1
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Filippova TA, Masamrekh RA, Khudoklinova YY, Shumyantseva VV, Kuzikov AV. The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity. Biochimie 2024; 222:169-194. [PMID: 38494106 DOI: 10.1016/j.biochi.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.
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Affiliation(s)
- Tatiana A Filippova
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Yulia Yu Khudoklinova
- Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia.
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2
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Nayak D, Dos Santos Bury P, Drag M, Nijkerk AN, El Oualid F, Olsen SK. Characterization of the Ubiquitin and ISG15 Deconjugase Activity of SARS-CoV-1 and SARS-CoV-2 Papain-Like Protease. Methods Mol Biol 2023; 2591:171-188. [PMID: 36350549 DOI: 10.1007/978-1-0716-2803-4_11] [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] [Indexed: 06/16/2023]
Abstract
Both severe acute respiratory syndrome coronavirus 1 and 2 (SARS-CoV-1 and SARS-CoV-2) encode a papain-like protease (PLpro), which plays a vital role in viral propagation. PLpro accomplishes this function by processing the viral polyproteins essential for viral replication and removing the small proteins, ubiquitin and ISG15 from the host's key immune signaling proteins, thereby preventing the host's innate immune response. Although PLpro from both SARS-CoV-1 and SARS-CoV-2 are structurally highly similar (83% sequence identity), they exhibit functional variability. Hence, to further elucidate the mechanism and aid in drug discovery efforts, the biochemical and kinetic characterization of PLpro is needed. This chapter describes step-by-step experimental procedures for evaluating PLpro activity in vitro using activity-based probes (ABPs) along with fluorescence-based substrates. Herein we describe a step-by-step experimental procedure to assess the activity of PLpro in vitro using a suite of activity-based probes (ABPs) and fluorescent substrates and how they can be applied as fast and yet sensitive methods to calculate kinetic parameters.
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Affiliation(s)
- Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | | | | | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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3
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Ripp S, Turunen P, Minot ED, Rowan AE, Blank KG. Deciphering Design Principles of Förster Resonance Energy Transfer-Based Protease Substrates: Thermolysin-Like Protease from Geobacillus stearothermophilus as a Test Case. ACS OMEGA 2018; 3:4148-4156. [PMID: 31458650 PMCID: PMC6641592 DOI: 10.1021/acsomega.7b02084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/19/2018] [Indexed: 06/10/2023]
Abstract
Protease activity is frequently assayed using short peptides that are equipped with a Förster resonance energy transfer (FRET) reporter system. Many frequently used donor-acceptor pairs are excited in the ultraviolet range and suffer from low extinction coefficients and quantum yields, limiting their usefulness in applications where a high sensitivity is required. A large number of alternative chromophores are available that are excited in the visible range, for example, based on xanthene or cyanine core structures. These alternatives are not only larger in size but also more hydrophobic. Here, we show that the hydrophobicity of these chromophores not only affects the solubility of the resulting FRET-labeled peptides but also their kinetic parameters in a model enzymatic reaction. In detail, we have compared two series of 4-8 amino acid long peptides, designed to serve as substrates for the thermolysin-like protease (TLP-ste) from Geobacillus stearothermophilus. These peptides were equipped with a carboxyfluorescein donor and either Cy5 or its sulfonated derivative Alexa Fluor 647 as the acceptor. We show that the turnover rate k cat is largely unaffected by the choice of the acceptor fluorophore, whereas the K M value is significantly lower for the Cy5- than for the Alexa Fluor 647-labeled substrates. TLP-ste is a rather nonspecific protease with a large number of hydrophobic amino acids surrounding the catalytic site, so that the fluorophore itself may form additional interactions with the enzyme. This hypothesis is supported by the result that the difference between Cy5- and Alexa Fluor 647-labeled substrates becomes less pronounced with increasing peptide length, that is, when the fluorophore is positioned at a larger distance from the catalytic site. These results suggest that fluorophores may become an integral part of FRET-labeled peptide substrates and that K M and k cat values are generally only valid for a specific combination of the peptide sequence and FRET pair.
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Affiliation(s)
- Sophie Ripp
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Petri Turunen
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ethan D. Minot
- Department
of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon 97331-6507, United States
| | - Alan E. Rowan
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin G. Blank
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Mechano(bio)chemistry,
Max Planck Institute of Colloids and Interfaces, Potsdam-Golm Science Park, 14424 Potsdam, Germany
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4
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Liu Y, Pujals S, Stals PJM, Paulöhrl T, Presolski SI, Meijer EW, Albertazzi L, Palmans ARA. Catalytically Active Single-Chain Polymeric Nanoparticles: Exploring Their Functions in Complex Biological Media. J Am Chem Soc 2018; 140:3423-3433. [PMID: 29457449 PMCID: PMC5997400 DOI: 10.1021/jacs.8b00122] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 01/01/2023]
Abstract
Dynamic single-chain polymeric nanoparticles (SCPNs) are intriguing, bioinspired architectures that result from the collapse or folding of an individual polymer chain into a nanometer-sized particle. Here we present a detailed biophysical study on the behavior of dynamic SCPNs in living cells and an evaluation of their catalytic functionality in such a complex medium. We first developed a number of delivery strategies that allowed the selective localization of SCPNs in different cellular compartments. Live/dead tests showed that the SCPNs were not toxic to cells while spectral imaging revealed that SCPNs provide a structural shielding and reduced the influence from the outer biological media. The ability of SCPNs to act as catalysts in biological media was first assessed by investigating their potential for reactive oxygen species generation. With porphyrins covalently attached to the SCPNs, singlet oxygen was generated upon irradiation with light, inducing spatially controlled cell death. In addition, Cu(I)- and Pd(II)-based SCPNs were prepared and these catalysts were screened in vitro and studied in cellular environments for the carbamate cleavage reaction of rhodamine-based substrates. This is a model reaction for the uncaging of bioactive compounds such as cytotoxic drugs for catalysis-based cancer therapy. We observed that the rate of the deprotection depends on both the organometallic catalysts and the nature of the protective group. The rate reduces from in vitro to the biological environment, indicating a strong influence of biomolecules on catalyst performance. The Cu(I)-based SCPNs in combination with the dimethylpropargyloxycarbonyl protective group showed the best performances both in vitro and in biological environment, making this group promising in biomedical applications.
