1
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Jang W, Song EL, Mun SJ, Bong KW. Efficient isolation of encoded microparticles in a degassed micromold for highly sensitive and multiplex immunoassay with signal amplification. Biosens Bioelectron 2024; 261:116465. [PMID: 38850735 DOI: 10.1016/j.bios.2024.116465] [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: 03/12/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Multiplex detection of low-abundance protein biomarkers in biofluids can contribute to diverse biomedical fields such as early diagnosis and precision medicine. However, conventional techniques such as digital ELISA, microarray, and hydrogel-based assay still face limitations in terms of efficient protein detection due to issues with multiplexing capability, sensitivity, or complicated assay procedures. In this study, we present the degassed micromold-based particle isolation technique for highly sensitive and multiplex immunoassay with enzymatic signal amplification. Using degassing treatment of nanoporous polydimethylsiloxane (PDMS) micromold, the encoded particles are isolated in the mold within 5 min absorbing trapped air bubbles into the mold by air suction capability. Through 10 min of signal amplification in the isolated spaces by fluorogenic substrate and horseradish peroxidase labeled in the particle, the assay signal is amplified with one order of magnitude compared to that of the standard hydrogel-based assay. Using the signal amplification assay, vascular endothelial growth factor (VEGF) and chorionic gonadotropin beta (CG beta), the preeclampsia-related protein biomarkers, are quantitatively detected with a limit of detection (LoD) of 249 fg/mL and 476 fg/mL in phosphate buffer saline. The multiplex immunoassay is conducted to validate negligible non-specific detection signals and robust recovery rates in the multiplex assay. Finally, the VEGF and CG beta in real urine samples are simultaneously and quantitatively detected by the developed assay. Given the high sensitivity, multiplexing capability, and process simplicity, the presented particle isolation-based signal amplification assay holds significant potential in biomedical and proteomic fields.
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Affiliation(s)
- Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - E Loomee Song
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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2
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Morajkar RV, Fatrekar AP, Vernekar AA. Approach of a small protein to the biomimetic bis-(μ-oxo) dicopper active-site installed in MOF-808 pores with restricted access perturbs substrate selectivity of oxidase nanozyme. Chem Sci 2024; 15:10810-10822. [PMID: 39027301 PMCID: PMC11253172 DOI: 10.1039/d4sc02136c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Advances in nanozymes have taken shape over the past few years in several domains. However, persisting challenging limitations of selectivity, specificity, and efficiency necessitate careful attention to aid in the development of next-generation artificial enzymes. Despite nanozymes having significant therapeutic and biotechnological prospects, the multienzyme mimetic activities can compromise their intended applications. Furthermore, the lack of substrate selectivity can hamper crucial biological pathways. While working on addressing the challenges of nanozymes, in this work, we aim to highlight the interplay between the substrates and bis-(μ-oxo) dicopper active site-installed MOF-808 for selectively mimicking oxidase. This oxidase mimetic with a small pore-aperture (1.4 nm), similar to the opening of enzyme binding pockets, projects a tight control over the dynamics and the reactivity of substrates, making it distinct from the general oxidase nanozymes. Interestingly, the design and the well-regulated activity of this nanozyme effectively thwart DNA from approaching the active site, thereby preventing its oxidative damage. Crucially, we also show that despite these merits, the oxidase selectivity is compromised by small proteins such as cytochrome c (Cyt c), having dimensions larger than the pore aperture of MOF-808. This reaction lucidly produces water molecules as a result of four electron transfer to an oxygen molecule. Such unintended side reactivities warrant special attention as they can perturb redox processes and several cellular energy pathways. Through this study, we provide a close look at designing next-generation artificial enzymes that can address the complex challenges for their utility in advanced applications.
