1
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Berg A, Velayuthan LP, Tågerud S, Ušaj M, Månsson A. Probing actin-activated ATP turnover kinetics of human cardiac myosin II by single molecule fluorescence. Cytoskeleton (Hoboken) 2024. [PMID: 38623952 DOI: 10.1002/cm.21858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Mechanistic insights into myosin II energy transduction in striated muscle in health and disease would benefit from functional studies of a wide range of point-mutants. This approach is, however, hampered by the slow turnaround of myosin II expression that usually relies on adenoviruses for gene transfer. A recently developed virus-free method is more time effective but would yield too small amounts of myosin for standard biochemical analyses. However, if the fluorescent adenosine triphosphate (ATP) and single molecule (sm) total internal reflection fluorescence microscopy previously used to analyze basal ATP turnover by myosin alone, can be expanded to actin-activated ATP turnover, it would appreciably reduce the required amount of myosin. To that end, we here describe zero-length cross-linking of human cardiac myosin II motor fragments (sub-fragment 1 long [S1L]) to surface-immobilized actin filaments in a configuration with maintained actin-activated ATP turnover. After optimizing the analysis of sm fluorescence events, we show that the amount of myosin produced from C2C12 cells in one 60 mm cell culture plate is sufficient to obtain both the basal myosin ATP turnover rate and the maximum actin-activated rate constant (kcat). Our analysis of many single binding events of fluorescent ATP to many S1L motor fragments revealed processes reflecting basal and actin-activated ATPase, but also a third exponential process consistent with non-specific ATP-binding outside the active site.
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Affiliation(s)
- Albin Berg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Science, Linnaeus University, Kalmar, Sweden
| | - Lok Priya Velayuthan
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Science, Linnaeus University, Kalmar, Sweden
| | - Sven Tågerud
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Science, Linnaeus University, Kalmar, Sweden
| | - Marko Ušaj
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Science, Linnaeus University, Kalmar, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Science, Linnaeus University, Kalmar, Sweden
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2
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Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
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Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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3
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Yu J, Zhang Y, Zhao Y, Zhang X, Ren H. Highly Sensitive and Selective Detection of Inorganic Phosphates in the Water Environment by Biosensors Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2023; 95:4904-4913. [PMID: 36942460 DOI: 10.1021/acs.analchem.2c04748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The accurate detection of phosphate in water is very important to prevent water eutrophication and ensure the health of water quality. However, traditional phosphomolybdenum blue spectrophotometry is not sensitive, is time-consuming, and demands large amounts of chemical reagents. Therefore, highly sensitive, rapid, and environmentally friendly Pi detection methods are urgently needed. Here, we developed a bioluminescence resonance energy transfer (BRET)-based biosensor, which can detect Pi in water quickly, highly sensitively, and highly selectively. The NanoLuc and the Venus fluorescent protein were selected as the bioluminescence donor and energy acceptor, respectively. The best-performing BRET sensor variant, VenusΔC10-PΔC12-ΔN4Nluc, was identified by Pi-specific binding protein (PiBP) screening and systematic truncation. Single-factor experiments optimized the key parameters affecting the detection performance of the sensor. Under the optimal detection conditions, the detection limit of this method was 1.3 μg·L-1, the detection range was 3.3-434 μg·L-1, and it had excellent selectivity, repeatability, and stability. This low-cost and environment-friendly BRET sensor showed a good application prospect in real water quality detection.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yanping Zhao
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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4
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Smith DD, Girodat D, Abbott DW, Wieden HJ. Construction of a highly selective and sensitive carbohydrate-detecting biosensor utilizing Computational Identification of Non-disruptive Conjugation sites (CINC) for flexible and streamlined biosensor design. Biosens Bioelectron 2022; 200:113899. [PMID: 34974264 DOI: 10.1016/j.bios.2021.113899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/18/2021] [Accepted: 12/16/2021] [Indexed: 01/30/2023]
Abstract
Fluorescently-labeled solute-binding proteins that alter their fluorescence output in response to ligand binding have been utilized as biosensors for a variety of applications. Coupling protein ligand binding to altered fluorescence output often requires trial and error-based testing of both multiple labeling positions and fluorophores to produce a functional biosensor with the desired properties. This approach is laborious and can lead to reduced ligand binding affinity or altered ligand specificity. Here we report the Computational Identification of Non-disruptive Conjugation sites (CINC) for streamlined identification of fluorophore conjugation sites. By exploiting the structural dynamics properties of proteins, CINC identifies positions where conjugation of a fluorophore results in a fluorescence change upon ligand binding without disrupting protein function. We show that a CINC-developed maltooligosaccharide (MOS)-detecting biosensor is capable of rapid (kon = 20 μM-1s-1), sensitive (sub-μM KD) and selective MOS detection. The MOS-detecting biosensor is modular with respect to the spectroscopic properties and demonstrates portability to detecting MOS released via α-amylase-catalyzed depolymerization of starch using both a stopped-flow and a microplate reader assay. Our MOS-detecting biosensor represents a first-in-class probe whose design was guided by changes in localized dynamics of individual amino acid positions, supporting expansion of the CINC pipeline as an indispensable tool for a wide range of protein engineering applications.
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Affiliation(s)
- Dustin D Smith
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Dylan Girodat
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - D Wade Abbott
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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5
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Development of a Real-Time Pectic Oligosaccharide-Detecting Biosensor Using the Rapid and Flexible Computational Identification of Non-Disruptive Conjugation Sites (CINC) Biosensor Design Platform. SENSORS 2022; 22:s22030948. [PMID: 35161692 PMCID: PMC8839585 DOI: 10.3390/s22030948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/25/2023]
Abstract
Fluorescently labeled, solute-binding proteins that change their fluorescent output in response to ligand binding are frequently used as biosensors for a wide range of applications. We have previously developed a "Computational Identification of Non-disruptive Conjugation sites" (CINC) approach, an in silico pipeline utilizing molecular dynamics simulations for the rapid design and construction of novel protein-fluorophore conjugate-type biosensors. Here, we report an improved in silico scoring algorithm for use in CINC and its use in the construction of an oligogalacturonide-detecting biosensor set. Using both 4,5-unsaturated and saturated oligogalacturonides, we demonstrate that signal transmission from the ligand-binding pocket of the starting protein scaffold to the CINC-selected reporter positions is effective for multiple different ligands. The utility of an oligogalacturonide-detecting biosensor is shown in Carbohydrate Active Enzyme (CAZyme) activity assays, where the biosensor is used to follow product release upon polygalacturonic acid (PGA) depolymerization in real time. The oligogalacturonide-detecting biosensor set represents a novel enabling tool integral to our rapidly expanding platform for biosensor-based carbohydrate detection, and moving forward, the CINC pipeline will continue to enable the rational design of biomolecular tools to detect additional chemically distinct oligosaccharides and other solutes.
