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Hou C, Sun S, Liu Z, Zhang H, Liu Y, An Q, Zhao J, Ma J, Sun Z, Chu W. Visible‐Light‐Induced Decarboxylative Acylation of Pyridine
N
‐Oxides with α‐Oxocarboxylic Acids Using Fluorescein Dimethylammonium as a Photocatalyst. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chuanfu Hou
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Shouneng Sun
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Ziqi Liu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Hui Zhang
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Yue Liu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Qi An
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Jian Zhao
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Junjie Ma
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Zhizhong Sun
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Wenyi Chu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
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Mukhopadhayay A, Singh D, Sharma KP. Neat Ionic liquid and α-Chymotrypsin-Polymer Surfactant Conjugate-Based Biocatalytic Solvent. Biomacromolecules 2020; 21:867-877. [PMID: 31841313 DOI: 10.1021/acs.biomac.9b01556] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Performing biocatalysis in nonaqueous solvents is advantageous as it imparts enhanced solubility to hydrophobic substrates and an ability to increase the temperature for shifting reaction equilibrium in the forward direction. In this work, we show the design and development of another class of nonaqueous composite solvent obtained by mixing surface modified enzyme and neat ionic liquid (IL). We systematically probe the interaction and solubility of industrially relevant α-chymotrypsin in its native or surface-bound polymer-surfactant bioconjugated form, with neat protic (N-methyl-2-pyrrolidonium trifluoromethanesulfonate; [NMP][OTf]), or aprotic (1-methyl-3-(4-sulfobutyl)-1H-imidazol-3-ium trifluoromethanesulfonate; [HO3S(CH2)4MIm][OTf]), ILs. Polarized optical micrographs show that the lyophilized powder of native α-chymotrypsin, nCT, does not disperse in either of the neat ILs, however, its polymer surfactant (PS)-coated bioconjugate counterparts, PScCT, in the waterless state, can be well-dispersed and solubilized in the neat [HO3S(CH2)4MIm][OTf]. The solubilization of waterless bioconjugates of PScCT in neat aprotic IL provides a composite liquid, WL-ImPScCT (WL: waterless, Im: [HO3S(CH2)4MIm][OTf]), having a viscosity of 69.6 Pa·s at 25 °C with a shear-thinning behavior, ≈ 15 w/w % α-chymotrypsin, and ≈ 1.2 w/w % residual water content. Detailed secondary structural analysis using circular dichroism and Fourier self-deconvolution on the ATR-FTIR data of WL-ImPScCT liquid reveals retention of the near native secondary structure of α-chymotrypsin. Further, using a combination of fluorescence spectroscopy and electron spray ionization mass spectrometry, we show that scattering of dry and powdered bovine serum albumin (BSA) protein on the WL-ImPScCT composite liquid results in the solubilization of the former, followed by limited proteolysis of BSA by the α-chymotrypsin. Our results, therefore, show the stabilization of α-chymotrypsin in a neat aprotic IL environment to yield a composite liquid, which not only acts as a nonaqueous, nonvolatile, and environmentally benign solvent, but also provides a biocatalytic platform capable of carrying out reactions relevant for biotransformations, food processing, drug delivery, and various other applications.
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Affiliation(s)
- Anasua Mukhopadhayay
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India
| | - Dharmendra Singh
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India
| | - Kamendra P Sharma
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076 , India
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4
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Ye R, Mao X, Sun X, Chen P. Analogy between Enzyme and Nanoparticle Catalysis: A Single-Molecule Perspective. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04926] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rong Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xiangcheng Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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5
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Xu Y, Gao Y, Su Y, Sun L, Xing F, Fan C, Li D. Single-Molecule Studies of Allosteric Inhibition of Individual Enzyme on a DNA Origami Reactor. J Phys Chem Lett 2018; 9:6786-6794. [PMID: 30412409 DOI: 10.1021/acs.jpclett.8b02992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Unraveling the conformational changes of enzymes together with inhibition kinetics during an enzymatic reaction has great potential in screening therapeutic candidates; however, it remains challenging due to the transient nature of each intermediate step. We report our study on the noncompetitive inhibition of horseradish peroxidase with single-turnover resolution using single-molecule fluorescence microscopy. By introducing DNA origami as an addressable nanoreactor, we observe the coexistence of nascent-formed fluorescent product on both catalytic and docking sites. We further propose a single-molecule kinetic model to reveal the interplay between product generation and noncompetitive inhibition and find three distinct inhibitor releasing pathways. Moreover, the kinetic isotope effect experiment indicates a strong correlation between catalytic and docking sites, suggesting an allosteric conformational change in noncompetitive inhibition. A memory effect is also observed. This work provides an in-depth understanding of the correlation between enzyme behavior and enzymatic conformational fluctuation, substrate conversion, and product releasing pathway and kinetics.
