1
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Ouyang J, Zhang Z, Li J, Wu C. Integrating Enzymes with Supramolecular Polymers for Recyclable Photobiocatalytic Catalysis. Angew Chem Int Ed Engl 2024; 63:e202400105. [PMID: 38386281 DOI: 10.1002/anie.202400105] [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: 01/02/2024] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024]
Abstract
Chemical modifications of enzymes excel in the realm of enzyme engineering due to its directness, robustness, and efficiency; however, challenges persist in devising versatile and effective strategies. In this study, we introduce a supramolecular modification methodology that amalgamates a supramolecular polymer with Candida antarctica lipase B (CalB) to create supramolecular enzymes (SupEnzyme). This approach features the straightforward preparation of a supramolecular amphiphilic polymer (β-CD@SMA), which was subsequently conjugated to the enzyme, resulting in a SupEnzyme capable of self-assembly into supramolecular nanoparticles. The resulting SupEnzyme nanoparticles can form micron-scale supramolecular aggregates through supramolecular and electrostatic interactions with guest entities, thus enhancing catalyst recycling. Remarkably, these aggregates maintain 80 % activity after seven cycles, outperforming Novozym 435. Additionally, they can effectively initiate photobiocatalytic cascade reactions using guest photocatalysts. As a consequence, our SupEnzyme methodology exhibits noteworthy adaptability in enzyme modification, presenting a versatile platform for various polymer, enzyme, and biocompatible catalyst pairings, with potential applications in the fields of chemistry and biology.
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Affiliation(s)
- Jingping Ouyang
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Zhenfang Zhang
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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2
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Kundu P, Saha S, Gangopadhyay G. A minimal kinetic model for the interpretation of complex catalysis in single enzyme molecules. Phys Chem Chem Phys 2023; 26:463-476. [PMID: 38078459 DOI: 10.1039/d3cp01720f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Multi-exponential waiting-time distribution and randomness parameter greater than unity ascribe dynamic disorder in single-enzyme catalysis corroborated to the interplay of transforming conformers [English et al., Nat. Chem. Biol., 2006, 2, 87]. The associated multi-state model of enzymatic turnovers with statically heterogeneous catalytic rates misdescribes the non-linear uprising of the randomness parameter from unity in relation to the attributes of the fall-offs of the waiting-time distribution at different substrate concentrations. To resolve this crucial issue, we first employ a comprehensive stochastic reaction scenario and further rationalize and work out the minimal indispensable dynamic-disorder model that ensures the foregoing relationship upon comparison with the data. We elucidate that specific disregard for the transition rate coefficients in the multi-state model on account of the especially slow conformational transitions is the underlying reason for not achieving interrelation between the observables.
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Affiliation(s)
- Prasanta Kundu
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Soma Saha
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, India.
| | - Gautam Gangopadhyay
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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3
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Ahn Y, Park M, Seo D. Observation of reactions in single molecules/nanoparticles using light microscopy. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yongdeok Ahn
- Department of Chemistry and Physics DGIST Daegu Republic of Korea
| | - Minsoo Park
- Department of Chemistry and Physics DGIST Daegu Republic of Korea
| | - Daeha Seo
- Department of Chemistry and Physics DGIST Daegu Republic of Korea
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4
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Dynamic single-molecule sensing by actively tuning binding kinetics for ultrasensitive biomarker detection. Proc Natl Acad Sci U S A 2022; 119:e2120379119. [PMID: 35238650 PMCID: PMC8916011 DOI: 10.1073/pnas.2120379119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
SignificanceThe detection of low-abundance molecular biomarkers is key to the liquid-biopsy-based disease diagnosis. Existing methods are limited by the affinity and specificity of recognition probes and the mass transportation of analyte molecules onto the sensor surfaces, resulting in insufficient sensitivity and long assay time. This work establishes a rapid and ultrasensitive approach by actively tuning binding kinetics and accelerating the mass transportation via nanoparticle micromanipulations. This is significant because it permits extremely sensitive measurements within clinically acceptable assay time. It is incubation-free, washing-free, and compatible with low- and high-affinity probes.
