PR China.
| | - Tianhong Wang
- State Key Laboratory of Microbial Technology of China, Shandong University, Jinan 250100, PR China.
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22
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Conzuelo F, Gamella M, Campuzano S, Martínez-Ruiz P, Esteban-Torres M, de las Rivas B, Reviejo AJ, Muñoz R, Pingarrón JM. Integrated Amperometric Affinity Biosensors Using Co2+–Tetradentate Nitrilotriacetic Acid Modified Disposable Carbon Electrodes: Application to the Determination of β-Lactam Antibiotics. Anal Chem 2013; 85:3246-54. [DOI: 10.1021/ac303604b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - María Esteban-Torres
- Laboratorio de Biotecnología
Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, C/Juan de la Cierva
3, 28006 Madrid, Spain
| | - Blanca de las Rivas
- Laboratorio de Biotecnología
Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, C/Juan de la Cierva
3, 28006 Madrid, Spain
| | | | - Rosario Muñoz
- Laboratorio de Biotecnología
Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, C/Juan de la Cierva
3, 28006 Madrid, Spain
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23
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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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24
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Electrocatalytic oxidation of tyrosines shows signal enhancement in label-free protein biosensors. Trends Analyt Chem 2012. [DOI: 10.1016/j.trac.2012.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Dacres H, Michie M, Anderson A, Trowell SC. Advantages of substituting bioluminescence for fluorescence in a resonance energy transfer-based periplasmic binding protein biosensor. Biosens Bioelectron 2012; 41:459-64. [PMID: 23083905 DOI: 10.1016/j.bios.2012.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 11/26/2022]
Abstract
A genetically encoded maltose biosensor was constructed, comprising maltose binding protein (MBP) flanked by a green fluorescent protein (GFP(2)) at the N-terminus and a Renilla luciferase variant (RLuc2) at the C-terminus. This Bioluminescence resonance energy transfer(2) (BRET(2)) system showed a 30% increase in the BRET ratio upon maltose binding, compared with a 10% increase with an equivalent fluorescence resonance energy transfer (FRET) biosensor. BRET(2) provides a better matched Förster distance to the known separation of the N and C termini of MBP than FRET. The sensor responded to maltose and maltotriose and the response was completely abolished by introduction of a single point mutation in the BRET(2) tagged MBP protein. The half maximal effective concentration (EC(50)) was 0.37 μM for maltose and the response was linear over almost three log units ranging from 10nM to 3.16 μM maltose for the BRET(2) system compared to an EC(50) of 2.3 μM and a linear response ranging from 0.3 μM to 21.1 μM for the equivalent FRET-based biosensor. The biosensor's estimate of maltose in beer matched that of a commercial enzyme-linked assay but was quicker and more precise, demonstrating its applicability to real-world samples. A similar BRET(2)-based transduction scheme approach would likely be applicable to other binding proteins that have a "venus-fly-trap" mechanism.
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Affiliation(s)
- Helen Dacres
- CSIRO Food Futures National Research Flagship & Ecosystem Sciences, Australia, Canberra ACT 2601, Australia.
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26
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Vallée-Bélisle A, Ricci F, Uzawa T, Xia F, Plaxco KW. Bioelectrochemical switches for the quantitative detection of antibodies directly in whole blood. J Am Chem Soc 2012; 134:15197-200. [PMID: 22913425 DOI: 10.1021/ja305720w] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The development of rapid, low-cost point-of-care approaches for the quantitative detection of antibodies would drastically impact global health by shortening the delay between sample collection and diagnosis and by improving the penetration of modern diagnostics into the developing world. Unfortunately, however, current methods for the quantitative detection of antibodies, including ELISAs, Western blots, and fluorescence polarization assays, are complex, multiple-step processes that rely on well-trained technicians working in well-equipped laboratories. In response, we describe here a versatile, DNA-based electrochemical "switch" for the rapid, single-step measurement of specific antibodies directly in undiluted whole blood at clinically relevant low-nanomolar concentrations.
