1
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Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH. Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2321017121. [PMID: 38990947 PMCID: PMC11260103 DOI: 10.1073/pnas.2321017121] [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: 11/30/2023] [Accepted: 05/23/2024] [Indexed: 07/13/2024] Open
Abstract
RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology by transcribing DNA into RNA. Despite their importance, much about how RNAPs work remains unclear, in part because the small (3.4 Angstrom) and fast (~40 ms/nt) steps during transcription were difficult to resolve. Here, we used high-resolution nanopore tweezers to observe the motion of single Escherichia coli RNAP molecules as it transcribes DNA ~1,000 times improved temporal resolution, resolving single-nucleotide and fractional-nucleotide steps of individual RNAPs at saturating nucleoside triphosphate concentrations. We analyzed RNAP during processive transcription elongation and sequence-dependent pausing at the yrbL elemental pause sequence. Each time RNAP encounters the yrbL elemental pause sequence, it rapidly interconverts between five translocational states, residing predominantly in a half-translocated state. The kinetics and force-dependence of this half-translocated state indicate it is a functional intermediate between pre- and post-translocated states. Using structural and kinetics data, we show that, in the half-translocated and post-translocated states, sequence-specific protein-DNA interaction occurs between RNAP and a guanine base at the downstream end of the transcription bubble (core recognition element). Kinetic data show that this interaction stabilizes the half-translocated and post-translocated states relative to the pre-translocated state. We develop a kinetic model for RNAP at the yrbL pause and discuss this in the context of key structural features.
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Affiliation(s)
- Ian C. Nova
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Abhishek Mazumder
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Andrew H. Laszlo
- Department of Physics, University of Washington, Seattle, WA98195
| | | | | | | | - Shuya Yang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | | | - Lingting Li
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | | | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Richard H. Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA98195
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2
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Melkonian AV, Gilboa T, Walt DR. Disulfide Bonds Are Not Necessary for Intrinsic TNSALP Activity. J Phys Chem B 2023; 127:1744-1748. [PMID: 36795426 DOI: 10.1021/acs.jpcb.2c08392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Recent developments in single-molecule enzymology (SME) have allowed for the observation of subpopulations present in enzyme ensembles. Tissue-nonspecific alkaline phosphatase (TNSALP), a homodimeric monophosphate esterase central to bone metabolism, has become a model enzyme for SME studies. TNSALP contains two internal disulfide bonds that are critical for its effective dimerization; mutations in its disulfide bonding framework have been reported in patients with hypophosphatasia, a rare disease characterized by impaired bone and tooth mineralization. In this paper, we present the kinetics of these mutants and show that these disulfide bonds are not crucial for TNSALP enzymatic function. This surprising result reveals that the enzyme's active conformation does not rely on its disulfide bonds. We posit that the signs and symptoms seen in hypophosphatasia are likely not primarily due to impaired enzyme function, but rather decreased enzyme expression and trafficking.
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Affiliation(s)
- Arek V Melkonian
- Harvard Medical School, Boston, Massachusetts 02115, United States.,Brigham and Women's Hospital, Department of Pathology, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Tal Gilboa
- Harvard Medical School, Boston, Massachusetts 02115, United States.,Brigham and Women's Hospital, Department of Pathology, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - David R Walt
- Harvard Medical School, Boston, Massachusetts 02115, United States.,Brigham and Women's Hospital, Department of Pathology, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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3
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Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution. Proc Natl Acad Sci U S A 2022; 119:e2202489119. [PMID: 36037333 PMCID: PMC9457475 DOI: 10.1073/pnas.2202489119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule picometer-resolution nanopore tweezers (SPRNT) to resolve the millisecond single-nucleotide steps of superfamily 1 helicase PcrA as it translocates on, or unwinds, several kilobase-long DNA molecules. We recorded more than two million enzyme steps under various assisting and opposing forces in diverse adenosine tri- and diphosphate conditions to comprehensively explore the mechanochemistry of PcrA motion. Forces applied in SPRNT mimic forces and physical barriers PcrA experiences in vivo, such as when the helicase encounters bound proteins or duplex DNA. We show how PcrA's kinetics change with such stimuli. SPRNT allows for direct association of the underlying DNA sequence with observed enzyme kinetics. Our data reveal that the underlying DNA sequence passing through the helicase strongly influences the kinetics during translocation and unwinding. Surprisingly, unwinding kinetics are not solely dominated by the base pairs being unwound. Instead, the sequence of the single-stranded DNA on which the PcrA walks determines much of the kinetics of unwinding.