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Affiliation(s)
- Yan Xu
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- National Engineering Research Center for Nanotechnology , Shanghai 200241 , China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yingying Su
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Department of Chemistry, College of Science , Shanghai University , Shanghai 200444 , China
| | - Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Feifei Xing
- Department of Chemistry, College of Science , Shanghai University , Shanghai 200444 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Di Li
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
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6
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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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7
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Cooperative communication within and between single nanocatalysts. Nat Chem 2018; 10:607-614. [DOI: 10.1038/s41557-018-0022-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/05/2018] [Indexed: 11/08/2022]
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8
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Wu L, Yang SH, Xiong H, Yang JQ, Guo J, Yang WC, Yang GF. Nonpeptide-Based Small-Molecule Probe for Fluorogenic and Chromogenic Detection of Chymotrypsin. Anal Chem 2017; 89:3687-3693. [DOI: 10.1021/acs.analchem.6b05115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Lei Wu
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Shu-Hou Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Hao Xiong
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jia-Qian Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jun Guo
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen-Chao Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
- Collaborative Innovation Center of Chemical Science
and Engineering, Tianjin 30071, P.R. China
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9
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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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Abstract
Over the last decade, femtoliter arrays have been used as a simple and robust way to encapsulate and monitor the kinetics of single enzyme molecules. Encapsulating individual enzyme molecules within a femtoliter-sized reaction chamber does not require immobilization of the enzyme molecules or fluorescent tagging of the enzyme molecules, which offers the unique advantage of observing unmodified single enzyme molecules free in solution. Several fascinating details about enzyme kinetics have been revealed using these femtoliter arrays, which were unattainable from traditional ensemble experiments. Here, we discuss various considerations to take into account when developing single-molecule enzyme assays in femtoliter arrays and the advantages and disadvantages of various protocols.
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Affiliation(s)
| | - D R Walt
- Tufts University, Medford, MA, United States.
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11
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Loring RF. Lattice model of spatial correlations in catalysis. J Chem Phys 2016; 145:134508. [DOI: 10.1063/1.4964282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Roger F. Loring
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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12
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Ristanović Z, Hofmann JP, De Cremer G, Kubarev AV, Rohnke M, Meirer F, Hofkens J, Roeffaers MBJ, Weckhuysen BM. Quantitative 3D Fluorescence Imaging of Single Catalytic Turnovers Reveals Spatiotemporal Gradients in Reactivity of Zeolite H-ZSM-5 Crystals upon Steaming. J Am Chem Soc 2015; 137:6559-68. [PMID: 25867455 PMCID: PMC4448181 DOI: 10.1021/jacs.5b01698] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Optimizing the number, distribution,
and accessibility of Brønsted
acid sites in zeolite-based catalysts is of a paramount importance
to further improve their catalytic performance. However, it remains
challenging to measure real-time changes in reactivity of single zeolite
catalyst particles by ensemble-averaging characterization methods.
In this work, a detailed 3D single molecule, single turnover sensitive
fluorescence microscopy study is presented to quantify the reactivity
of Brønsted acid sites in zeolite H-ZSM-5 crystals upon steaming.
This approach, in combination with the oligomerization of furfuryl
alcohol as a probe reaction, allowed the stochastic behavior of single
catalytic turnovers and temporally resolved turnover frequencies of
zeolite domains smaller than the diffraction limited resolution to
be investigated with great precision. It was found that the single
turnover kinetics of the parent zeolite crystal proceeds with significant
spatial differences in turnover frequencies on the nanoscale and noncorrelated
temporal fluctuations. Mild steaming of zeolite H-ZSM-5 crystals at
500 °C led to an enhanced surface reactivity, with up to 4 times
higher local turnover rates than those of the parent H-ZSM-5 crystals,
and revealed remarkable heterogeneities in surface reactivity. In
strong contrast, severe steaming at 700 °C significantly dealuminated
the zeolite H-ZSM-5 material, leading to a 460 times lower turnover
rate. The differences in measured turnover activities are explained
by changes in the 3D aluminum distribution due to migration of extraframework
Al-species and their subsequent effect on pore accessibility, as corroborated
by time-of-flight secondary ion mass spectrometry (TOF-SIMS) sputter
depth profiling data.