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6
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Bianco PR. Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays. Methods 2021; 204:348-360. [PMID: 34896247 PMCID: PMC9534331 DOI: 10.1016/j.ymeth.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
There are multiple assays available that can provide insight into the biochemical mechanism of DNA helicases. For the first 22 years since their discovery, bulk-phase assays were used. These include gel-based, spectrophotometric, and spectrofluorometric assays that revealed many facets of these enzymes. From 2001, single-molecule studies have contributed additional insight into these DNA nanomachines to reveal details on energy coupling, step size, processivity as well as unique aspects of individual enzyme behavior that were masked in the averaging inherent in ensemble studies. In this review, important aspects of the study of helicases are discussed including beginning with active, nuclease-free enzyme, followed by several bulk-phase approaches that have been developed and still find widespread use today. Finally, two single-molecule approaches are discussed, and the resulting findings are related to the results obtained in bulk-phase studies.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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7
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Measurement of Nucleotide Hydrolysis Using Fluorescent Biosensors for Phosphate. Methods Mol Biol 2021; 2263:289-318. [PMID: 33877604 DOI: 10.1007/978-1-0716-1197-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Assays for the detection of inorganic phosphate (Pi) are widely used to measure the activity of nucleotide hydrolyzing enzymes, such as ATPases and GTPases. The fluorescent biosensors for Pi, described here, are based on fluorescently labeled versions of E. coli phosphate-binding protein (PBP), which translates Pi binding into a large change in fluorescence intensity. In comparison with other Pi-detection systems, these biosensors are characterized by a high sensitivity (sub-micromolar Pi concentrations) and high time resolution (tens of milliseconds), and they are therefore particularly well suited for measurements of phosphate ester hydrolysis in real time. In this chapter, it is described how the Pi biosensors can be used to measure kinetics of ATPase and GTPase reactions, both under steady state and pre-steady state conditions. An example protocol is given for determining steady state kinetic parameters, Km and kcat, of the ATP-dependent chromatin remodeler Chd1, in a plate reader format. In addition, the measurement of Pi release kinetics under pre-steady state conditions is described, including a detailed experimental procedure for a single turnover measurement of ATP hydrolysis by the ABC-type ATPase SufBC using rapid mixing.
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8
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Franz P, Gassl V, Topf A, Eckelmann L, Iorga B, Tsiavaliaris G. A thermophoresis-based biosensor for real-time detection of inorganic phosphate during enzymatic reactions. Biosens Bioelectron 2020; 169:112616. [PMID: 32979591 DOI: 10.1016/j.bios.2020.112616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 01/07/2023]
Abstract
Inorganic phosphate (Pi)-sensing is a key application in many disciplines, and biosensors emerged as powerful analytic tools for use in environmental Pi monitoring, food quality control, basic research, and medical diagnosis. Current sensing techniques exploit either electrochemical or optical detection approaches for Pi quantification. Here, by combining the advantages of a biological Pi-receptor based on the bacterial phosphate binding protein with the principle of thermophoresis, i.e. the diffusional motion of particles in response to a temperature gradient, we developed a continuous, sensitive, and versatile method for detecting and quantifying free Pi in the subnanomolar to micromolar range in sample volumes ≤10 μL. By recording entropy-driven changes in the directed net diffusional flux of the Pi-sensor in a temperature gradient at defined time intervals, we validate the method for analyzing steady-state enzymatic reactions associated with Pi liberation in real-time for adenosine triphosphate (ATP) turnover by myosin, the actomyosin system and for insoluble, high molecular weight enzyme-protein assemblies in biopsy derived myofibrils. Particular features of the method are: (1) high Pi-sensitivity and selectivity, (2) uncoupling of the read-out signal from potential chemical and spectroscopic interferences, (3) minimal sample volumes and nanogram protein amounts, (4) possibility to run several experiments in parallel, and (5) straightforward data analysis. The present work establishes thermophoresis as powerful sensing method in microscale format for a wide range of applications, augmenting the current set of detection principles in biosensor technology.
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Affiliation(s)
- Peter Franz
- Cellular Biophysics, Institute for Biophysical Chemistry, OE 4350, Hannover Medical School, 30625, Hannover, Germany
| | - Vincent Gassl
- Cellular Biophysics, Institute for Biophysical Chemistry, OE 4350, Hannover Medical School, 30625, Hannover, Germany
| | - Andrea Topf
- Cellular Biophysics, Institute for Biophysical Chemistry, OE 4350, Hannover Medical School, 30625, Hannover, Germany
| | - Luca Eckelmann
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Bogdan Iorga
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany; Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
| | - Georgios Tsiavaliaris
- Cellular Biophysics, Institute for Biophysical Chemistry, OE 4350, Hannover Medical School, 30625, Hannover, Germany.
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9
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Structural and kinetic basis for the regulation and potentiation of Hsp104 function. Proc Natl Acad Sci U S A 2020; 117:9384-9392. [PMID: 32277033 DOI: 10.1073/pnas.1921968117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Hsp104 provides a valuable model for the many essential proteostatic functions performed by the AAA+ superfamily of protein molecular machines. We developed and used a powerful hydrogen exchange mass spectrometry (HX MS) analysis that can provide positionally resolved information on structure, dynamics, and energetics of the Hsp104 molecular machinery, even during functional cycling. HX MS reveals that the ATPase cycle is rate-limited by ADP release from nucleotide-binding domain 1 (NBD1). The middle domain (MD) serves to regulate Hsp104 activity by slowing ADP release. Mutational potentiation accelerates ADP release, thereby increasing ATPase activity. It reduces time in the open state, thereby decreasing substrate protein loss. During active cycling, Hsp104 transits repeatedly between whole hexamer closed and open states. Under diverse conditions, the shift of open/closed balance can lead to premature substrate loss, normal processing, or the generation of a strong pulling force. HX MS exposes the mechanisms of these functions at near-residue resolution.