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Affiliation(s)
- Rasmi V Morajkar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Adarsh P Fatrekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Amit A Vernekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
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3
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Tsai YH, Milbrandt NB, Prado RC, Ponce NB, Alam MM, Qiu SR, Yu X, Burda C, Kim TKJ, Samia ACS. Effect of Nitrogen Doping on the Photocatalytic Properties and Antibiofilm Efficacy of Reduced TiO 2 Nanoparticles. ACS APPLIED BIO MATERIALS 2024; 7:4580-4592. [PMID: 38958462 DOI: 10.1021/acsabm.4c00459] [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] [Indexed: 07/04/2024]
Abstract
Nanomaterial-mediated antibacterial photodynamic therapy (aPDT) emerges as a promising treatment against antibiotic-resistant bacterial biofilms. Specifically, titanium dioxide nanoparticles (TiO2 NPs) are being investigated as photosensitizers in aPDT to address biofilm related diseases. To enhance their photocatalytic performance in the visible spectral range for biomedical applications, various strategies have been adopted, including reduction of TiO2 NPs. However, despite improvements in visible-light photoactivity, reduced TiO2 NPs have yet to reach their expected performance primarily due to the instability of oxygen vacancies and their tendency to reoxidize easily. To address this, we present a two-step approach to fabricate highly visible-light active and stable TiO2 NP photocatalysts, involving nitrogen doping followed by a magnesium-assisted reductive annealing process. X-ray photoelectron spectroscopy analysis of the synthesized reduced nitrogen-doped TiO2 NPs (H:Mg-N-TiO2 NPs) reveals that the presence of nitrogen stabilizes oxygen vacancies and reduced Ti species, leading to increased production of reactive oxygen species under visible-light excitation. The improved aPDT efficiency translates to a 3-fold enhancement in the antibiofilm activity of nitrogen-doped compared to undoped reduced TiO2 NPs against both Gram-positive (Streptococcus mutans) and Gram-negative (Porphyromonas gingivalis, Fusobacterium nucleatum) oral pathogens. These results underscore the potential of H:Mg-N-TiO2 NPs in aPDT for combating bacterial biofilms effectively.
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Affiliation(s)
- Yu Hsin Tsai
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathalie B Milbrandt
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Ross Clark Prado
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nicole Beatrice Ponce
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Md Masud Alam
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - S Roger Qiu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratyory, Livermore, California 94551, United States
| | - Xiong Yu
- Department of Civil and Environmental Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Clemens Burda
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Tae Kyong John Kim
- Swagelok Center for Surface Analysis of Materials, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Anna Cristina S Samia
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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4
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Gines G, Espada R, Dramé-Maigné A, Baccouche A, Larrouy N, Rondelez Y. Functional analysis of single enzymes combining programmable molecular circuits with droplet-based microfluidics. NATURE NANOTECHNOLOGY 2024; 19:800-809. [PMID: 38409552 DOI: 10.1038/s41565-024-01617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024]
Abstract
The analysis of proteins at the single-molecule level reveals heterogeneous behaviours that are masked in ensemble-averaged techniques. The digital quantification of enzymes traditionally involves the observation and counting of single molecules partitioned into microcompartments via the conversion of a profluorescent substrate. This strategy, based on linear signal amplification, is limited to a few enzymes with sufficiently high turnover rate. Here we show that combining the sensitivity of an exponential molecular amplifier with the modularity of DNA-enzyme circuits and droplet readout makes it possible to specifically detect, at the single-molecule level, virtually any D(R)NA-related enzymatic activity. This strategy, denoted digital PUMA (Programmable Ultrasensitive Molecular Amplifier), is validated for more than a dozen different enzymes, including many with slow catalytic rate, and down to the extreme limit of apparent single turnover for Streptococcus pyogenes Cas9. Digital counting uniquely yields absolute molar quantification and reveals a large fraction of inactive catalysts in all tested commercial preparations. By monitoring the amplification reaction from single enzyme molecules in real time, we also extract the distribution of activity among the catalyst population, revealing alternative inactivation pathways under various stresses. Our approach dramatically expands the number of enzymes that can benefit from quantification and functional analysis at single-molecule resolution. We anticipate digital PUMA will serve as a versatile framework for accurate enzyme quantification in diagnosis or biotechnological applications. These digital assays may also be utilized to study the origin of protein functional heterogeneity.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France.