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Affiliation(s)
- Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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27
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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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28
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Ley C, Holtmann D, Mangold KM, Schrader J. Immobilization of histidine-tagged proteins on electrodes. Colloids Surf B Biointerfaces 2011; 88:539-51. [PMID: 21840689 DOI: 10.1016/j.colsurfb.2011.07.044] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/19/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
Abstract
The development of new enzyme immobilization techniques that do not affect catalytic activity or conformation of a protein is an important research task in biotechnology including biosensor applications and heterogeneous reaction systems. One of the most promising approaches for controlled protein immobilization is based on the immobilized metal ion affinity chromatography (IMAC) principle originally developed for protein purification. Here we describe the current status and future perspectives of immobilization of His-tagged proteins on electrode surfaces. Recombinant proteins comprising histidine-tags or histidine rich native proteins have a strong affinity to transition metal ions. For metal ion immobilization at the electrode surface different matrices can be used such as self-assembled monolayers or conductive polymers. This specific technique allows a reversible immobilization of histidine-tagged proteins at electrodes in a defined orientation which is an important prerequisite for efficient electron transfer between the electrode and the biomolecule. Any application requiring immobilized biocatalysts on electrodes can make use of this immobilization approach, making future biosensors and biocatalytic technologies more sensitive, simpler, reusable and less expensive while only requiring mild enzyme modifications.
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Affiliation(s)
- Claudia Ley
- Biochemical Engineering Group, Karl-Winnacker-Institut, DECHEMA e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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29
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Asghar W, Ilyas A, Deshmukh RR, Sumitsawan S, Timmons RB, Iqbal SM. Pulsed plasma polymerization for controlling shrinkage and surface composition of nanopores. NANOTECHNOLOGY 2011; 22:285304. [PMID: 21636880 DOI: 10.1088/0957-4484/22/28/285304] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.
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Affiliation(s)
- Waseem Asghar
- Department of Electrical Engineering, University of Texas at Arlington, TX 76011, USA
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30
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Recent progress in protein drug design and discovery with a focus on novel approaches to the development of anti-cocaine medications. Future Med Chem 2011; 1:515-28. [PMID: 20161378 DOI: 10.4155/fmc.09.20] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cocaine is highly addictive and no anti-cocaine medication is currently available. Accelerating cocaine metabolism, producing biologically inactive metabolites, is recognized as an ideal anti-cocaine medication strategy, especially for the treatment of acute cocaine toxicity. However, currently known wild-type enzymes have either too low a catalytic efficiency against the abused cocaine, in other words (-)-cocaine, or the in vivo half-life is too short. Novel computational strategies and design approaches have been developed recently to design and discover thermostable or high-activity mutants of enzymes based on detailed structures and catalytic/inactivation mechanisms. The structure- and mechanism-based computational design efforts have led to the discovery of high-activity mutants of butyrylcholinesterase and thermostable mutants of cocaine esterase as promising anti-cocaine therapeutics. The structure- and mechanism-based computational strategies and design approaches may be used to design high-activity and/or thermostable mutants of many other proteins that have clear therapeutic potentials and to design completely new therapeutic enzymes.
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31
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Sharabi O, Yanover C, Dekel A, Shifman JM. Optimizing energy functions for protein-protein interface design. J Comput Chem 2011; 32:23-32. [PMID: 20623647 DOI: 10.1002/jcc.21594] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.
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Affiliation(s)
- Oz Sharabi
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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32
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Yoon H, Ahn JH, Barone PW, Yum K, Sharma R, Boghossian AA, Han JH, Strano MS. Periplasmic Binding Proteins as Optical Modulators of Single-Walled Carbon Nanotube Fluorescence: Amplifying a Nanoscale Actuator. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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33
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Yoon H, Ahn JH, Barone PW, Yum K, Sharma R, Boghossian AA, Han JH, Strano MS. Periplasmic Binding Proteins as Optical Modulators of Single-Walled Carbon Nanotube Fluorescence: Amplifying a Nanoscale Actuator. Angew Chem Int Ed Engl 2011; 50:1828-31. [DOI: 10.1002/anie.201006167] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 12/13/2010] [Indexed: 02/05/2023]
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34
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Plaxco KW, Soh HT. Switch-based biosensors: a new approach towards real-time, in vivo molecular detection. Trends Biotechnol 2011; 29:1-5. [PMID: 21106266 PMCID: PMC3010506 DOI: 10.1016/j.tibtech.2010.10.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/18/2010] [Accepted: 10/25/2010] [Indexed: 01/21/2023]
Abstract
Although the ability to monitor specific molecules in vivo in real-time could revolutionize many aspects of healthcare, the technological challenges that stand in the way of reaching this goal are considerable and are poorly met by most existing analytical approaches. Nature, however, has already solved the problem of real-time molecular detection in complex media by employing biomolecular "switches". That is, protein and nucleic acids that sense chemical cues and, by undergoing specific, binding-induced conformational changes, transduce this recognition into high-gain signal outputs. Here, we argue that devices that employ such switches represent a promising route towards versatile, real-time molecular monitoring in vivo.