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5
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Zhang L, Fan W, Jia D, Feng Q, Ren W, Liu C. Microchamber-Free Digital Flow Cytometric Analysis of T4 Polynucleotide Kinase Phosphatase Based on Single-Enzyme-to-Single-Bead Space-Confined Reaction. Anal Chem 2021; 93:14828-14836. [PMID: 34713697 DOI: 10.1021/acs.analchem.1c03724] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Digital bioassays have attracted extensive attention in biomedical applications due to their ultrahigh sensitivity. However, traditional digital bioassays require numerous microchambers such as droplets or microwells, which restricts their application scope. Herein, we propose a microchamber-free flow cytometric method for the digital quantification of T4 polynucleotide kinase phosphatase (T4 PNKP) based on an unprecedented phenomenon that each T4 PNKP molecule-catalyzed reaction can be spatially self-confined on a single microbead, which ultimately enables the one-target-to-one-fluorescence-positive microbead digital signal transduction. The digital signal-readout mode can clearly detect T4 PNKP concentrations as low as 1.28 × 10-10 U/μL, making it most sensitive method to date. Significantly, T4 PNKP can be specifically distinguished from other phosphatases and nucleases in complex samples by digitally counting the fluorescence-positive microbeads, which cannot be realized by traditional bulk measurement-based methods. Taking advantage of the novel space-confined enzymatic feature of T4 PNKP, this digital mechanism can use T4 PNKP as the enzyme label to fabricate digital sensing systems toward various biomolecules such as digital enzyme-linked immunosorbent assay (ELISA). Therefore, this work not only enlarges the toolbox for high-sensitivity biomolecule detection but also opens new gates to fabricate next-generation digital assays.
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Affiliation(s)
- Lijun Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Qinya Feng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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6
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Subramanian S, Jones HB, Frustaci S, Winter S, van der Kamp MW, Arcus VL, Pudney CR, Vollmer F. Sensing Enzyme Activation Heat Capacity at the Single-Molecule Level Using Gold-Nanorod-Based Optical Whispering Gallery Modes. ACS APPLIED NANO MATERIALS 2021; 4:4576-4583. [PMID: 34085031 PMCID: PMC8165693 DOI: 10.1021/acsanm.1c00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Here, we report a label-free gold nanoparticle-based single-molecule optical platform to study the immobilization, activity, and thermodynamics of single enzymes. The sensor uses plasmonic gold nanoparticles coupled to optical whispering gallery modes (WGMs) to probe enzyme conformational dynamics during turnover at a microsecond time resolution. Using a glucosidase enzyme as the model system, we explore the temperature dependence of the enzyme turnover at the single-molecule (SM) level. A recent physical model for understanding enzyme temperature dependencies (macromolecular rate theory; MMRT) has emerged as a powerful tool to study the relationship between enzyme turnover and thermodynamics. Using WGMs, SM enzyme measurements enable us to accurately track turnover as a function of conformational changes and therefore to quantitatively probe the key feature of the MMRT model, the activation heat capacity, at the ultimate level of SM. Our data shows that WGMs are extraordinarily sensitive to protein conformational change and can discern both multiple steps with turnover as well as microscopic conformational substates within those steps. The temperature dependence studies show that the MMRT model can be applied to a range of steps within turnover at the SM scale that is associated with conformational change. Our study validates the notion that MMRT captures differences in dynamics between states. The WGM sensors provide a platform for the quantitative analysis of SM activation heat capacity, applying MMRT to the label-free sensing of microsecond substates of active enzymes.
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Affiliation(s)
- Sivaraman Subramanian
- Living
Systems Institute, Department of Physics & Astronomy, University of Exeter, Exeter EX4 4QD, U.K.
| | - Hannah B.L. Jones
- Department
of Biology and Biochemistry, Centre for Biosensors, Bioelectronics
and Biodevices, University of Bath, Bath BA2 7AY, U.K.
| | - Simona Frustaci
- Living
Systems Institute, Department of Physics & Astronomy, University of Exeter, Exeter EX4 4QD, U.K.
| | - Samuel Winter
- Department
of Biology and Biochemistry, Centre for Biosensors, Bioelectronics
and Biodevices, University of Bath, Bath BA2 7AY, U.K.
| | | | - Vickery L. Arcus
- Te
Aka Ma̅tuatua - School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Christopher R. Pudney
- Department
of Biology and Biochemistry, Centre for Biosensors, Bioelectronics
and Biodevices, University of Bath, Bath BA2 7AY, U.K.
| | - Frank Vollmer
- Living
Systems Institute, Department of Physics & Astronomy, University of Exeter, Exeter EX4 4QD, U.K.
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7
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Abstract
Traditional studies of enzymatic activity rely on the combined kinetics of millions of enzyme molecules to produce a product, an experimental approach that may wash out heterogeneities that exist between individual enzymes. Evaluating these properties on an enzyme-by-enzyme basis represents an unambiguous means of elucidating heterogeneities; however, the quantification of enzymatic activity at the single-enzyme level is fundamentally limited by the maximum catalytic rate, kcat, inherent to a given enzyme. For electrochemical methods measuring current, single enzymes must turn over greater than 107 molecules per second to produce a measurable signal on the order of 10-12 A. Enzymes with this capability are extremely rare in nature, with typical kcat values for biologically relevant enzymes falling between 1 and 10 000 s-1. Thus, clever amplification strategies are necessary to electrochemically detect the vast majority of enzymes. This review details the progress toward the electroanalytical detection and evaluation of single enzyme kinetics largely focused on the nanoimpact method, a chronoamperometric detection strategy that monitors the change in the current-time profile associated with stochastic collisions of freely diffusing entities (e.g., enzymes) onto a microelectrode or nanoelectrode surface. We discuss the experimental setups and methods developed in the last decade toward the quantification of single molecule enzymatic rates. Special emphasis is given to the limitations of measurement science in the observation of single enzyme activity and feasible methods of signal amplification with reasonable bandwidth.