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10
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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Li Z, Wang W, Jian H, Li W, Dai B, He L. Synthesis of 9-phenol-substituted xanthenes by cascade O-insertion/1,6-conjugate addition of benzyne with ortho-hydroxyphenyl substituted para-quinone methides. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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12
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Donaphon B, Bloom LB, Levitus M. Photophysical characterization of interchromophoric interactions between rhodamine dyes conjugated to proteins. Methods Appl Fluoresc 2018; 6:045004. [PMID: 29985159 DOI: 10.1088/2050-6120/aad20f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rhodamine dyes in aqueous solution form non-fluorescent dimers with a plane-to-plane stacking geometry (H-dimers). The self-quenching properties of these dimers have been exploited to probe the conformation and dynamics of proteins using a variety of fluorescence approaches that require the interpretation of fluorescence intensities, lifetimes and fluctuations. Here, we report on a systematic study of the photophysical properties of three rhodamine dyes (tetramethylrhodamine, Alexa 488 and Alexa 546) covalently bound to the E. coli sliding clamp (β clamp) with emphasis on the properties of the H-dimers that form when the dimeric protein is labeled with one dye at each side of the dimer interface. Overall, results are consistent with an equilibrium between non-emissive dimers and unstacked monomers that experience efficient dynamic quenching Protein constructs labeled with tetramethylrhodamine show the characteristic features of H-dimers in their absorption spectra and a c.a. 40-fold quenching of fluorescence intensity. The degree of quenching decreases when samples are labeled with a tetramethylrhodamine derivative bearing a six-carbon linker. H-dimers do not form in samples labeled with Alexa 488 and A546, but fluorescence is still quenched in these samples through a dynamic mechanism. These results should help researchers design and interpret fluorescence experiments that take advantage of the properties of rhodamine dimers in protein research.
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Affiliation(s)
- Bryan Donaphon
- School of Molecular Sciences and Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States of America
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13
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Streamlined purification of fluorescently labeled Escherichia coli phosphate-binding protein (PhoS) suitable for rapid-kinetics applications. Anal Biochem 2017; 537:106-113. [PMID: 28941789 DOI: 10.1016/j.ab.2017.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 11/20/2022]
Abstract
Fluorescently labeled phosphate-binding proteins can be used as biomolecular tools to measure the release of inorganic phosphate (Pi) from enzymes in real time, enabling the detailed kinetic analysis of dephosphorylating enzymes using rapid-kinetics approaches. Previously reported methods to purify fluorescently labeled phosphate-binding proteins (PhoS) from Escherichia coli are laborious, and a simplified approach is needed. Here, we report the characterization of a cytosol-localized variant (A197C) of PhoS that allows a streamlined purification for subsequent covalent conjugation with a fluorescent dye. We show that export of PhoS into the periplasmic space is not required for the fluorescence-based detection of Pi binding. Furthermore, we report the addition of a C-terminal His-tag, simplifying the purification of PhoS from the cytosol via Ni2+-affinity chromatography, yielding a fully functional fusion protein (HC PhoS A197C). We demonstrate the utility of fluorescently labeled HC PhoS A197C for rapid-kinetics applications by measuring, using stopped-flow, the Pi release kinetics from LepA/EF4 following 70S ribosome-stimulated GTP hydrolysis. Altogether, the approach developed here allows for the high-yield and simplified in-house production of a Pi detection system suitable for rapid-kinetics approaches with comparable sensitivity to the commercially available Phosphate Sensor.
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14
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Vancraenenbroeck R, Kunzelmann S, Webb MR. Development of a range of fluorescent reagentless biosensors for ATP, based on malonyl-coenzyme A synthetase. PLoS One 2017; 12:e0179547. [PMID: 28636641 PMCID: PMC5479551 DOI: 10.1371/journal.pone.0179547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
The range of ATP concentrations that can be measured with a fluorescent reagentless biosensor for ATP has been increased by modulating its affinity for this analyte. The ATP biosensor is an adduct of two tetramethylrhodamines with MatB from Rhodopseudomonas palustris. Mutations were introduced into the binding site to modify ATP binding affinity, while aiming to maintain the concomitant fluorescence signal. Using this signal, the effect of mutations in different parts of the binding site was measured. This mutational analysis revealed three variants in particular, each with a single mutation in the phosphate-binding loop, which had potentially beneficial changes in ATP binding properties but preserving a fluorescence change of ~3-fold on ATP binding. Two variants (T167A and T303A) weakened the binding, changing the dissociation constant from the parent's 6 μM to 123 μM and 42 μM, respectively. Kinetic measurements showed that the effect of these mutations on affinity was by an increase in dissociation rate constants. These variants widen the range of ATP concentration that can be measured readily by this biosensor to >100 μM. In contrast, a third variant, S170A, decreased the dissociation constant of ATP to 3.8 μM and has a fluorescence change of 4.2 on binding ATP. This variant has increased selectivity for ATP over ADP of >200-fold. This had advantages over the parent by increasing sensitivity as well as increasing selectivity during ATP measurements in which ADP is present.
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Affiliation(s)
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
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15
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Jian H, Liu K, Wang WH, Li ZJ, Dai B, He L. Construction of 9-functionalized xanthenes via Diels-Alder reaction of stable ortho-quinone methides and arynes. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Patra C, Bhanja AK, Sen C, Ojha D, Chattopadhyay D, Mahapatra A, Sinha C. Imine-functionalized thioether Zn(ii) turn-on fluorescent sensor and its selective sequential logic operations with H2PO4−, DFT computation and live cell imaging. RSC Adv 2016. [DOI: 10.1039/c6ra07089b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Thioether Schiff base (H2L), a nontoxic Zn2+-sensor (LOD, 0.050 μM) has shown selective ON–OFF emission following INHIBIT logic circuit with H2PO4−and useful agent for the identification of Zn2+and H2PO4−in intracellular fluid in living cells.
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Affiliation(s)
- Chiranjit Patra
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | | | - Chandana Sen
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Durbadal Ojha
- ICMR Virus Unit
- Infectious Diseases & Beliaghata General Hospital
- Kolkata-700 010
- India
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17
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Vancraenenbroeck R, Webb MR. A Fluorescent, Reagentless Biosensor for ATP, Based on Malonyl-Coenzyme A Synthetase. ACS Chem Biol 2015; 10:2650-7. [PMID: 26355992 PMCID: PMC4655421 DOI: 10.1021/acschembio.5b00346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
A fluorescent reagentless biosensor
for ATP has been developed,
based on malonyl-coenzyme A synthetase from Rhodopseudomonas
palustris as the protein scaffold and recognition element.