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Affiliation(s)
- Zoran Ristanović
- †Inorganic Chemistry and Catalysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Jan P Hofmann
- †Inorganic Chemistry and Catalysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Gert De Cremer
- ‡Department of Chemistry, KU Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Alexey V Kubarev
- §Centre for Surface Chemistry and Catalysis, KU Leuven, Kasteelpark Arenberg 23, 3001 Heverlee, Belgium
| | - Marcus Rohnke
- ∥Institute of Physical Chemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Florian Meirer
- †Inorganic Chemistry and Catalysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Johan Hofkens
- ‡Department of Chemistry, KU Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Maarten B J Roeffaers
- §Centre for Surface Chemistry and Catalysis, KU Leuven, Kasteelpark Arenberg 23, 3001 Heverlee, Belgium
| | - Bert M Weckhuysen
- †Inorganic Chemistry and Catalysis, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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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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14
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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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15
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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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16
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Redefining the dry molten globule state of proteins. J Mol Biol 2014; 426:2520-8. [PMID: 24792909 DOI: 10.1016/j.jmb.2014.04.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/22/2022]
Abstract
Dynamics and function of proteins are governed by the structural and energetic properties of the different states they adopt and the barriers separating them. In earlier work, native-state triplet-triplet energy transfer (TTET) on the villin headpiece subdomain (HP35) revealed an equilibrium between a locked native state and an unlocked native state, which are structurally similar but have different dynamic properties. The locked state is restricted to low amplitude motions, whereas the unlocked state shows increased conformational flexibility and undergoes local unfolding reactions. This classified the unlocked state as a dry molten globule (DMG), which was proposed to represent an expanded native state with loosened side-chain interactions and a solvent-shielded core. To test whether the unlocked state of HP35 is actually expanded compared to the locked state, we performed high-pressure TTET measurements. Increasing pressure shifts the equilibrium from the locked toward the unlocked state, with a small negative reaction volume for unlocking (ΔV(0)=-1.6±0.5cm(3)/mol). Therefore, rather than being expanded, the unlocked state represents an alternatively packed, compact state, demonstrating that native proteins can exist in several compact folded states, an observation with implications for protein function. The transition state for unlocking/locking, in contrast, has a largely increased volume relative to the locked and unlocked state, with respective activation volumes of 7.1±0.4cm(3)/mol and 8.7±0.9cm(3)/mol, indicating an expansion of the protein during the locking/unlocking transition. The presented results demonstrate the existence of both compact, low-energy and expanded, high-energy DMGs, prompting a broader definition of this state.
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17
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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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18
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Laursen T, Singha A, Rantzau N, Tutkus M, Borch J, Hedegård P, Stamou D, Møller BL, Hatzakis NS. Single molecule activity measurements of cytochrome P450 oxidoreductase reveal the existence of two discrete functional states. ACS Chem Biol 2014; 9:630-4. [PMID: 24359083 DOI: 10.1021/cb400708v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electron transfer between membrane spanning oxidoreductase enzymes controls vital metabolic processes. Here we studied for the first time with single molecule resolution the function of P450 oxidoreductase (POR), the canonical membrane spanning activator of all microsomal cytochrome P450 enzymes. Measurements and statistical analysis of individual catalytic turnover cycles shows POR to sample at least two major functional states. This phenotype may underlie regulatory interactions with different cytochromes P450 but to date has remained masked in bulk kinetics. To ensure that we measured the inherent behavior of POR, we reconstituted the full length POR in "native like" membrane patches, nanodiscs. Nanodisc reconstitution increased stability by ∼2-fold as compared to detergent solubilized POR and showed significantly increased activity at biologically relevant ionic strength conditions, highlighting the importance of studying POR function in a membrane environment. This assay paves the way for studying the function of additional membrane spanning oxidoreductases with single molecule resolution.