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Affiliation(s)
- Kathryn J Vannoy
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Andrey Ryabykh
- Department of Physical and Inorganic Chemistry, Altai State University, Barnaul, Altai Krai, Russia656049
| | - Andrei I Chapoval
- Russian-American Anti-Cancer Center, Altai State University, Barnaul, Altai Krai, Russia656049
| | - Jeffrey E Dick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. and Lineberger Comprehensive Cancer Center, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Bohr SSR, Lund PM, Kallenbach AS, Pinholt H, Thomsen J, Iversen L, Svendsen A, Christensen SM, Hatzakis NS. Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition. Sci Rep 2019; 9:16169. [PMID: 31700110 PMCID: PMC6838188 DOI: 10.1038/s41598-019-52539-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Lipases are interfacially activated enzymes that catalyze the hydrolysis of ester bonds and constitute prime candidates for industrial and biotechnological applications ranging from detergent industry, to chiral organic synthesis. As a result, there is an incentive to understand the mechanisms underlying lipase activity at the molecular level, so as to be able to design new lipase variants with tailor-made functionalities. Our understanding of lipase function primarily relies on bulk assay averaging the behavior of a high number of enzymes masking structural dynamics and functional heterogeneities. Recent advances in single molecule techniques based on fluorogenic substrate analogues revealed the existence of lipase functional states, and furthermore so how they are remodeled by regulatory cues. Single particle studies of lipases on the other hand directly observed diffusional heterogeneities and suggested lipases to operate in two different modes. Here to decipher how mutations in the lid region controls Thermomyces lanuginosus lipase (TLL) diffusion and function we employed a Single Particle Tracking (SPT) assay to directly observe the spatiotemporal localization of TLL and rationally designed mutants on native substrate surfaces. Parallel imaging of thousands of individual TLL enzymes and HMM analysis allowed us to observe and quantify the diffusion, abundance and microscopic transition rates between three linearly interconverting diffusional states for each lipase. We proposed a model that correlate diffusion with function that allowed us to predict that lipase regulation, via mutations in lid region or product inhibition, primarily operates via biasing transitions to the active states.
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Affiliation(s)
- Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philip M Lund
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Pinholt
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Lars Iversen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark.
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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9
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Popov R, Shankara GK, von Bojničić-Kninski C, Nesterov-Mueller A. Renaissance Distribution for Statistically Failed Experiments. Int J Mol Sci 2019; 20:ijms20133250. [PMID: 31269680 PMCID: PMC6651062 DOI: 10.3390/ijms20133250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 11/25/2022] Open
Abstract
Much of the experimental data, especially in life sciences, is considered to be useless if it demonstrates a large standard deviation from the mean value. The Renaissance distribution, as presented in this study, allows one to extract true values from such statistical data with large noise. To obtain proof of the Renaissance distribution, high-throughput synthesis of deep substitutions for a target amino acid sequence was performed, and the known epitope was identified in assay with human serum antibodies. In addition, the Renaissance distribution was shown to approach the epitope affinity maturation by the deep alanine substitution. The Renaissance distribution may have an impact in the development of novel specific drugs.
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Affiliation(s)
- Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Girish Karadka Shankara
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Clemens von Bojničić-Kninski
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany.
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10
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Wang Y, Zijlstra P. Plasmon-Enhanced Single-Molecule Enzymology. ACS PHOTONICS 2018; 5:3073-3081. [PMID: 30148184 PMCID: PMC6105035 DOI: 10.1021/acsphotonics.8b00327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 05/06/2023]
Abstract
We present a numerical study on plasmon-enhanced single-molecule enzymology. We combine Brownian dynamics and electromagnetic simulations to calculate the enhancement of fluorescence signals of fluorogenic substrate converted by an enzyme conjugated to a plasmonic particle. We simulate the Brownian motion of a fluorescent product away from the active site of the enzyme, and calculate the photon detection rate taking into account modifications of the excitation and emission processes by coupling to the plasmon. We show that plasmon enhancement can boost the signal-to-noise ratio (SNR) of single turnovers by up to 100 fold compared to confocal microscopy. This enhancement factor is a trade-off between the reduced residence time in the near-field of the particle, and the enhanced emission intensity due to coupling to the plasmon. The enhancement depends on the size, shape and material of the particle and the photophysical properties of the fluorescent product. Our study provides guidelines on how to enhance the SNR of single-molecule enzyme studies and may aid in further understanding and quantifying static and dynamic heterogeneity.