Two 5-iodoacetamidotetramethylrhodamines were covalently bound to
this protein to provide the readout. This adduct couples ATP binding
to a 3.7-fold increase in fluorescence intensity with excitation at
553 nm and emission at 575 nm. It measures ATP concentrations with
micromolar sensitivity and is highly selective for ATP relative to
ADP. Its ability to monitor enzymatic ATP production or depletion
was demonstrated in steady-state kinetic assays in which ATP is a
product or substrate, respectively.
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Affiliation(s)
- Renée Vancraenenbroeck
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Martin R. Webb
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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18
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Solscheid C, Kunzelmann S, Davis C, Hunter JL, Nofer A, Webb MR. Development of a Reagentless Biosensor for Inorganic Phosphate, Applicable over a Wide Concentration Range. Biochemistry 2015; 54:5054-62. [PMID: 26199994 PMCID: PMC4741387 DOI: 10.1021/acs.biochem.5b00449] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/22/2015] [Indexed: 11/30/2022]
Abstract
A fluorescent reagentless biosensor for inorganic phosphate (Pi), based on the E. coli PstS phosphate binding protein, was redesigned to allow measurements of higher Pi concentrations and at low, substoichiometric concentrations of biosensor. This was achieved by weakening Pi binding of the previous biosensor, and different approaches are described that could enable this change in properties. The readout, providing response to the Pi concentration, is delivered by tetramethylrhodamine fluorescence. In addition to two cysteine mutations for rhodamine labeling at positions 17 and 197, the final variant had an I76G mutation in the hinge region between the two lobes that make up the protein. Upon Pi binding, the lobes rotate on this hinge and the mutation on the hinge lowers affinity ∼200-fold, with a dissociation constant now in the tens to hundreds micromolar range, depending on solution conditions. The signal change on Pi binding was up to 9-fold, depending on pH. The suitability of the biosensor for steady-state ATPase assays was demonstrated with low biosensor usage and its advantage in ability to cope with Pi contamination.
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Affiliation(s)
- Claudia Solscheid
- The Francis Crick
Institute, Mill Hill Laboratory, The
Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Simone Kunzelmann
- The Francis Crick
Institute, Mill Hill Laboratory, The
Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Colin
T. Davis
- The Francis Crick
Institute, Mill Hill Laboratory, The
Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Jackie L. Hunter
- MRC National Institute
for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Annie Nofer
- MRC National Institute
for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Martin R. Webb
- The Francis Crick
Institute, Mill Hill Laboratory, The
Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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19
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Recent advances in phosphate biosensors. Biotechnol Lett 2015; 37:1335-45. [DOI: 10.1007/s10529-015-1823-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
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20
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Duan XL, Liu NN, Yang YT, Li HH, Li M, Dou SX, Xi XG. G-quadruplexes significantly stimulate Pif1 helicase-catalyzed duplex DNA unwinding. J Biol Chem 2015; 290:7722-35. [PMID: 25627683 DOI: 10.1074/jbc.m114.628008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation. Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures. Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability. Cells have evolved highly specific helicases to resolve G4 structures. We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation. We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA. Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding. This finding provides new insights into the properties and functions of G4s. We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation.
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Affiliation(s)
- Xiao-Lei Duan
- From the College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- From the College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yan-Tao Yang
- From the College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Hai-Hong Li
- From the College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Ming Li
- the CAS Key Laboratory of Soft Matter Physics, International Associated Laboratory of CNRS-Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China, and
| | - Shuo-Xing Dou
- the CAS Key Laboratory of Soft Matter Physics, International Associated Laboratory of CNRS-Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China, and
| | - Xu-Guang Xi
- From the College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China, the Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, CNRS, 61 Avenue du Président Wilson, 94235 Cachan, France
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21
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Toseland CP. Fluorescence to study the ATPase mechanism of motor proteins. ACTA ACUST UNITED AC 2014; 105:67-86. [PMID: 25095991 DOI: 10.1007/978-3-0348-0856-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This chapter provides an overview of different methodologies to dissect the ATPase mechanism of motor proteins. The use of ATP is fundamental to how these molecular engines work and how they can use the energy to perform various cellular roles. Rapid reaction and single-molecule techniques will be discussed to monitor reactions in real time through the application of fluorescence intensity, anisotropy and FRET. These approaches utilise fluorescent nucleotides and biosensors. While not every technique may be suitable for your motor protein, the different ways to determine the ATPase mechanism should allow a good evaluation of the kinetic parameters.
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Affiliation(s)
- Christopher P Toseland
- Chromosome Organisation and Dynamics, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany,
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22
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Mukherjea M, Ali MY, Kikuti C, Safer D, Yang Z, Sirkia H, Ropars V, Houdusse A, Warshaw DM, Sweeney HL. Myosin VI must dimerize and deploy its unusual lever arm in order to perform its cellular roles. Cell Rep 2014; 8:1522-32. [PMID: 25159143 DOI: 10.1016/j.celrep.2014.07.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/13/2014] [Accepted: 07/22/2014] [Indexed: 12/21/2022] Open
Abstract
It is unclear whether the reverse-direction myosin (myosin VI) functions as a monomer or dimer in cells and how it generates large movements on actin. We deleted a stable, single-α-helix (SAH) domain that has been proposed to function as part of a lever arm to amplify movements without impact on in vitro movement or in vivo functions. A myosin VI construct that used this SAH domain as part of its lever arm was able to take large steps in vitro but did not rescue in vivo functions. It was necessary for myosin VI to internally dimerize, triggering unfolding of a three-helix bundle and calmodulin binding in order to step normally in vitro and rescue endocytosis and Golgi morphology in myosin VI-null fibroblasts. A model for myosin VI emerges in which cargo binding triggers dimerization and unfolds the three-helix bundle to create a lever arm essential for in vivo functions.