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Affiliation(s)
- Tomas Laursen
- Plant
Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
| | - Aparajita Singha
- Bio-Nanotechnology
Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
| | - Nicolai Rantzau
- Bio-Nanotechnology
Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
| | - Marijonas Tutkus
- Bio-Nanotechnology
Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
| | - Jonas Borch
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK−5230 Odense M, Denmark
| | - Per Hedegård
- Nano-Science
Center, Niels Bohr Institute, University of Copenhagen, Denmark
| | - Dimitrios Stamou
- Bio-Nanotechnology
Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck
Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant
Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark
- bioSYNergy,
Center for Synthetic Biology, University of 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
- bioSYNergy,
Center for Synthetic Biology, University of Copenhagen, Denmark
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19
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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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20
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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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21
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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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22
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Bally M, Rydell GE, Zahn R, Nasir W, Eggeling C, Breimer ME, Svensson L, Höök F, Larson G. Norovirus GII.4 Virus-like Particles Recognize Galactosylceramides in Domains of Planar Supported Lipid Bilayers. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Bally M, Rydell GE, Zahn R, Nasir W, Eggeling C, Breimer ME, Svensson L, Höök F, Larson G. Norovirus GII.4 virus-like particles recognize galactosylceramides in domains of planar supported lipid bilayers. Angew Chem Int Ed Engl 2012; 51:12020-4. [PMID: 23097253 PMCID: PMC3546384 DOI: 10.1002/anie.201205972] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 01/13/2023]
Affiliation(s)
- Marta Bally
- Department of Applied Physics, Chalmers University of TechnologySE-41133 Göteborg (Sweden)
| | - Gustaf E Rydell
- Traffic, Signaling, and Delivery Laboratory, Centre de Recherche, Institut CurieCNRS UMR144 (France)
| | - Raphael Zahn
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, Universität Zürich und ETH Zürich(Switzerland)
| | - Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg(Sweden)
| | - Christian Eggeling
- Department of Applied Physics, Chalmers University of TechnologySE-41133 Göteborg (Sweden)
| | - Michael E Breimer
- Department of Surgery, Sahlgrenska Academy, University of Gothenburg(Sweden)
| | | | - Fredrik Höök
- Department of Applied Physics, Chalmers University of TechnologySE-41133 Göteborg (Sweden)
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, University of Gothenburg(Sweden)
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24
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Hatzakis NS, Wei L, Jorgensen SK, Kunding AH, Bolinger PY, Ehrlich N, Makarov I, Skjot M, Svendsen A, Hedegård P, Stamou D. Single enzyme studies reveal the existence of discrete functional states for monomeric enzymes and how they are "selected" upon allosteric regulation. J Am Chem Soc 2012; 134:9296-302. [PMID: 22489643 DOI: 10.1021/ja3011429] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.
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Affiliation(s)
- Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, University of Copenhagen, Denmark.
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25
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Ochoa MA, Zhou X, Chen P, Loring RF. Interpreting single turnover catalysis measurements with constrained mean dwell times. J Chem Phys 2012; 135:174509. [PMID: 22070308 DOI: 10.1063/1.3657855] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Observation of a chemical transformation at the single-molecule level yields a detailed view of kinetic pathways contributing to the averaged results obtained in a bulk measurement. Studies of a fluorogenic reaction catalyzed by gold nanoparticles have revealed heterogeneous reaction dynamics for these catalysts. Measurements on single nanoparticles yield binary trajectories with stochastic transitions between a dark state in which no product molecules are adsorbed and a fluorescent state in which one product molecule is present. The mean dwell time in either state gives information corresponding to a bulk measurement. Quantifying fluctuations from mean kinetics requires identifying properties of the fluorescence trajectory that are selective in emphasizing certain dynamic processes according to their time scales. We propose the use of constrained mean dwell times, defined as the mean dwell time in a state with the constraint that the immediately preceding dwell time in the other state is, for example, less than a variable time. Calculations of constrained mean dwell times for a kinetic model with dynamic disorder demonstrate that these quantities reveal correlations among dynamic fluctuations at different active sites on a multisite catalyst. Constrained mean dwell times are determined from measurements of single nanoparticle catalysis. The results indicate that dynamical fluctuations at different active sites are correlated, and that especially rapid reaction events produce particularly slowly desorbing product molecules.