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11
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Mickert MJ, Gorris HH. Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis. J Phys Chem B 2018; 122:5809-5819. [DOI: 10.1021/acs.jpcb.8b02297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Matthias J. Mickert
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Hans H. Gorris
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
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12
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Direct observation of multiple conformational states in Cytochrome P450 oxidoreductase and their modulation by membrane environment and ionic strength. Sci Rep 2018; 8:6817. [PMID: 29717147 PMCID: PMC5931563 DOI: 10.1038/s41598-018-24922-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450 oxidoreductase (POR) is the primary electron donor in eukaryotic cytochrome P450 (CYP) containing systems. A wealth of ensemble biophysical studies of Cytochrome P450 oxidoreductase (POR) has reported a binary model of the conformational equilibrium directing its catalytic efficiency and biomolecular recognition. In this study, full length POR from the crop plant Sorghum bicolor was site-specifically labeled with Cy3 (donor) and Cy5 (acceptor) fluorophores and reconstituted in nanodiscs. Our single molecule fluorescence resonance energy transfer (smFRET) burst analyses of POR allowed the direct observation and quantification of at least three dominant conformational sub-populations, their distribution and occupancies. Moreover, the state occupancies were remodeled significantly by ionic strength and the nature of reconstitution environment, i.e. phospholipid bilayers (nanodiscs) composed of different lipid head group charges vs. detergent micelles. The existence of conformational heterogeneity in POR may mediate selective activation of multiple downstream electron acceptors and association in complexes in the ER membrane.
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13
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Benítez-Mateos AI, Nidetzky B, Bolivar JM, López-Gallego F. Single-Particle Studies to Advance the Characterization of Heterogeneous Biocatalysts. ChemCatChem 2018. [DOI: 10.1002/cctc.201701590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ana I. Benítez-Mateos
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
| | - Juan M. Bolivar
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
- IKERBASQUE; Basque Foundation for Science; Bilbao Spain
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14
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Craig DB, King SD, Reinfelds G, Henderson AR, Wood TE. Electrophoretic mobility, catalytic rate, and activation energy of catalysis of single molecules of the enzyme β-glucuronidase from Escherichia coli. Int J Biol Macromol 2017; 96:669-674. [DOI: 10.1016/j.ijbiomac.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 10/12/2016] [Accepted: 12/12/2016] [Indexed: 12/28/2022]
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15
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Zhang Y, Chen T, Song P, Xu W. Recent progress on single-molecule nanocatalysis based on single-molecule fluorescence microscopy. Sci Bull (Beijing) 2017; 62:290-301. [PMID: 36659357 DOI: 10.1016/j.scib.2017.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 01/21/2023]
Abstract
Understanding the heterogeneous catalytic properties of nanoparticles is of great significance for the development of high efficient nanocatalysts, but the intrinsic heterogeneities of nanocatalysts were always covered in traditional ensemble studies. This issue can be overcome if one can follow the catalysis of individual nanoparticles in real time. This paper mainly summarizes recent developments in single-molecule nanocatalysis at single particle level in Changchun Institute of Applied Chemistry, Chinese Academy of Sciences. These developments include the revealing of catalytic kinetics of different types (plane & edge) of surface atoms on individual Pd nanocubes, the observing of in situ deactivation of individual carbon-supported Pt nanoparticles during the electrocatalytic hydrogen-oxidation reaction, and the measurement of catalytic activation energies on single nanocatalysts for both product formation process and dissociation process, etc. These studies further indicate the advantages or unique abilities of single-molecule methods in the studies of nanocatalysis or even chemical reactions.
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Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Provincial Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Tao Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Provincial Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Song
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Provincial Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Weilin Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Provincial Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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16
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Münninghoff JAW, Elemans JAAW. Chemistry at the square nanometer: reactivity at liquid/solid interfaces revealed with an STM. Chem Commun (Camb) 2017; 53:1769-1788. [DOI: 10.1039/c6cc07862a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An overview is given of single molecule reactivity at a liquid/solid interface employing a scanning tunneling microscope.
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17
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Hwang W, Lee IB, Hong SC, Hyeon C. Decoding Single Molecule Time Traces with Dynamic Disorder. PLoS Comput Biol 2016; 12:e1005286. [PMID: 28027304 PMCID: PMC5226833 DOI: 10.1371/journal.pcbi.1005286] [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: 08/11/2016] [Revised: 01/11/2017] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm—Variational Bayes-double chain Markov model (VB-DCMM)—to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA. We have developed a new algorithm to better decode single molecule data with dynamic disorder. Our new algorithm, which represents a substantial improvement over other methodologies, can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy landscape. As a model system, we applied our algorithm to the single molecule FRET time traces of H-DNA. While duplex-triplex transitions of H-DNA are conventionally interpreted in terms of two-state kinetics, slowly varying dynamic patterns corresponding to hidden internal states can also be identified from the individual time traces. Our algorithm reveals that at least 4 distinct internal states are required to correctly interpret the data.