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Affiliation(s)
- Monalisa Mukherjea
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, 415 Curie Boulevard, 700 CRB, Philadelphia, PA 19104-6085, USA
| | - M Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405, USA
| | - Carlos Kikuti
- Structural Motility, Centre de Recherche, Institut Curie, 75248 Paris, France; CNRS, UMR144, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Daniel Safer
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, 415 Curie Boulevard, 700 CRB, Philadelphia, PA 19104-6085, USA
| | - Zhaohui Yang
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, 415 Curie Boulevard, 700 CRB, Philadelphia, PA 19104-6085, USA
| | - Helena Sirkia
- Structural Motility, Centre de Recherche, Institut Curie, 75248 Paris, France; CNRS, UMR144, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Virginie Ropars
- Structural Motility, Centre de Recherche, Institut Curie, 75248 Paris, France; CNRS, UMR144, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Anne Houdusse
- Structural Motility, Centre de Recherche, Institut Curie, 75248 Paris, France; CNRS, UMR144, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - David M Warshaw
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405, USA
| | - H Lee Sweeney
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, 415 Curie Boulevard, 700 CRB, Philadelphia, PA 19104-6085, USA.
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23
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Biochemical and antiparasitic properties of inhibitors of the Plasmodium falciparum calcium-dependent protein kinase PfCDPK1. Antimicrob Agents Chemother 2014; 58:6032-43. [PMID: 25070106 PMCID: PMC4187893 DOI: 10.1128/aac.02959-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PfCDPK1 is a Plasmodium falciparum calcium-dependent protein kinase, which has been identified as a potential target for novel antimalarial chemotherapeutics. In order to further investigate the role of PfCDPK1, we established a high-throughput in vitro biochemical assay and used it to screen a library of over 35,000 small molecules. Five chemical series of inhibitors were initially identified from the screen, from which series 1 and 2 were selected for chemical optimization. Indicative of their mechanism of action, enzyme inhibition by these compounds was found to be sensitive to both the ATP concentration and substitution of the amino acid residue present at the “gatekeeper” position at the ATP-binding site of the enzyme. Medicinal chemistry efforts led to a series of PfCDPK1 inhibitors with 50% inhibitory concentrations (IC50s) below 10 nM against PfCDPK1 in a biochemical assay and 50% effective concentrations (EC50s) less than 100 nM for inhibition of parasite growth in vitro. Potent inhibition was combined with acceptable absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties and equipotent inhibition of Plasmodium vivax CDPK1. However, we were unable to correlate biochemical inhibition with parasite growth inhibition for this series overall. Inhibition of Plasmodium berghei CDPK1 correlated well with PfCDPK1 inhibition, enabling progression of a set of compounds to in vivo evaluation in the P. berghei rodent model for malaria. These chemical series have potential for further development as inhibitors of CDPK1.
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24
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Fluorescent biosensors: design and application to motor proteins. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:25-47. [PMID: 25095989 DOI: 10.1007/978-3-0348-0856-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reagentless biosensors are single molecular species that report the concentration of a specific target analyte, while having minimal impact on the system being studied. This chapter reviews such biosensors with emphasis on the ones that use fluorescence as readout and can be used for real-time assays of concentration changes with reasonably high time resolution and sensitivity. Reagentless biosensors can be designed with different types of recognition elements, particularly specific binding proteins and nucleic acids, including aptamers. Different ways are described in which a fluorescence signal can be used to report the target concentration. These include the use of single, environmentally sensitive fluorophores; FRET pairs, often used in genetically encoded biosensors; and pairs of identical fluorophores that undergo reversible stacking interactions to change fluorescence intensity. The applications of these biosensors in different types of real-time assays with motor proteins are described together with some specific examples. These encompass regulation and mechanism of motor proteins, using both steady-state assays and single-turnover measurements.
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25
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Deacon LJ, Billones H, Galyean AA, Donaldson T, Pennacchio A, Iozzino L, D'Auria S, Dattelbaum JD. Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein. Biochimie 2013; 99:208-14. [PMID: 24370478 DOI: 10.1016/j.biochi.2013.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
The Thermotoga maritima arginine binding protein (TmArgBP) is a member of the periplasmic binding protein superfamily. As a highly thermostable protein, TmArgBP has been investigated for the potential to serve as a protein scaffold for the development of fluorescent protein biosensors. To establish a relationship between structural dynamics and ligand binding capabilities, we constructed single tryptophan mutants to probe the arginine binding pocket. Trp residues placed around the binding pocket reveal a strong dependence on fluorescence emission of the protein with arginine for all but one of the mutants. Using these data, we calculated dissociation constants of 1.9-3.3 μM for arginine. Stern-Volmer quenching analysis demonstrated that the protein undergoes a large conformational change upon ligand binding, which is a common feature of this protein superfamily. While still active at room temperature, time-resolved intensity and anisotropy decay data suggest that the protein exists as a highly rigid structure under these conditions. Interestingly, TmArgBP exists as a dimer at room temperature in both the presence and absence of arginine, as determined by asymmetric flow field flow fractionation (AF4) and supported by native gel-electrophoresis and time-resolved anisotropy. Our data on dynamics and stability will contribute to our understanding of hyperthermophilic proteins and their potential biotechnological applications.
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Affiliation(s)
- Lindsay J Deacon
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Hilbert Billones
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anne A Galyean
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Teraya Donaldson
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA
| | - Anna Pennacchio
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Luisa Iozzino
- Department of Chemistry, University of Richmond, Richmond, VA 23173, USA; Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
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26
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Ozyurt C, Evran S, Telefoncu A. Development of a novel fluorescent protein construct by genetically fusing green fluorescent protein to the N-terminal of aspartate dehydrogenase. Biotechnol Appl Biochem 2013; 60:399-404. [PMID: 24033594 DOI: 10.1002/bab.1107] [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: 10/16/2012] [Accepted: 02/06/2013] [Indexed: 11/11/2022]
Abstract
We developed a fluorescent protein construct by genetically fusing green fluorescent protein (GFP) to aspartate dehydrogenase from Thermotoga maritima. The fusion protein was cloned, heterologously expressed in Escherichia coli cells, and purified by Ni-chelate affinity chromatography. It was then introduced into a measurement cuvette to monitor its fluorescence signal. Aspartate dehydrogenase functioned as the biorecognition element, and aspartate-induced conformational change was converted to a fluorescence signal by GFP. The recombinant protein responded to l-aspartate (l-Asp) linearly within the concentration range of 1-50 mM, and it was capable of giving a fluorescence signal in 1 Min. Although a linear response was also observed for l-Glu, the fluorescence signal was 2.7 times lower than that observed for l-Asp. In the present study, we describe two novelties: development of a genetically encoded fluorescent protein construct for monitoring of l-Asp in vitro, and employment of aspartate dehydrogenase scaffold as a biorecognition element. A few genetically encoded amino-acid biosensors have been described in the literature, but to our knowledge, a protein has not been constructed solely for determination of l-Asp. Periplasmic ligand binding proteins offer high binding affinity in the micromolar range, and they are frequently used as biorecognition elements. Instead of choosing a periplasmic l-Asp binding protein, we attempted to use the substrate specificity of aspartate dehydrogenase enzyme.