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4
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Baek S, Han D, Kwon SR, Sundaresan V, Bohn PW. Electrochemical Zero-Mode Waveguide Potential-Dependent Fluorescence of Glutathione Reductase at Single-Molecule Occupancy. Anal Chem 2022; 94:3970-3977. [PMID: 35213143 PMCID: PMC8904319 DOI: 10.1021/acs.analchem.1c05091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding functional states of individual redox enzymes is important because electron-transfer reactions are fundamental to life, and single-enzyme molecules exhibit molecule-to-molecule heterogeneity in their properties, such as catalytic activity. Zero-mode waveguides (ZMW) constitute a powerful tool for single-molecule studies, enabling investigations of binding reactions up to the micromolar range due to the ability to trap electromagnetic radiation in zeptoliter-scale observation volumes. Here, we report the potential-dependent fluorescence dynamics of single glutathione reductase (GR) molecules using a bimodal electrochemical ZMW (E-ZMW), where a single-ring electrode embedded in each of the nanopores of an E-ZMW array simultaneously serves to control electrochemical potential and to confine optical radiation within the nanopores. Here, the redox state of GR is manipulated using an external potential control of the Au electrode in the presence of a redox mediator, methyl viologen (MV). Redox-state transitions in GR are monitored by correlating electrochemical and spectroscopic signals from freely diffusing MV/GR in 60 zL effective observation volumes at single GR molecule average pore occupancy, ⟨n⟩ ∼ 0.8. Fluorescence intensities decrease (increase) at reducing (oxidizing) potentials for MV due to the MV-mediated control of the GR redox state. The spectroelectrochemical response of GR to the enzyme substrate, i.e., glutathione disulfide (GSSG), shows that GSSG promotes GR oxidation via enzymatic reduction. The capabilities of E-ZMWs to probe spectroelectrochemical phenomena in zL-scale-confined environments show great promise for the study of single-enzyme reactions and can be extended to important technological applications, such as those in molecular diagnostics.
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Affiliation(s)
- Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, South Korea
| | - Seung-Ryong Kwon
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, South Korea
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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5
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Wang L, Zhang J, Han M, Zhang L, Chen C, Huang A, Xie R, Wang G, Zhu J, Wang Y, Liu X, Zhuang W, Li Y, Wang J. A Genetically Encoded Two‐Dimensional Infrared Probe for Enzyme Active‐Site Dynamics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Li Wang
- School of Life Sciences University of Chinese Academy of Sciences Yuquan Road, Shijingshan District Beijing 100049 China
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
| | - Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Ming‐Jie Han
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou 350002 China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guosheng Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
| | - Xiaohong Liu
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou 350002 China
- Institute of urban environment Chinese Academy of Sciences Xiamen Fujian 361021 China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
| | - Jiangyun Wang
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
- School of Life Sciences University of Chinese Academy of Sciences Yuquan Road, Shijingshan District Beijing 100049 China
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6
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Jordan JW, Fung KLY, Skowron ST, Allen CS, Biskupek J, Newton GN, Kaiser U, Khlobystov AN. Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions. Chem Sci 2021; 12:7377-7387. [PMID: 34163827 PMCID: PMC8171355 DOI: 10.1039/d1sc01874d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3- (Keggin) and [P2W18O62]6- (Wells-Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W-O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.