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Affiliation(s)
- Wonseok Hwang
- Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Il-Buem Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Seok-Cheol Hong
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- * E-mail:
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Moses M, Hedegård P, Hatzakis N. Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout. Methods Enzymol 2016; 581:227-256. [DOI: 10.1016/bs.mie.2016.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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20
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Enzyme molecules in solitary confinement. Molecules 2014; 19:14417-45. [PMID: 25221867 PMCID: PMC6271441 DOI: 10.3390/molecules190914417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 11/17/2022] Open
Abstract
Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.
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21
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Turunen P, Rowan AE, Blank K. Single-enzyme kinetics with fluorogenic substrates: lessons learnt and future directions. FEBS Lett 2014; 588:3553-63. [DOI: 10.1016/j.febslet.2014.06.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 01/05/2023]
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22
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Khatua S, Paulo PMR, Yuan H, Gupta A, Zijlstra P, Orrit M. Resonant plasmonic enhancement of single-molecule fluorescence by individual gold nanorods. ACS NANO 2014; 8:4440-9. [PMID: 24684549 DOI: 10.1021/nn406434y] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhancing the fluorescence of a weak emitter is important to further extend the reach of single-molecule fluorescence imaging to many unexplored systems. Here we study fluorescence enhancement by isolated gold nanorods and explore the role of the surface plasmon resonance (SPR) on the observed enhancements. Gold nanorods can be cheaply synthesized in large volumes, yet we find similar fluorescence enhancements as literature reports on lithographically fabricated nanoparticle assemblies. The fluorescence of a weak emitter, crystal violet, can be enhanced more than 1000-fold by a single nanorod with its SPR at 629 nm excited at 633 nm. This strong enhancement results from both an excitation rate enhancement of ∼130 and an effective emission enhancement of ∼9. The fluorescence enhancement, however, decreases sharply when the SPR wavelength moves away from the excitation laser wavelength or when the SPR has only a partial overlap with the emission spectrum of the fluorophore. The reported measurements of fluorescence enhancement by 11 nanorods with varying SPR wavelengths are consistent with numerical simulations.
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Affiliation(s)
- Saumyakanti Khatua
- Huygens-Kamerlingh Onnes Laboratory, Universiteit Leiden , 2300 RA Leiden, The Netherlands
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23
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Liebherr RB, Renner M, Gorris HH. A single molecule perspective on the functional diversity of in vitro evolved β-glucuronidase. J Am Chem Soc 2014; 136:5949-55. [PMID: 24684619 DOI: 10.1021/ja412379p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms that drive the evolution of new enzyme activity have been investigated by comparing the kinetics of wild-type and in vitro evolved β-glucuronidase (GUS) at the single molecule level. Several hundred single GUS molecules were separated in large arrays of 62,500 ultrasmall reaction chambers etched into the surface of a fused silica slide to observe their individual substrate turnover rates in parallel by fluorescence microscopy. Individual GUS molecules feature long-lived but divergent activity states, and their mean activity is consistent with classic Michaelis-Menten kinetics. The large number of single molecule substrate turnover rates is representative of the activity distribution within an entire enzyme population. Partially evolved GUS displays a much broader activity distribution among individual enzyme molecules than wild-type GUS. The broader activity distribution indicates a functional division of work between individual molecules in a population of partially evolved enzymes that-as so-called generalists-are characterized by their promiscuous activity with many different substrates.