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Affiliation(s)
- Canan Ozyurt
- Department of Biochemistry, Faculty of Science, Ege University, Izmir, Turkey
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27
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Progress and recent advances in phosphate sensors: A review. Talanta 2013; 114:191-203. [DOI: 10.1016/j.talanta.2013.03.031] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/25/2022]
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28
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Toseland CP, Webb MR. ATPase mechanism of the 5'-3' DNA helicase, RecD2: evidence for a pre-hydrolysis conformation change. J Biol Chem 2013; 288:25183-25193. [PMID: 23839989 PMCID: PMC3757182 DOI: 10.1074/jbc.m113.484667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The superfamily 1 helicase, RecD2, is a monomeric, bacterial enzyme with a role in DNA repair, but with 5′-3′ activity unlike most enzymes from this superfamily. Rate constants were determined for steps within the ATPase cycle of RecD2 in the presence of ssDNA. The fluorescent ATP analog, mantATP (2′(3′)-O-(N-methylanthraniloyl)ATP), was used throughout to provide a complete set of rate constants and determine the mechanism of the cycle for a single nucleotide species. Fluorescence stopped-flow measurements were used to determine rate constants for adenosine nucleotide binding and release, quenched-flow measurements were used for the hydrolytic cleavage step, and the fluorescent phosphate biosensor was used for phosphate release kinetics. Some rate constants could also be measured using the natural substrate, ATP, and these suggested a similar mechanism to that obtained with mantATP. The data show that a rearrangement linked to Mg2+ coordination, which occurs before the hydrolysis step, is rate-limiting in the cycle and that this step is greatly accelerated by bound DNA. This is also shown here for the PcrA 3′-5′ helicase and so may be a general mechanism governing superfamily 1 helicases. The mechanism accounts for the tight coupling between translocation and ATPase activity.
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Affiliation(s)
- Christopher P Toseland
- From the MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom and; Institut für Zelluläre Physiologie and Center for NanoScience, Physiologisches Institut, Ludwig Maximilians Universität, Munich 80336, Germany
| | - Martin R Webb
- From the MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom and.
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29
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Abstract
Noncovalently "stacked" tetramethylrhodamine (TMR) dimers have been used to both report and perturb the allosteric equilibrium in GroEL. A GroEL mutant (K242C) has been labeled with TMR, close to the peptide-binding site in the apical domain, such that TMR molecules on adjacent subunits are able to form dimers in the T allosteric state. Addition of ATP induces the transition to the R state and the separation of the peptide-binding sites, with concomitant unstacking of the TMR dimers. A statistical analysis of the spectra allowed us to compute the number and orientation of TMR dimers per ring as a function of the average number of TMR molecules per ring. The TMR dimers thus serve as quantitative reporter of the allosteric state of the system. The TMR dimers also serve as a surrogate for substrate protein, substituting in a more homogeneous, quantifiable manner for the heterogeneous intersubunit, intraring, noncovalent cross-links provided by the substrate protein. The characteristic stimulation of the ATPase activity by substrate protein is also mimicked by the TMR dimers. Using an expanded version of the nested cooperativity model, we determine values for the free energy of the TT to TR and TR to RR allosteric equilibria to be 27 ± 11 and 46 ± 2 kJ/mol, respectively. The free energy of unstacking of the TMR dimers was estimated at 2.6 ± 1.0 kJ/mol dimer. These results demonstrate that GroEL can perform work during the T to R transition, supporting the iterative annealing model of chaperonin function.
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30
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Wan Y, Zhang XX, Wang C, Zhao LL, Chen LF, Liu GX, Huang SY, Yue SN, Zhang WL, Wu H. The first example of glucose-containing Brønsted acid synthesis and catalysis: efficient synthesis of tetrahydrobenzo[α]xanthens and tetrahydrobenzo[α]acridines in water. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Lawal AT, Adeloju SB. Polypyrrole based amperometric and potentiometric phosphate biosensors: A comparative study B. Biosens Bioelectron 2013; 40:377-84. [DOI: 10.1016/j.bios.2012.08.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 08/03/2012] [Accepted: 08/07/2012] [Indexed: 10/28/2022]
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32
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Abstract
Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.
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Affiliation(s)
- Peter N Lowe
- Biomolecular Interactions Consultancy, Hertford, UK
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33
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Gonçalves MB, Dreyer J, Lupieri P, Barrera-Patiño C, Ippoliti E, Webb MR, Corrie JET, Carloni P. Structural prediction of a rhodamine-based biosensor and comparison with biophysical data. Phys Chem Chem Phys 2013; 15:2177-83. [DOI: 10.1039/c2cp42396k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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34
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Time-dependent, reversible, oxaborole inhibition of Escherichia coli leucyl-tRNA synthetase measured with a continuous fluorescence assay. Anal Biochem 2012; 431:48-53. [DOI: 10.1016/j.ab.2012.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022]
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35
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Abstract
Helicases are an important and much studied group of enzymes that generally couple ATP hydrolysis to the separation of strands of base-paired nucleic acids. Studying their biochemistry at different levels of organization requires assays that measure the progress of the reaction in different ways. One such method makes use of the single-stranded DNA-binding protein (SSB) from Escherichia coli. This is used as a protein framework to produce a "reagentless biosensor," making use of its tight and specific binding of single-stranded DNA. The attachment of a fluorophore to this protein produces a signal in response to that binding. Thus the (G26C)SSB, labeled with a diethylaminocoumarin, gives a ~5-fold fluorescence increase on binding to single-stranded DNA and this can be used to assay the progress of helicase action along double-stranded DNA. A protocol for this is described along with a variant that can be used to follow the unwinding on a single molecule scale.