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Affiliation(s)
- Jack W Jordan
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Kayleigh L Y Fung
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Stephen T Skowron
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Christopher S Allen
- Electron Physical Science Imaging Center, Diamond Light Source Ltd. Didcot OX11 0DE UK
- Department of Materials, University of Oxford Oxford OX1 3HP UK
| | - Johannes Biskupek
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Graham N Newton
- GSK Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham Nottingham NG7 2TU UK
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Ulm University 89081 Ulm Germany
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
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7
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Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT). Essays Biochem 2021; 65:109-127. [PMID: 33491732 DOI: 10.1042/ebc20200027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT's spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT's ability to discern an enzyme's nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
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8
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Wang L, Zhang J, Han MJ, Zhang L, Chen C, Huang A, Xie R, Wang G, Zhu J, Wang Y, Liu X, Zhuang W, Li Y, Wang J. A Genetically Encoded Two-Dimensional Infrared Probe for Enzyme Active-Site Dynamics. Angew Chem Int Ed Engl 2021; 60:11143-11147. [PMID: 33644946 DOI: 10.1002/anie.202016880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/10/2021] [Indexed: 11/08/2022]
Abstract
While two-dimensional infrared (2D-IR) spectroscopy is uniquely suitable for monitoring femtosecond (fs) to picosecond (ps) water dynamics around static protein structures, its utility for probing enzyme active-site dynamics is limited due to the lack of site-specific 2D-IR probes. We demonstrate the genetic incorporation of a novel 2D-IR probe, m-azido-L-tyrosine (N3Y) in the active-site of DddK, an iron-dependent enzyme that catalyzes the conversion of dimethylsulfoniopropionate to dimethylsulphide. Our results show that both the oxidation of active-site iron to FeIII , and the addition of denaturation reagents, result in significant decrease in enzyme activity and active-site water motion confinement. As tyrosine residues play important roles, including as general acids and bases, and electron transfer agents in many key enzymes, the genetically encoded 2D-IR probe N3Y should be broadly applicable to investigate how the enzyme active-site motions at the fs-ps time scale direct reaction pathways to facilitating specific chemical reactions.
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Affiliation(s)
- Li Wang
- School of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China.,Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guosheng Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China.,Institute of urban environment, Chinese Academy of Sciences, Xiamen, Fujian, 361021, China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.,Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China.,School of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China
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9
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Menges JA, Clasen A, Jourdain M, Beckmann J, Hoffmann C, König J, Jung G. Surface Preparation for Single-Molecule Chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2506-2516. [PMID: 30664351 DOI: 10.1021/acs.langmuir.8b03603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Immobilization procedures, intended to enable prolonged observation of single molecules by fluorescence microscopy, may generate heterogeneous microenvironments, thus inducing heterogeneity in the molecular behavior. On that account, we propose a straightforward surface preparation procedure for studying chemical reactions on the single-molecule level. Sensor fluorophores were developed, which exhibit dual-emissive characteristics in a homogeneously catalyzed showcase reaction. These molecules undergo a shift of fluorescence wavelength of about 100 nm upon Pd(0)-induced deallylation in the Tsuji-Trost reaction, allowing for separate visualization of the starting material and product. Whereas a simultaneous immobilization of dye and inert silane leads to strongly polydisperse reaction kinetics, a consecutive immobilization routine with deposition of dye molecules as the last step provides substrates underlying the kinetics of ensemble experiments. Also, the found kinetics are unaffected by the chemical variation of inert silanes, nearly uniform, and therefore well reproducible. Additional parameters like photostability, signal-to-noise ratio, dye-molecule density, and spatial distribution of dye molecules are, as well, hardly affected by surface modification in the successive immobilization scheme.