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Affiliation(s)
- Maicol A Ochoa
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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26
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Campos D, Méndez V. Two-point approximation to the Kramers problem with coloured noise. J Chem Phys 2012; 136:074506. [PMID: 22360247 DOI: 10.1063/1.3685418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We present a method, founded on previous renewal approaches as the classical Wilemski-Fixman approximation, to describe the escape dynamics from a potential well of a particle subject to non-Markovian fluctuations. In particular, we show how to provide an approximated expression for the distribution of escape times if the system is governed by a generalized Langevin equation (GLE). While we show that the method could apply to any friction kernel in the GLE, we focus here on the case of power-law kernels, for which extensive literature has appeared in the last years. The method presented (termed as two-point approximation) is able to fit the distribution of escape times adequately for low potential barriers, even if conditions are far from Markovian. In addition, it confirms that non-exponential decays arise when a power-law friction kernel is considered (in agreement with related works published recently), which questions the existence of a characteristic reaction rate in such situations.
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Affiliation(s)
- Daniel Campos
- Grup de Física Estadística, Departament de Física, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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27
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Terentyeva TG, Engelkamp H, Rowan AE, Komatsuzaki T, Hofkens J, Li CB, Blank K. Dynamic disorder in single-enzyme experiments: facts and artifacts. ACS NANO 2012; 6:346-54. [PMID: 22133314 DOI: 10.1021/nn203669r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Using a single-molecule fluorescence approach, the time series of catalytic events of an enzymatic reaction can be monitored, yielding a sequence of fluorescent "on"- and "off"-states. An accurate on/off-assignment is complicated by the intrinsic and extrinsic noise in every single-molecule fluorescence experiment. Using simulated data, the performance of the most widely employed binning and thresholding approach was systematically compared to change point analysis. It is shown that the underlying on- and off-histograms as well as the off-autocorrelation are not necessarily extracted from the "signal'' buried in noise. The shapes of the on- and off-histograms are affected by artifacts introduced by the analysis procedure and depend on the signal-to-noise ratio and the overall fluorescence intensity. For experimental data where the background intensity is not constant over time we consider change point analysis to be more accurate. When using change point analysis for data of the enzyme α-chymotrypsin, no characteristics of dynamic disorder was found. In light of these results, dynamic disorder might not be a general sign of enzymatic reactions.
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Affiliation(s)
- Tatyana G Terentyeva
- Photochemistry & Spectroscopy, Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium
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28
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Terentyeva TG, Van Rossom W, Van der Auweraer M, Blank K, Hofkens J. Morpholinecarbonyl-Rhodamine 110 Based Substrates for the Determination of Protease Activity with Accurate Kinetic Parameters. Bioconjug Chem 2011; 22:1932-8. [DOI: 10.1021/bc2001038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatyana G. Terentyeva
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Wim Van Rossom
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Mark Van der Auweraer
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kerstin Blank
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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29
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Esfandiari NM, Wang Y, Bass JY, Blum SA. Deconvoluting Subensemble Chemical Reaction Kinetics of Platinum–Sulfur Ligand Exchange Detected with Single-Molecule Fluorescence Microscopy. Inorg Chem 2011; 50:9201-3. [DOI: 10.1021/ic2007952] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. Melody Esfandiari
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yong Wang
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Jonathan Y. Bass
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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30
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Roeffaers MBJ, De Cremer G, Libeert J, Ameloot R, Dedecker P, Bons AJ, Bückins M, Martens JA, Sels BF, De Vos DE, Hofkens J. Super-resolution reactivity mapping of nanostructured catalyst particles. Angew Chem Int Ed Engl 2010; 48:9285-9. [PMID: 19890928 DOI: 10.1002/anie.200904944] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maarten B J Roeffaers
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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31
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Claessen VI, Engelkamp H, Christianen PCM, Maan JC, Nolte RJM, Blank K, Rowan AE. Single-biomolecule kinetics: the art of studying a single enzyme. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:319-340. [PMID: 20636045 DOI: 10.1146/annurev.anchem.111808.073638] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The potential of single-enzyme studies to unravel the complex energy landscape of these polymeric catalysts is the next critical step in enzymology. From its inception in Rotman's emulsion experiments in the 1960s, the field of single-molecule enzymology has now advanced into the time-resolved age. Technological advances have enabled individual enzymatic turnover reactions to be observed with a millisecond time resolution. A number of initial studies have revealed the underlying static and dynamic disorder in the catalytic rates originating from conformational fluctuations. Although these experiments are still in their infancy, they may be able to relate the topography of the energy landscape to the biological function and regulation of enzymes. This review summarizes some of the experimental techniques and data-analysis methods that have been used to study individual enzyme molecules in search of a deeper understanding of their kinetics.