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36
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Zhou R, Kunzelmann S, Webb MR, Ha T. Detecting intramolecular conformational dynamics of single molecules in short distance range with subnanometer sensitivity. NANO LETTERS 2011; 11:5482-8. [PMID: 22023515 PMCID: PMC3237907 DOI: 10.1021/nl2032876] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single molecule detection is useful for characterizing nanoscale objects such as biological macromolecules, nanoparticles and nanodevices with nanometer spatial resolution. Fluorescence resonance energy transfer (FRET) is widely used as a single-molecule assay to monitor intramolecular dynamics in the distance range of 3-8 nm. Here we demonstrate that self-quenching of two rhodamine derivatives can be used to detect small conformational dynamics corresponding to subnanometer distance changes in a FRET-insensitive short-range at the single molecule level. A ParM protein mutant labeled with two rhodamines works as a single molecule adenosine 5'-diphosphate (ADP) sensor that has 20 times brighter fluorescence signal in the ADP bound state than the unbound state. Single molecule time trajectories show discrete transitions between fluorescence on and off states that can be directly ascribed to ADP binding and dissociation events. The conformational changes observed with 20:1 contrast are only 0.5 nm in magnitude and are between crystallographic distances of 1.6 and 2.1 nm, demonstrating exquisite sensitivity to short distance scale changes. The systems also allowed us to gain information on the photophysics of self-quenching induced by rhodamine stacking: (1) photobleaching of either of the two rhodamines eliminates quenching of the other rhodamine fluorophore and (2) photobleaching from the highly quenched, stacked state is only 2-fold slower than from the unstacked state.
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Affiliation(s)
- Ruobo Zhou
- Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Illinois 61801, United States
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Shapiro AB, Livchak S, Gao N, Whiteaker J, Thresher J, Jahić H, Huang J, Gu RF. A homogeneous, high-throughput-compatible, fluorescence intensity-based assay for UDP-N-acetylenolpyruvylglucosamine reductase (MurB) with nanomolar product detection. ACTA ACUST UNITED AC 2011; 17:327-38. [PMID: 22068704 DOI: 10.1177/1087057111425188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A novel assay for the NADPH-dependent bacterial enzyme UDP-N-acetylenolpyruvylglucosamine reductase (MurB) is described that has nanomolar sensitivity for product formation and is suitable for high-throughput applications. MurB catalyzes an essential cytoplasmic step in the synthesis of peptidoglycan for the bacterial cell wall, reduction of UDP-N-acetylenolpyruvylglucosamine to UDP-N-acetylmuramic acid (UNAM). Interruption of this biosynthetic pathway leads to cell death, making MurB an attractive target for antibacterial drug discovery. In the new assay, the UNAM product of the MurB reaction is ligated to L-alanine by the next enzyme in the peptidoglycan biosynthesis pathway, MurC, resulting in hydrolysis of adenosine triphosphate (ATP) to adenosine diphosphate (ADP). The ADP is detected with nanomolar sensitivity by converting it to oligomeric RNA with polynucleotide phosphorylase and detecting the oligomeric RNA with a fluorescent dye. The product sensitivity of the new assay is 1000-fold greater than that of the standard assay that follows the absorbance decrease resulting from the conversion of NADPH to NADP(+). This sensitivity allows inhibitor screening to be performed at the low substrate concentrations needed to make the assay sensitive to competitive inhibition of MurB.
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Affiliation(s)
- Adam B Shapiro
- Bioscience Department, Infection Innovative Medicines, AstraZeneca R&D Boston, Waltham, MA 02451, USA.
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Ho CL, Koh SL, Chuah MLC, Luo Z, Tan WJ, Low DKS, Liang ZX. Rational design of fluorescent biosensor for cyclic di-GMP. Chembiochem 2011; 12:2753-8. [PMID: 22021215 DOI: 10.1002/cbic.201100557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 01/19/2023]
Abstract
Messenger bagged: The design of a fluorophore-labeled protein biosensor for the bacterial messenger cyclic di-GMP is described. The biosensor responds to c-di-GMP with sub-micromolar sensitivity in a real-time fashion. The biosensor can be used for enzyme assays for diguanylate cyclases and c-di-GMP phosphodiesterases as well as the high-throughput screening of inhibitors.
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Affiliation(s)
- Chun Loong Ho
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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Chang CC, Cheng SF, Lin CH, Chen SSL, Chang DK. Stability of gp41 hairpin and helix bundle assembly probed by combined stacking and circular dichroic approaches. J Struct Biol 2011; 175:406-14. [DOI: 10.1016/j.jsb.2011.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/17/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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Fabrication of a bilayer potentiometric phosphate biosensor by cross-link immobilization with bovine serum albumin and glutaraldehyde. Anal Chim Acta 2011; 691:89-94. [DOI: 10.1016/j.aca.2011.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/31/2011] [Accepted: 02/07/2011] [Indexed: 11/30/2022]
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Shapiro AB, Gao N, Thresher J, Walkup GK, Whiteaker J. A high-throughput absorbance-based assay for methionine produced by methionine aminopeptidase using S-adenosyl-L-methionine synthetase. ACTA ACUST UNITED AC 2011; 16:494-505. [PMID: 21402755 DOI: 10.1177/1087057111398934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methionine aminopeptidase (MAP) (E.C. 3.4.11.18) is a metallopeptidase that cleaves the N-terminal methionine (Met) residue from some proteins. MAP is essential for growth of several bacterial pathogens, making it a target for antibacterial drug discovery. MAP enzymes are also present in eukaryotic cells, and one is a target for antiangiogenic cancer therapy. To screen large compound libraries for MAP inhibitors as the starting point for drug discovery, a high-throughput-compatible assay is valuable. Here the authors describe a novel assay, which detects the Met product of MAP-catalyzed peptide cleavage by coupling it to adenosine triphosphate (ATP)-dependent production of S-adenosyl-L-methionine (SAM) and inorganic phosphate (P(i)) by SAM synthetase (MetK) combined with inorganic pyrophosphatase. The three P(i) ions produced for each Met consumed are detected using Malachite Green/molybdate reagent. This assay can use any unmodified peptide MAP substrate with an N-terminal Met. The assay was used to measure kinetic constants for Escherichia coli MAP using Mn(2+) as the activator and the peptide Met-Gly-Met-Met as the substrate, as well as to measure the potency of a MAP inhibitor. A Mn(2+) buffer is described that can be used to prevent free Mn(2+) depletion by chelating compounds from interfering in screens for MAP inhibitors.