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Affiliation(s)
- Johannes A Menges
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Anne Clasen
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Matthias Jourdain
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julian Beckmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Caroline Hoffmann
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Julien König
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
| | - Gregor Jung
- Biophysical Chemistry , Saarland University , Building B2.2 , 66123 Saarbrücken , Germany
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10
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Gao Y, Liu X, Sun L, Xu Y, Yang S, Fan C, Li D. Alleviated Inhibition of Single Enzyme in Confined and Crowded Environment. J Phys Chem Lett 2019; 10:82-89. [PMID: 30565943 DOI: 10.1021/acs.jpclett.8b03736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Most proteins perform functions in intracellular milieu. The crowding, compartmentalized cytosol environment affects the protein structure, folding, conformational stability, substrate diffusion, and substrate-enzyme binding. Moreover, enzymes are available at single or very low copy numbers in a cell, and thus the conformation fluctuations of a single enzyme in a crowding environment could also greatly influence its kinetics. However, the crowding effect is poorly understood in the kinetical aspect of enzymatic reactions. In the present study, individual horseradish peroxidase (HRP) is encapsulated in a liposome containing crowding reagents as mimics of viscous cytosol. The confined crowding environment possesses a profound influence on both the catalytic activity and the product inhibition of enzymes. By analyzing the correlation between product generation and product inhibition, we find that the allosteric noncompetitive inhibition of HRP is alleviated in the crowded and confined milieu. Small-angle X-ray scattering experiments provide straightforward proofs of structural changes of enzymes in crowding environments, which are responsible for the reduced enzyme activity and increased enzyme-substrate affinity. We expect that this work may deepen the understanding of correlations between enzymatic conformations and activity performance in real cellular environments.
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Affiliation(s)
- 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
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , 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
| | - Yan Xu
- 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
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - 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
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Di Li
- 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
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
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11
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Fontana M, Fijen C, Lemay SG, Mathwig K, Hohlbein J. High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices. LAB ON A CHIP 2018; 19:79-86. [PMID: 30468446 DOI: 10.1039/c8lc01175c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.
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Affiliation(s)
- Mattia Fontana
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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12
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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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13
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Robin T, Reuveni S, Urbakh M. Single-molecule theory of enzymatic inhibition. Nat Commun 2018; 9:779. [PMID: 29472579 PMCID: PMC5823943 DOI: 10.1038/s41467-018-02995-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
The classical theory of enzymatic inhibition takes a deterministic, bulk based approach to quantitatively describe how inhibitors affect the progression of enzymatic reactions. Catalysis at the single-enzyme level is, however, inherently stochastic which could lead to strong deviations from classical predictions. To explore this, we take the single-enzyme perspective and rebuild the theory of enzymatic inhibition from the bottom up. We find that accounting for multi-conformational enzyme structure and intrinsic randomness should strongly change our view on the uncompetitive and mixed modes of inhibition. There, stochastic fluctuations at the single-enzyme level could make inhibitors act as activators; and we state—in terms of experimentally measurable quantities—a mathematical condition for the emergence of this surprising phenomenon. Our findings could explain why certain molecules that inhibit enzymatic activity when substrate concentrations are high, elicit a non-monotonic dose response when substrate concentrations are low. Single molecule approaches demonstrated that enzymatic catalysis is stochastic which could lead to deviations from classical predictions. Here authors rebuild the theory of enzymatic inhibition to show that stochastic fluctuations on the single enzyme level could make inhibitors act as activators.
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Affiliation(s)
- Tal Robin
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Shlomi Reuveni
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Department of Systems Biology, HMS, Harvard University, 200 Longwood Avenue, Boston, MA, 02115, USA.