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Affiliation(s)
- Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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35
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Vallée-Bélisle A, Plaxco KW. Structure-switching biosensors: inspired by Nature. Curr Opin Struct Biol 2010; 20:518-26. [PMID: 20627702 DOI: 10.1016/j.sbi.2010.05.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/03/2010] [Accepted: 05/04/2010] [Indexed: 01/30/2023]
Abstract
Chemosensing in nature relies on biomolecular switches, biomolecules that undergo binding-induced changes in conformation or oligomerization to transduce chemical information into specific biochemical outputs. Motivated by the impressive performance of these natural 'biosensors,' which support continuous, real-time detection in highly complex environments, significant efforts have gone into the adaptation of such switches into artificial chemical sensors. Ongoing advances in the fields of protein and nucleic acid engineering (e.g. computational protein design, directed evolution, selection strategies and labeling chemistries) have greatly enhanced our ability to design new structure-switching sensors. Coupled with the development of advanced optical readout mechanisms, including genetically encoded fluorophores, and electrochemical readouts supporting detection directly in highly complex sample matrices, switch-based sensors have already seen deployment in applications ranging from real time, in vivo imaging to the continuous monitoring of drugs in blood serum.
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Affiliation(s)
- Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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36
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Siqueira JR, Caseli L, Crespilho FN, Zucolotto V, Oliveira ON. Immobilization of biomolecules on nanostructured films for biosensing. Biosens Bioelectron 2010; 25:1254-63. [DOI: 10.1016/j.bios.2009.09.043] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/14/2009] [Accepted: 09/30/2009] [Indexed: 01/18/2023]
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37
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Udit AK, Hollingsworth W, Choi K. Metal- and Metallocycle-Binding Sites Engineered into Polyvalent Virus-Like Scaffolds. Bioconjug Chem 2010; 21:399-404. [DOI: 10.1021/bc900399e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew K. Udit
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
| | - William Hollingsworth
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
| | - Kang Choi
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
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38
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Caruana DJ, Howorka S. Biosensors and biofuel cells with engineered proteins. MOLECULAR BIOSYSTEMS 2010; 6:1548-56. [DOI: 10.1039/c004951d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Kuiper JM, Pluta R, Huibers WHC, Fusetti F, Geertsma ER, Poolman B. A method for site-specific labeling of multiple protein thiols. Protein Sci 2009; 18:1033-41. [PMID: 19388048 DOI: 10.1002/pro.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a generic method for the site-specific and differential labeling of multiple cysteine residues in one protein. Phenyl arsenic oxide has been employed as a protecting group of two closely spaced thiols, allowing first labeling of a single thiol. Subsequently, the protecting group is removed, making available a reactive dithiol site for labeling with a second probe. For proof-of-principle, single and triple Cys mutants of the sulphate binding protein of an ABC transporter were constructed. The closely spaced thiols were engineered on the basis of the crystal structure of the protein and placed in different types of secondary structure elements and at different spacing. We show that phenyl arsenic oxide is a good protecting group for thiols spaced 6.3-7.3 A. Proteins were labeled with two different fluorescent labels and the labeling ratios were determined with UV-Vis spectroscopy and MALDI-Tof mass spectrometry. The average labeling efficiency was approximately 80% for the single thiol and 65-90% for the dithiol site.