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Abstract
The interconversion of nucleoside triphosphate (NTP) and diphosphate occurs in some of the most -important cellular reactions. It is catalyzed by diverse classes of enzymes, such as nucleoside triphosphatases, kinases, and ATP synthases. Triphosphatases include helicases, myosins, and G-proteins, as well as many other energy-transducing enzymes. The transfer of phosphate by kinases is involved in many metabolic pathways and in control of enzyme activity through protein phosphorylation. To understand the processes catalyzed by these enzymes, it is important to measure the kinetics of individual elementary steps and conformation changes. Fluorescent nucleotides can directly report on the binding and release steps, and conformational changes associated with these processes. In single-molecule studies, fluorescent nucleotides can allow their role to be explored by following precisely the temporal and spatial changes in the bound nucleotide. Here, the selection of fluorophores and nucleotide modifications are discussed and methods are described to prepare ATP analogs with examples of two alternate fluorophores, diethylaminocoumarin and Cy3.
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Toseland CP, Webb MR. Fluorescence tools to measure helicase activity in real time. Methods 2010; 51:259-68. [DOI: 10.1016/j.ymeth.2010.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 02/03/2010] [Accepted: 02/12/2010] [Indexed: 11/16/2022] Open
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Abstract
ATP-driven translocation of helicases along DNA can be assayed in several ways. Reagentless biosensors, based on fluorophore-protein adducts, provide convenient ways for real-time assays of both the separation of dsDNA and the hydrolysis of ATP. Single-stranded DNA can be assayed using a modified single-stranded DNA-binding protein (SSB), and phosphate production during ATP hydrolysis can be measured by a modified phosphate-binding protein. Advantages and limitations of these approaches are compared with those of other types of measurements.
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Affiliation(s)
- Martin R Webb
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK
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Hackney DD. When is weaker better? Design of an ADP sensor with weak ADP affinity, but still selective against ATP. ACS Chem Biol 2010; 5:353-4. [PMID: 20394442 DOI: 10.1021/cb1000839] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A simple ADP biosensor would be of broad usefulness in monitoring the large number of metabolic processes that produce ADP. Several new systems have been recently described including one in the current issue of ACS Chemical Biology that provides a simple readout of the ADP concentration without significant interference by ATP.
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Affiliation(s)
- David D. Hackney
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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Kunzelmann S, Webb MR. A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM. ACS Chem Biol 2010; 5:415-25. [PMID: 20158267 PMCID: PMC2855616 DOI: 10.1021/cb9003173] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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Fluorescence assays for ADP detection are of considerable current interest, both in basic research and in drug discovery, as they provide a generic method for measuring the activity of ATPases and kinases. The development of a novel fluorescent biosensor is described that is based on a tetramethylrhodamine-labeled, bacterial actin homologue, ParM. The design of the biosensor takes advantage of the large conformational change of ParM on ADP binding and the strong quenching of the tetramethylrhodamine fluorescence by stacking of the dye. ParM was labeled with two tetramethylrhodamines in close proximity, whereby the fluorophores are able to interact with each other. ADP binding alters the distance and relative orientation of the tetramethylrhodamines, which leads to a change in this stacking interaction and so in the fluorescence intensity. The final ADP biosensor shows ∼15-fold fluorescence increase in response to ADP binding. It has relatively weak affinity for ADP (Kd = 30 μM), enabling it to be used at substoichiometric concentrations relative to ADP, while reporting ADP concentration changes in a wide range around the Kd value, namely, submicromolar to tens of micromolar. The biosensor strongly discriminates against ATP (>100-fold), allowing ADP detection against a background of millimolar ATP. At 20 °C, the labeled ParM binds ADP with a rate constant of 9.5 × 104 M−1 s−1 and the complex dissociates at 2.9 s−1. Thus, the biosensor is suitable for real-time measurements, and its performance in such assays is demonstrated using a sugar kinase and a mammalian protein kinase.
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Affiliation(s)
- Simone Kunzelmann
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Martin R. Webb
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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Huang X, Zhang T. Cascade nucleophilic addition-cyclic Michael addition of arynes and phenols/anilines bearing ortho alpha,beta-unsaturated groups: facile synthesis of 9-functionalized xanthenes/acridines. J Org Chem 2010; 75:506-9. [PMID: 20020766 DOI: 10.1021/jo902311a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile synthesis of xanthenes and acridines based on a cascade nucleophilic addition-cyclic Michael addition process of arynes and phenols/anilines substituted with alpha,beta-unsaturated groups at the ortho positions is described. The reaction has also been successfully extended to the synthesis of 9-spiro-xanthene and acridine derivatives with potential biochemical interest.
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Affiliation(s)
- Xian Huang
- Department of Chemistry, Zhejiang University (Xixi Campus), Hangzhou 310028, People's Republic of China.
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Comparison of enzyme immobilisation methods for potentiometric phosphate biosensors. Biosens Bioelectron 2009; 25:406-10. [DOI: 10.1016/j.bios.2009.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/10/2009] [Accepted: 07/23/2009] [Indexed: 11/19/2022]
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Kunzelmann S, Webb MR. A biosensor for fluorescent determination of ADP with high time resolution. J Biol Chem 2009; 284:33130-8. [PMID: 19801632 PMCID: PMC2785155 DOI: 10.1074/jbc.m109.047118] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nearly every cellular process requires the presence of ATP. This is reflected in the vast number of enzymes like kinases or ATP hydrolases, both of which cleave the terminal phosphate from ATP, thereby releasing ADP. Despite the fact that ATP hydrolysis is one of the most fundamental reactions in biological systems, there are only a few methods available for direct measurements of enzymatic-driven ATP conversion. Here we describe the development of a reagentless biosensor for ADP, the common product of all ATPases and kinases, which allows the real-time detection of ADP, produced enzymatically. The biosensor is derived from a bacterial actin homologue, ParM, as protein framework. A single fluorophore (a diethylaminocoumarin), attached to ParM at the edge of the nucleotide binding site, couples ADP binding to a >3.5-fold increase in fluorescence intensity. The labeled ParM variant has high affinity for ADP (0.46 μm) and a fast signal response, controlled by the rate of ADP binding to the sensor (0.65 μm−1s−1). Amino acids in the active site were mutated to reduce ATP affinity and achieve a >400-fold discrimination against triphosphate binding. A further mutation ensured that the final sensor did not form filaments and, as a consequence, has extremely low ATPase activity. The broad applicability of N-[2-(1-maleimidyl)ethyl]-7-diethylaminocoumarin-3-carboxamide (MDCC)-ParM as a sensitive probe for ADP is demonstrated in real-time kinetic assays on two different ATPases and a protein kinase.
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Affiliation(s)
- Simone Kunzelmann
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
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