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Affiliation(s)
- Raphaela B Liebherr
- Institute of Analytical Chemistry, Chemo- and Biosensors and ‡Institute of Biophysics and Physical Biochemistry, University of Regensburg , 93040 Regensburg, Germany
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Affiliation(s)
- Justin B. Sambur
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850;
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850;
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25
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Yildiz UH, De Hoog HPM, Fu Z, Tomczak N, Parikh AN, Nallani M, Liedberg B. Third-party ATP sensing in polymersomes: a label-free assay of enzyme reactions in vesicular compartments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:442-7, 441. [PMID: 23963775 DOI: 10.1002/smll.201300060] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 05/28/2013] [Indexed: 05/02/2023]
Affiliation(s)
- Umit Hakan Yildiz
- Centre for Biomimetic Sensor Science, School of Materials Science & Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 6375532
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26
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Hatzakis NS. Single molecule insights on conformational selection and induced fit mechanism. Biophys Chem 2014; 186:46-54. [DOI: 10.1016/j.bpc.2013.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 01/24/2023]
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JØRGENSEN SUNEK, HATZAKIS NIKOSS. INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins. [Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41
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Affiliation(s)
- SUNE K. JØRGENSEN
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
| | - NIKOS S. HATZAKIS
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
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28
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Abstract
In this article, we talk about the ways that scientists can solve single molecule trajectories. Solving single molecules, that is, finding the model from the data, is complicated at least as much as measuring single molecules. We must filter the noise and take care of every step in the analysis when constructing the most accurate model from the data. Here, we present valuable solutions. Ways that solve clean discrete data are first presented. We review here our reduced dimensions forms (RDFs): unique models that are canonical forms of discrete data, and the statistical and numerical toolbox that builds a RDF from finite, clean, two-state data. We then review our most recent filter that "tackles" the noise when measuring two state noisy photon trajectories. The filter is a numerical algorithm with various special statistical treatments that is based on a general likelihood function that we have developed recently. We show the strengths of the filter (also over other approaches) and talk about its various new variants. This filter (with minor adjustments) can solve the noise in any discrete state trajectories, yet, extensions are needed in "tackling" the noise from other data, e.g. continuous data. Only the combined procedures enable creating the most accurate model from noisy discrete trajectories from single molecules. These concepts and methods (with adjustments) are valuable also when solving continuous trajectories and fluorescence resonance energy transfer trajectories. We also present a set of simple methods that can help any scientist with treating the trajectory perhaps encouraging applying the involved methods. The involved methods will appear in software that we are developing now, helping therefore the experimentalists utilizing these methods on real data. Comparisons with other known methods in this field are made. [Formula: see text]Special Issue Comment: This article about mathematical treatments when solving single molecules is related to the reviews in this Special Issue about measuring enzymes67 and about FRET experiments2 and about the software QUB.6
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Affiliation(s)
- OPHIR FLOMENBOM
- Flomenbom-BPS Ltd, 19 Louis Marshal Street, Tel Aviv, 62668, Israel
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29
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Chauhan DP, Saha T, Lahiri M, Talukdar P. BODIPY based ‘click on’ fluorogenic dyes: application in live cell imaging. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Mogalisetti P, Gorris HH, Rojek MJ, Walt DR. Elucidating the relationship between substrate and inhibitor binding to the active sites of tetrameric β-galactosidase. Chem Sci 2014. [DOI: 10.1039/c4sc01437e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The stochastic binding and release of two different inhibitors from a tetrameric enzyme is described at the single molecule level.
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Affiliation(s)
| | - Hans H. Gorris
- University of Regensburg, Institute of Analytical Chemistry
- Chemo- and Biosensors
- 93040 Regensburg, Germany
| | | | - David R. Walt
- Tufts University, Department of Chemistry
- Medford, USA
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31
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Chen P, Zhou X, Andoy NM, Han KS, Choudhary E, Zou N, Chen G, Shen H. Spatiotemporal catalytic dynamics within single nanocatalysts revealed by single-molecule microscopy. Chem Soc Rev 2014; 43:1107-17. [DOI: 10.1039/c3cs60215j] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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32
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Janssen KPF, De Cremer G, Neely RK, Kubarev AV, Van Loon J, Martens JA, De Vos DE, Roeffaers MBJ, Hofkens J. Single molecule methods for the study of catalysis: from enzymes to heterogeneous catalysts. Chem Soc Rev 2014; 43:990-1006. [DOI: 10.1039/c3cs60245a] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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33
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34
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Holzmeister P, Acuna GP, Grohmann D, Tinnefeld P. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev 2013; 43:1014-28. [PMID: 24019005 DOI: 10.1039/c3cs60207a] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach.
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Affiliation(s)
- Phil Holzmeister
- Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany.
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35
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Schwabe A, Maarleveld TR, Bruggeman FJ. Exploration of the spontaneous fluctuating activity of single enzyme molecules. FEBS Lett 2013; 587:2744-52. [PMID: 23850890 DOI: 10.1016/j.febslet.2013.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 11/30/2022]
Abstract
Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activity, such as transcription, replication, translation, and histone modifications. Here we introduce the main theoretical concepts of stochastic single-enzyme activity starting from the Michaelis-Menten enzyme mechanism. Next, we discuss stochasticity of multi-substrate enzymes, of enzymes and receptors with multiple conformational states and finally, how fluctuations in receptor activity arise from fluctuations in signal concentration. This paper aims to introduce the exciting field of single-molecule enzyme kinetics and stochasticity to a wider audience of biochemists and systems biologists.