| | - Michael Urbakh
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, 6997801, Tel Aviv, Israel
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14
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XU Y, SUN LL, GAO YJ, QIN WW, PENG TH, LI D. Research Progresses in Single Molecule Enzymology. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Mathwig K, Chi Q, Lemay SG, Rassaei L. Handling and Sensing of Single Enzyme Molecules: From Fluorescence Detection towards Nanoscale Electrical Measurements. Chemphyschem 2015; 17:452-7. [DOI: 10.1002/cphc.201500686] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Klaus Mathwig
- Pharmaceutical Analysis; Groningen Research Institute of Pharmacy; University of Groningen; P.O. Box 196 9700 AD Groningen The Netherlands
| | - Qijin Chi
- Department of Chemistry; Technical University of Denmark; 2800 Kongens Lyngby Denmark
| | - Serge G. Lemay
- MESA+ Institute for Nanotechnology; University of Twente; P.O. Box 217 7500 AE Enschede The Netherlands
| | - Liza Rassaei
- Laboratory of Organic Materials and Interfaces; Department of Chemical Engineering; Delft University of Technology; Julianalaan 136 2628 BL Delft The Netherlands
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16
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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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17
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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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18
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Zheng D, Lu HP. Single-molecule enzymatic conformational dynamics: spilling out the product molecules. J Phys Chem B 2014; 118:9128-40. [PMID: 25025461 PMCID: PMC4126733 DOI: 10.1021/jp5014434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 07/14/2014] [Indexed: 12/19/2022]
Abstract
Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses.
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Affiliation(s)
- Desheng Zheng
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling
Green State University, Bowling
Green, Ohio 43403, United States
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19
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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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20
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Abstract
The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.
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21
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Balasubramanian K, Kern K. 25th anniversary article: label-free electrical biodetection using carbon nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1154-75. [PMID: 24452968 DOI: 10.1002/adma.201304912] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/25/2013] [Indexed: 05/07/2023]
Abstract
Nanostructures are promising candidates for use as active materials for the detection of chemical and biological species, mainly due to the high surface-to-volume ratio and the unique physical properties arising at the nanoscale. Among the various nanostructures, materials comprised of sp(2) -carbon enjoy a unique position due to the possibility to readily prepare them in various dimensions ranging from 0D, through 1D to 2D. This review focuses on the use of 1D (carbon nanotubes) and 2D (graphene) carbon nanostructures for the detection of biologically relevant molecules. A key advantage is the possibility to perform the sensing operation without the use of any labels or complex reaction schemes. Along this spirit, various strategies reported for the label-free electrical detection of biomolecules using carbon nanostructures are discussed. With their promise for ultimate sensitivity and the capability to attain high selectivity through controlled chemical functionalization, carbon-based nanobiosensors are expected to open avenues to novel diagnostic tools as well as to obtain new fundamental insight into biomolecular interactions down to the single molecule level.
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Affiliation(s)
- Kannan Balasubramanian
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D70569, Stuttgart, Germany
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22
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Serdjukow S, Kink F, Steigenberger B, Tomás-Gamasa M, Carell T. Synthesis of γ-labeled nucleoside 5'-triphosphates using click chemistry. Chem Commun (Camb) 2014; 50:1861-3. [PMID: 24402283 DOI: 10.1039/c3cc48937j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Real-time enzymatic studies are gaining importance as their chemical and technical instrumentation improves. Here we report the efficient synthesis of γ-alkyne modified triphosphate amidates that are converted into a variety of γ-fluorophore labeled triphosphates by Cu(I) catalyzed alkyne/azide click reactions. The synthesized triphosphates are incorporated into DNA by DNA polymerases.
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Affiliation(s)
- S Serdjukow
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstraße 5-13, 81377 Munich, Germany.
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23
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Yuan H, Orrit M. Temperature cycles unravel the dynamics of single biomolecules. Biophys J 2014; 106:3-4. [PMID: 24411230 PMCID: PMC3907218 DOI: 10.1016/j.bpj.2013.11.1120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022] Open
Affiliation(s)
- Haifeng Yuan
- MoNOS, LION, Leiden University, Leiden, The Netherlands
| | - Michel Orrit
- MoNOS, LION, Leiden University, Leiden, The Netherlands.
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24
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Akkilic N, van der Grient F, Kamran M, Sanghamitra NJM. Chemically-induced redox switching of a metalloprotein reveals thermodynamic and kinetic heterogeneity, one molecule at a time. Chem Commun (Camb) 2014; 50:14523-6. [DOI: 10.1039/c4cc06334a] [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]
Abstract
FRET-based detection of individual azurin–Cy5 molecules shows an on (reduction)–off (oxidation) fluorescence switching, reveals the redox parameters.