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Affiliation(s)
- Yiliu Liu
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sílvia Pujals
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Patrick J. M. Stals
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Thomas Paulöhrl
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Stanislav I. Presolski
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - E. W. Meijer
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Anja R. A. Palmans
- Laboratory
for Macromolecular and Organic Chemistry and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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5
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MacDonald MJ, Lavis LD, Hilvert D, Gellman SH. Evaluation of the Ser-His Dipeptide, a Putative Catalyst of Amide and Ester Hydrolysis. Org Lett 2016; 18:3518-21. [PMID: 27400366 DOI: 10.1021/acs.orglett.6b01279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient hydrolysis of amide bonds has long been a reaction of interest for organic chemists. The rate constants of proteases are unmatched by those of any synthetic catalyst. It has been proposed that a dipeptide containing serine and histidine is an effective catalyst of amide hydrolysis, based on an apparent ability to degrade a protein. The capacity of the Ser-His dipeptide to catalyze the hydrolysis of several discrete ester and amide substrates is investigated using previously described conditions. This dipeptide does not catalyze the hydrolysis of amide or unactivated ester groups in any of the substrates under the conditions evaluated.
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Affiliation(s)
- Melissa J MacDonald
- Department of Chemistry, University of Wisconsin-Madison , Wisconsin 53706, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia 20147, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich , 8093 Zürich, Switzerland
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Wisconsin 53706, United States
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6
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Hameed DS, Sapmaz A, Ovaa H. How Chemical Synthesis of Ubiquitin Conjugates Helps To Understand Ubiquitin Signal Transduction. Bioconjug Chem 2016; 28:805-815. [PMID: 27077728 DOI: 10.1021/acs.bioconjchem.6b00140] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ubiquitin (Ub) is a small post-translational modifier protein involved in a myriad of biochemical processes including DNA damage repair, proteasomal proteolysis, and cell cycle control. Ubiquitin signaling pathways have not been completely deciphered due to the complex nature of the enzymes involved in ubiquitin conjugation and deconjugation. Hence, probes and assay reagents are important to get a better understanding of this pathway. Recently, improvements have been made in synthesis procedures of Ub derivatives. In this perspective, we explain various research reagents available and how chemical synthesis has made an important contribution to Ub research.
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Affiliation(s)
- Dharjath S Hameed
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aysegul Sapmaz
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center , Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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7
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Zisis T, Freddolino PL, Turunen P, van Teeseling MCF, Rowan AE, Blank KG. Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation. Biochemistry 2015; 54:5969-79. [PMID: 26346632 DOI: 10.1021/acs.biochem.5b00586] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipase immobilization is frequently used for altering the catalytic properties of these industrially used enzymes. Many lipases bind strongly to hydrophobic surfaces where they undergo interfacial activation. Candida antarctica lipase B (CalB), one of the most commonly used biocatalysts, is frequently discussed as an atypical lipase lacking interfacial activation. Here we show that CalB displays an enhanced catalytic rate for large, bulky substrates when adsorbed to a hydrophobic interface composed of densely packed alkyl chains. We attribute this increased activity of more than 7-fold to a conformational change that yields a more open active site. This hypothesis is supported by molecular dynamics simulations that show a high mobility for a small "lid" (helix α5) close to the active site. Molecular docking calculations confirm that a highly open conformation of this helix is required for binding large, bulky substrates and that this conformation is favored in a hydrophobic environment. Taken together, our combined approach provides clear evidence for the interfacial activation of CalB on highly hydrophobic surfaces. In contrast to other lipases, however, the conformational change only affects large, bulky substrates, leading to the conclusion that CalB acts like an esterase for small substrates and as a lipase for substrates with large alcohol substituents.
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Affiliation(s)
- Themistoklis Zisis
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Petri Turunen
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Muriel C F van Teeseling
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Alan E Rowan
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin G Blank
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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8
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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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9
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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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10
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Strategies in the Design of Small-Molecule Fluorescent Probes for Peptidases. Med Res Rev 2014; 34:1217-41. [DOI: 10.1002/med.21316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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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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12
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Henares TG, Uenoyama Y, Nogawa Y, Ikegami K, Citterio D, Suzuki K, Funano SI, Sueyoshi K, Endo T, Hisamoto H. Novel fluorescent probe for highly sensitive bioassay using sequential enzyme-linked immunosorbent assay-capillary isoelectric focusing (ELISA-cIEF). Analyst 2013; 138:3139-41. [DOI: 10.1039/c3an00098b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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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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