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Affiliation(s)
- Johanna M Kuiper
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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40
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Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors. Proc Natl Acad Sci U S A 2009; 106:13802-7. [PMID: 19666496 DOI: 10.1073/pnas.0904005106] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding-induced biomolecular switches are used throughout nature and, increasingly, throughout biotechnology for the detection of chemical moieties and the subsequent transduction of this detection into useful outputs. Here we show that the thermodynamics of these switches are quantitatively described by a simple 3-state population-shift model, in which the equilibrium between a nonbinding, nonsignaling state and the binding-competent, signaling state is shifted toward the latter upon target binding. Because of this, their performance is determined by the tradeoff inherent to their switching thermodynamics; while a switching equilibrium constant favoring the nonbinding, nonsignaling, conformation ensures a larger signal change (more molecules are poised to respond), it also reduces affinity (binding must overcome a more unfavorable conformational free energy). We then derive and employ the relationship between switching thermodynamics and switch signaling to rationally tune the dynamic range and detection limit of a representative structure-switching biosensor, a molecular beacon, over 4 orders of magnitude. These findings demonstrate that the performance of biomolecular switches can be rationally tuned via mutations that alter their switching thermodynamics and suggest a mechanism by which the performance of naturally occurring switches may have evolved.
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41
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Udit AK, Brown S, Baksh MM, Finn M. Immobilization of bacteriophage Qβ on metal-derivatized surfaces via polyvalent display of hexahistidine tags. J Inorg Biochem 2008; 102:2142-6. [DOI: 10.1016/j.jinorgbio.2008.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Revised: 08/07/2008] [Accepted: 08/13/2008] [Indexed: 11/16/2022]
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42
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Goujon F, Bonal C, Limoges B, Malfreyt P. Molecular Dynamics Description of Grafted Monolayers: Effect of the Surface Coverage. J Phys Chem B 2008; 112:14221-9. [DOI: 10.1021/jp8028825] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Goujon
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - C. Bonal
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - B. Limoges
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - P. Malfreyt
- Laboratoire de Thermodynamique et Interactions Moléculaires de lʼUniversité Blaise Pascal (Clermont-Ferrand II), FRE 3099, 24 Avenue des Landais, 63177 Aubière Cedex, and Laboratoire dʼElectrochimie Moléculaire de lʼUniversité Denis Diderot (Paris 7), UMR CNRS 7591, 2 Place Jussieu, 75251 Paris Cedex 05, France
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43
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Balland V, Hureau C, Cusano AM, Liu Y, Tron T, Limoges B. Oriented immobilization of a fully active monolayer of histidine-tagged recombinant laccase on modified gold electrodes. Chemistry 2008; 14:7186-92. [PMID: 18600817 DOI: 10.1002/chem.200800368] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The formation of a dense monolayer of histidine-tagged recombinant laccase on gold electrodes by using a short thiol-NTA linker is described, as well as a kinetic analysis of the process by cyclic voltammetry. From a detailed analysis of the catalytic reduction of dioxygen by laccase in the presence of a one-electron redox mediator it can be concluded that the immobilized enzyme remains as active as in homogeneous solution.
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Affiliation(s)
- Véronique Balland
- Laboratoire d'Electrochimie Moléculaire, UMR CNRS 7591, Université Paris Diderot, 2 place Jussieu, Paris Cedex 05, France.
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44
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Hasegawa T, Hagihara M, Fukuda M, Nakano S, Fujieda N, Morii T. Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide. J Am Chem Soc 2008; 130:8804-12. [PMID: 18597435 DOI: 10.1021/ja801734f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.