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Affiliation(s)
- Anne Schwabe
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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36
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Xu A, Li F, Robinson H, Yeung ES. Can Protein Conformers Be Fractionated by Crystallization? Anal Chem 2013; 85:6372-7. [DOI: 10.1021/ac400762x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aoshuang Xu
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Fenglei Li
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Howard Robinson
- Biology Department, 463, Brookhaven National Laboratory,
Upton, New York 11973-5000, United States
| | - Edward S. Yeung
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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37
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Ehrl BN, Liebherr RB, Gorris HH. Single molecule kinetics of horseradish peroxidase exposed in large arrays of femtoliter-sized fused silica chambers. Analyst 2013; 138:4260-5. [PMID: 23752650 DOI: 10.1039/c3an00809f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large arrays of femtoliter-sized chambers were etched into the surface of fused silica slides to enclose and observe hundreds of single horseradish peroxidase (HRP) molecules in parallel. Individual molecules of HRP oxidize the fluorogenic substrate Amplex Red to fluorescent resorufin in separate chambers, which was monitored by fluorescence microscopy. Photooxidation of Amplex Red and photobleaching of resorufin have previously limited the analysis of HRP in femtoliter arrays. We have strongly reduced these effects by optimizing the fluorescence excitation and detection scheme to yield accurate single molecule substrate turnover rates. We demonstrate the presence of long-lived kinetic states of single HRP molecules that are individually different for each molecule in the array. The large number of molecules investigated in parallel provides excellent statistics on the activity distribution in the enzyme population, which is similar to that reported for other enzymes such as β-galactosidase. We have further confirmed that the product formation of HRP in femtoliter chambers is 10-fold lower than that in the bulk solution due to the particular two-step redox reaction mechanism of HRP.
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Affiliation(s)
- Benno N Ehrl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany
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38
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Arayanarakool R, Shui L, Kengen SWM, van den Berg A, Eijkel JCT. Single-enzyme analysis in a droplet-based micro- and nanofluidic system. LAB ON A CHIP 2013; 13:1955-62. [PMID: 23546540 DOI: 10.1039/c3lc41100a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The kinetic activity of individual enzyme molecules was determined in aqueous droplets generated in a nano- and microfluidic device. To avoid high background noise, the enzyme and substrate solution was confined into femtoliter carriers, achieving high product concentrations from single-molecule encapsulation. The tiny droplets (φ ~ 2.5-3 μm) generated from this fluidic system were highly monodisperse, beneficial for an analysis of single enzyme activity. The method presented here allows to follow large numbers of individual droplets over time. The instrumental requirements are furthermore modest, since the small droplet size allows to use of standard microscope and standard Pyrex glass chips as well as the use of relatively high enzyme concentrations (nM range) for single molecule encapsulation.
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Affiliation(s)
- Rerngchai Arayanarakool
- BIOS/Lab-on-chip group, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
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39
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Rybina A, Lang C, Wirtz M, Grußmayer K, Kurz A, Maier F, Schmitt A, Trapp O, Jung G, Herten DP. Direkte Beobachtung alternativer Reaktionswege an einzelnen Molekülen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Rybina A, Lang C, Wirtz M, Grußmayer K, Kurz A, Maier F, Schmitt A, Trapp O, Jung G, Herten DP. Distinguishing Alternative Reaction Pathways by Single-Molecule Fluorescence Spectroscopy. Angew Chem Int Ed Engl 2013; 52:6322-5. [DOI: 10.1002/anie.201300100] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 02/25/2013] [Indexed: 11/07/2022]
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41
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Sharpless KB, Manetsch R. In situ click chemistry: a powerful means for lead discovery. Expert Opin Drug Discov 2013; 1:525-38. [PMID: 23506064 DOI: 10.1517/17460441.1.6.525] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.
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Affiliation(s)
- K Barry Sharpless
- WM Keck Professor, Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-315 La Jolla, CA 92037, USA.