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Affiliation(s)
- Victor I Claessen
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
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32
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De Cremer G, Sels BF, De Vos DE, Hofkens J, Roeffaers MBJ. Fluorescence micro(spectro)scopy as a tool to study catalytic materials in action. Chem Soc Rev 2010; 39:4703-17. [DOI: 10.1039/c0cs00047g] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Roeffaers M, Deâ
Cremer G, Libeert J, Ameloot R, Dedecker P, Bons AJ, Bückins M, Martens J, Sels B, Deâ
Vos D, Hofkens J. Super-Resolution Reactivity Mapping of Nanostructured Catalyst Particles. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904944] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Gumpp H, Puchner EM, Zimmermann JL, Gerland U, Gaub HE, Blank K. Triggering enzymatic activity with force. NANO LETTERS 2009; 9:3290-3295. [PMID: 19658405 DOI: 10.1021/nl9015705] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Integrating single molecule force spectroscopy with fluorescence-based techniques allows the manipulation of an enzyme with a periodic stretching and relaxation protocol while simultaneously monitoring its catalytic activity. After releasing the stretching force we observe a higher probability for enzymatic activity at a time of 1.7 s. A detailed theoretical analysis reveals that the relaxation from the force-induced enzyme conformation to the observed active conformation follows a cascade reaction with several steps and a free energy difference of at least 8 k(B)T. Our study clearly points out the direct influence of force on enzymatic activity and opens up a new way to study and manipulate (bio)catalytic reactions at the single molecule level.
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Affiliation(s)
- Hermann Gumpp
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Center for Integrated Protein Science Munich, LMU München, D-80799 München, Germany
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35
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Chen AY, Jani AS, Zheng L, Burke PJ, Brody JP. Microfabricated arrays of cylindrical wells facilitate single-molecule enzymology of α-chymotrypsin. Biotechnol Prog 2009; 25:929-37. [DOI: 10.1002/btpr.283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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36
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Blank K, De Cremer G, Hofkens J. Fluorescence-based analysis of enzymes at the single-molecule level. Biotechnol J 2009; 4:465-79. [DOI: 10.1002/biot.200800262] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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37
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Rocha S, Hutchison JA, Peneva K, Herrmann A, Müllen K, Skjøt M, Jørgensen CI, Svendsen A, De Schryver FC, Hofkens J, Uji-i H. Linking Phospholipase Mobility to Activity by Single-Molecule Wide-Field Microscopy. Chemphyschem 2009; 10:151-61. [DOI: 10.1002/cphc.200800537] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Chen Q, Groote R, Schönherr H, Vancso GJ. Probing single enzyme kinetics in real-time. Chem Soc Rev 2009; 38:2671-83. [DOI: 10.1039/b903638e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Ameloot R, Roeffaers M, Baruah M, De Cremer G, Sels B, De Vos D, Hofkens J. Towards direct monitoring of discrete events in a catalytic cycle at the single molecule level. Photochem Photobiol Sci 2009; 8:453-6. [DOI: 10.1039/b821657f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Roeffaers MBJ, Ameloot R, Bons AJ, Mortier W, De Cremer G, de Kloe R, Hofkens J, De Vos DE, Sels BF. Relating pore structure to activity at the subcrystal level for ZSM-5: an electron backscattering diffraction and fluorescence microscopy study. J Am Chem Soc 2008; 130:13516-7. [PMID: 18800795 DOI: 10.1021/ja8048767] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic performance of microporous materials such as zeolites is determined not only by the active sites' molecular architecture, but also by the organization of the surrounding pores with varying diameter, shape, and directionality. These pores control transport of reagents and products and induce shape selectivity. Rather than being ideal single crystals, zeolites often have complex 3-dimensional morphologies, comprising intergrowths and various defect types. Here, the underlying pore architecture of the hexagonal facet of an individual zeolite ZSM-5 crystal is successfully determined by electron beam scattering diffraction and is correlated with the initial reactivity toward the acid-catalyzed oligomerization of furfuryl alcohol using polarized fluorescence microscopy.
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Affiliation(s)
- Maarten B J Roeffaers
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 23, B-3001 Leuven, Belgium
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