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Affiliation(s)
- Tetsuya Hasegawa
- Institute of Advanced Energy, Institute of Sustainability Science, and Pioneering Research Unit for Next Generation, Kyoto University, Uji, Kyoto 611-0011, Japan
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45
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East AK, Mauchline TH, Poole PS. Biosensors for ligand detection. ADVANCES IN APPLIED MICROBIOLOGY 2008; 64:137-66. [PMID: 18485284 DOI: 10.1016/s0065-2164(08)00405-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alison K East
- Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom
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46
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47
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Chan PH, So PK, Ma DL, Zhao Y, Lai TS, Chung WH, Chan KC, Yiu KF, Chan HW, Siu FM, Tsang CW, Leung YC, Wong KY. Fluorophore-Labeled β-Lactamase as a Biosensor for β-Lactam Antibiotics: A Study of the Biosensing Process. J Am Chem Soc 2008; 130:6351-61. [DOI: 10.1021/ja076111g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pak-Ho Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Pui-Kin So
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Dik-Lung Ma
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Tat-Shing Lai
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Wai-Hong Chung
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Chu Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Ka-Fai Yiu
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Hoi-Wan Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Fung-Ming Siu
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Chun-Wai Tsang
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
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48
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Theegala CS, Small DD, Monroe WT. Oxygen electrode-based single antibody amperometric biosensor for qualitative detection of E. coli and bacteria in water. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2008; 43:478-487. [PMID: 18324534 DOI: 10.1080/10934520701796325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Design and performance of an amperometric biosensor for E. coli O157:H7 that is based on a common dissolved oxygen probe is discussed. Anti-E. coli O157:H7 antibody was conjugated to horseradish peroxidase and immobilized on a nitrocellulose membrane that was placed over the oxygen probe membrane using a custom-fabricated polyvinyl chloride (PVC) insert. Upon bacterial cell binding, a decrease in enzyme activity resulted in a change in oxygen concentration that was detected with a Clark-type oxygen electrode probe. Validation experiments determined the effect of the outer membrane and insert on the Clarke electrode performance and linearity, and the effects of stirring on sensor response. The mechanism of enzymatic disruption is presumably steric hindrance due to binding of the bacterial cell and conformational change in antibody structure. Sampling various dilutions of heat-sterilized E. coli O157:H7 cells in water, as little as 50 bacterial cells/mL could be detected in approximately 20 minutes of sampling and processing procedures. Bacterial concentrations from 0 to 5000 cells/mL were tested, with 2.52 mg/L +/- 0.37 mg/L equivalents of oxygen produced from as few as 50 cells/mL, versus 6.26 +/- 0.64 mg/L when no cells were present in solution. Overall, the developed amperometric biosensor technology offered an efficient means of detection primarily due to its ease of use, cost-effectiveness, portability, and amenability to incorporation at existing water quality gaging stations.
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Affiliation(s)
- Chandra S Theegala
- Department of Biological and Agricultural Engineering, Louisiana State University and LSU Agricultural Center, Baton Rouge, Louisiana, USA.
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49
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Der BS, Dattelbaum JD. Construction of a reagentless glucose biosensor using molecular exciton luminescence. Anal Biochem 2008; 375:132-40. [DOI: 10.1016/j.ab.2007.11.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 11/07/2007] [Indexed: 11/17/2022]
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50
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Jones LM, Yang W, Maniccia AW, Harrison A, van der Merwe PA, Yang JJ. Rational design of a novel calcium-binding site adjacent to the ligand-binding site on CD2 increases its CD48 affinity. Protein Sci 2008; 17:439-49. [PMID: 18287277 PMCID: PMC2248323 DOI: 10.1110/ps.073328208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 12/04/2007] [Accepted: 12/07/2007] [Indexed: 10/22/2022]
Abstract
Electrostatic interactions are important for molecular recognition processes including Ca2+-binding and cell adhesion. To understand these processes, we have successfully introduced a novel Ca2+-binding site into the non-Ca2+-dependent cell adhesion protein CD2 using our criteria that are specifically tailored to the structural and functional properties of the protein environment and charged adhesion surface. This designed site with ligand residues exclusively from the beta-sheets selectively binds to Ca2+ and Ln3+ over other mono- and divalent cations. While Ca2+ and Ln3+ binding specifically alters the local environment of the designed Ca2+-binding site, the designed protein undergoes a significantly smaller conformation change compared with those observed in naturally occurring Ca2+-binding sites that are composed of at least part of the flexible loop and helical regions. In addition, the CD2-CD48-binding affinity increased approximately threefold after protein engineering, suggesting that the cell adhesion of CD2 can be modulated by altering the local electrostatic environment. The study provides site-specific information for regulating cell adhesion within CD2 and gives insight into the structural factors required for Ca2+-modulated biological processes.
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Affiliation(s)
- Lisa M Jones
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, Georgia 30303, USA
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