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42
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Terentyeva TG, Hofkens J, Komatsuzaki T, Blank K, Li CB. Time-Resolved Single Molecule Fluorescence Spectroscopy of an α-Chymotrypsin Catalyzed Reaction. J Phys Chem B 2013; 117:1252-60. [DOI: 10.1021/jp310663v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatyana G. Terentyeva
- Photochemistry & Spectroscopy, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Johan Hofkens
- Photochemistry & Spectroscopy, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Tamiki Komatsuzaki
- Molecule & Life Nonlinear Sciences, Research Institute for Electronic Science (RIES), Hokkaido University, Sapporo, Japan
| | - Kerstin Blank
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Chun-Biu Li
- Molecule & Life Nonlinear Sciences, Research Institute for Electronic Science (RIES), Hokkaido University, Sapporo, Japan
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43
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Yuan H, Khatua S, Zijlstra P, Yorulmaz M, Orrit M. Thousand-fold Enhancement of Single-Molecule Fluorescence Near a Single Gold Nanorod. Angew Chem Int Ed Engl 2012; 52:1217-21. [DOI: 10.1002/anie.201208125] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Indexed: 11/06/2022]
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44
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Yuan H, Khatua S, Zijlstra P, Yorulmaz M, Orrit M. Thousand-fold Enhancement of Single-Molecule Fluorescence Near a Single Gold Nanorod. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201208125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Lente G. Stochastic mapping of first order reaction networks: a systematic comparison of the stochastic and deterministic kinetic approaches. J Chem Phys 2012; 137:164101. [PMID: 23126689 DOI: 10.1063/1.4758458] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stochastic maps are developed and used for first order reaction networks to decide whether the deterministic kinetic approach is appropriate for a certain evaluation problem or the use of the computationally more demanding stochastic approach is inevitable. On these maps, the decision between the two approaches is based on the standard deviation of the expectation of detected variables: when the relative standard deviation is larger than 1%, the use of the stochastic method is necessary. Four different systems are considered as examples: the irreversible first order reaction, the reversible first order reaction, two consecutive irreversible first order reactions, and the unidirectional triangle reaction. Experimental examples are used to illustrate the practical use of the theoretical results. It is shown that the maps do not only depend on particle numbers, but the influence of parameters such as time, rate constants, and the identity of the detected target variable is also an important factor.
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Affiliation(s)
- Gábor Lente
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary.
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Affiliation(s)
- Elias M. Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
| | - Hermann E. Gaub
- Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany;
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47
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Mandal PK, Cattiaux L, Bensimon D, Mallet JM. Monogalactopyranosides of fluorescein and fluorescein methyl ester: synthesis, enzymatic hydrolysis by biotnylated β-galactosidase, and determination of translational diffusion coefficient. Carbohydr Res 2012; 358:40-6. [PMID: 22817995 DOI: 10.1016/j.carres.2012.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/11/2012] [Accepted: 05/15/2012] [Indexed: 10/28/2022]
Abstract
Fluorescein monoglycosides (D-galactopyranoside (FMG) and D-glucopyranoside) and their methyl ester (MFMG) have been prepared from acetobromoglucose/galactose and fluorescein methyl ester in good yields. Enzymatic hydrolysis experiments (using biotinylated β-galactosidase) of the galacto derivatives have been performed and kinetic parameters were calculated. A 15-20 times increase of the fluorescence intensity has been observed during the hydrolysis. A linear increase of fluorescence has been noted at short time and low concentration of substrate, making these compounds useful and sensitive probes for galactosidases. The magnitude of the Michaelis-Menten constant (K(m)) value for MFMG is higher than that of FMG suggesting a possible conformational change of the fluorogenic substrate. K(m) value for biotinylated β-Gal with FMG is lower than that for the native enzyme. This observation indicates higher substrate affinity of the biotinylated enzyme in comparison to the native enzyme. Translational diffusion coefficients have been measured, for both fluorogenic substrates and both the products, employing fluorescence correlation spectroscopy. Translational diffusion coefficients for fluorogenic substrates and the enzymatic hydrolysis products have been measured to be similar, in the range of 3.5-4.5×10(-10) m(2) s(-1). Thus an enhancement or retardation of the enzymatic kinetics due to difference in translational mobility of substrate and product is not that apparent.
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Affiliation(s)
- Prasun K Mandal
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, Département de Physique, UMR CNRS-ENS 8550, Paris, France
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48
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Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles. Proc Natl Acad Sci U S A 2012; 109:E1437-43. [PMID: 22562794 DOI: 10.1073/pnas.1116670109] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule level. Individual HRP molecules are trapped within surface-tethered lipid vesicles, and their reaction with a fluorogenic substrate is probed. While the substrate readily penetrates into the vesicles, the charged product (resorufin) gets trapped and accumulates inside the vesicles. Surprisingly, individual enzyme molecules are found to stall when a few tens of product molecules accumulate. Bulk enzymology experiments verify that the enzyme is noncompetitively inhibited by resorufin. The initial reaction velocity of individual enzyme molecules and the number of product molecules required for their complete inhibition are broadly distributed and dynamically disordered. The two seemingly unrelated parameters, however, are found to be substantially correlated with each other in each enzyme molecule and over long times. These results suggest that, as a way to counter disorder, enzymes have evolved the means to correlate fluctuations at structurally distinct functional sites.
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49
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Lim YR, Park SJ, Lee SY, Sung JY. Nonclassical Chemical Kinetics for Description of Chemical Fluctuation in a Dynamically Heterogeneous Biological System. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.3.963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Lim YR, Park SJ, Park BJ, Cao J, Silbey RJ, Sung J. Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity. J Chem Theory Comput 2012; 8:1415-25. [DOI: 10.1021/ct200785q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Rim Lim
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Seong Jun Park
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Bo Jung Park
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Jianshu Cao
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert J. Silbey
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jaeyoung Sung
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
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