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Affiliation(s)
- Namik Akkilic
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
| | - Fenna van der Grient
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
| | - Muhammad Kamran
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
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25
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Jacobs MJ, Blank K. Joining forces: integrating the mechanical and optical single molecule toolkits. Chem Sci 2014. [DOI: 10.1039/c3sc52502c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Combining single molecule force measurements with fluorescence detection opens up exciting new possibilities for the characterization of mechanoresponsive molecules in Biology and Materials Science.
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Affiliation(s)
- Monique J. Jacobs
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Department of Molecular Materials
- 6525 AJ Nijmegen, The Netherlands
| | - Kerstin Blank
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Department of Molecular Materials
- 6525 AJ Nijmegen, The Netherlands
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26
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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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27
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Moffitt JR, Bustamante C. Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations. FEBS J 2013; 281:498-517. [PMID: 24428386 DOI: 10.1111/febs.12545] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/17/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models.
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Affiliation(s)
- Jeffrey R Moffitt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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28
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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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29
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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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30
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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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31
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Kleijn SEF, Serrano-Bou B, Yanson AI, Koper MTM. Influence of hydrazine-induced aggregation on the electrochemical detection of platinum nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:2054-2064. [PMID: 23320415 DOI: 10.1021/la3040566] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To study the catalytic activity of single nanoparticles (NPs) electrochemically, we investigated the applicability of a novel method for nanoparticle detection as a means to immobilize individual NPs. This method consists of analyzing the current steps that can be measured at an ultramicroelectrode (UME) when a colloid of NPs is injected into an electrolyte containing an electroactive species, that is turned over at the NP but not the UME surface. We have measured these current steps for the hydrazine oxidation at Pt NPs landing on a lithographically fabricated Au UME, showing a mean step size comparable to theory and prior measurements. We found a reduced landing frequency with respect to values reported in the literature and those predicted from theory, while the current step distribution showed a long tail of large current steps. This could be explained by the particle aggregation, which would lower the effective NP concentration and therefore lower the landing frequency and would result in higher current steps when aggregates reach the electrode. Cyclic voltammetry (CV) measurements of the Pt-modified Au UME showed a signal characteristic of the presence of Pt, while electron microscopy revealed aggregated NPs, after landings were performed in the presence of hydrazine or hydrogen gas. Conversely, no aggregates were found after particles were injected in absence of such reducing agents, while CV still suggested the presence of Pt, indicating individual particles. The finding, that landing nanoparticles in the presence of hydrazine yields NP aggregates on the surface, means that this particular method is currently not suited for the preparation of individually immobilized particles to facilitate catalysis studies at individual nanoparticles.
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Affiliation(s)
- Steven E F Kleijn
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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32
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Gatti-Lafranconi P, Hollfelder F. Flexibility and reactivity in promiscuous enzymes. Chembiochem 2013; 14:285-92. [PMID: 23362046 DOI: 10.1002/cbic.201200628] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Indexed: 11/10/2022]
Abstract
Best of both worlds: The interplay of active site reactivity and the dynamic character of proteins allows enzymes to be promiscuous and--sometimes--remarkably efficient at the same time. This review analyses the roles structural flexibility and chemical reactivity play in the catalytic mechanism of selected enzymes.
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33
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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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34
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Liu C, Fan D, Shi Y, Zhou Q. A glimpse of enzymology within the idea of systems. SCIENCE CHINA. LIFE SCIENCES 2012; 55:826-33. [PMID: 23015132 PMCID: PMC7088909 DOI: 10.1007/s11427-012-4371-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/21/2012] [Indexed: 12/21/2022]
Affiliation(s)
- ChuanPeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.
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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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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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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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Fange D, Lovmar M, Pavlov MY, Ehrenberg M. Identification of enzyme inhibitory mechanisms from steady-state kinetics. Biochimie 2011; 93:1623-9. [DOI: 10.1016/j.biochi.2011.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
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