| | - Rocίo Espada
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Adèle Dramé-Maigné
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Alexandre Baccouche
- LIMMS, IRL 2820 CNRS-Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Nicolas Larrouy
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
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Metternich JT, Hill B, Wartmann JAC, Ma C, Kruskop RM, Neutsch K, Herbertz S, Kruss S. Signal Amplification and Near-Infrared Translation of Enzymatic Reactions by Nanosensors. Angew Chem Int Ed Engl 2024; 63:e202316965. [PMID: 38100133 DOI: 10.1002/anie.202316965] [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: 11/08/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic reactions are used to detect analytes in a range of biochemical methods. To measure the presence of an analyte, the enzyme is conjugated to a recognition unit and converts a substrate into a (colored) product that is detectable by visible (VIS) light. Thus, the lowest enzymatic turnover that can be detected sets a limit on sensitivity. Here, we report that substrates and products of horseradish peroxidase (HRP) and β-galactosidase change the near-infrared (NIR) fluorescence of (bio)polymer modified single-walled carbon nanotubes (SWCNTs). They translate a VIS signal into a beneficial NIR signal. Moreover, the affinity of the nanosensors leads to a higher effective local concentration of the reactants. This causes a non-linear sensor-based signal amplification and translation (SENSAT). We find signal enhancement up to ≈120x for the HRP substrate p-phenylenediamine (PPD), which means that reactions below the limit of detection in the VIS can be followed in the NIR (≈1000 nm). The approach is also applicable to other substrates such as 3,3'-5,5'-tetramethylbenzidine (TMB). An adsorption-based theoretical model fits the observed signals and corroborates the sensor-based enhancement mechanism. This approach can be used to amplify signals, translate them into the NIR and increase sensitivity of biochemical assays.
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Affiliation(s)
- Justus T Metternich
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Björn Hill
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Janus A C Wartmann
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chen Ma
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Rebecca M Kruskop
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Krisztian Neutsch
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Svenja Herbertz
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Sebastian Kruss
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
- Center for Nanointegration Duisburg-Essen (CENIDE), Carl-Benz-Strasse 199, 47057, Duisburg, Germany
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6
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Zhou K, Su H, Gao J, Li H, Liu S, Yi X, Zhang Z, Wang W. Deciphering the Kinetics of Spontaneous Generation of H 2O 2 in Individual Water Microdroplets. J Am Chem Soc 2024; 146:2445-2451. [PMID: 38230586 DOI: 10.1021/jacs.3c09864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Spontaneous generation of H2O2 in sub-10 μm-sized water microdroplets has received increasing interest since its first discovery in 2019. On the other hand, due to the short lifetime of these microdroplets (rapid evaporation) and lack of suitable tools to real-time monitor the generation of H2O2 in individual microdroplets, such a seemingly thermodynamically unfavorable process has also raised vigorous debates on the origin of H2O2 and the underlying mechanism. Herein, we prepared water microdroplets with a long lifetime (>1 h) by virtue of microwell confinement and dynamically monitored the spontaneous generation of H2O2 in individual microdroplets via time-lapsed fluorescence imaging. It was unveiled that H2O2 was continuously generated in the as-prepared water microdroplets and an apparent equilibrium concentration of ∼3 μM of H2O2 in the presence of a H2O2-consuming reaction can be obtained. Through engineering the geometry of these microdroplets, we further revealed that the generation rates of H2O2 in individual microdroplets were positively proportional to their surface-to-volume ratios. This also allowed us to extract a maximal H2O2 generation rate of 7.7 nmol m-2 min-1 in the presence of a H2O2-consuming reaction and derive the corresponding probability of spontaneous conversion of interfacial H2O into H2O2 for the first time, that is, ∼1 of 65,000 water molecules in 1 s. These findings delivered strong evidence that the spontaneous generation of H2O2 indeed occurs at the surface of microdroplets and provided us with an important starting point to further enhance the yield of H2O2 in water microdroplets for future applications.
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Affiliation(s)
- Kai Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hua Su
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shasha Liu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xuannuo Yi
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhibing Zhang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education (MOE), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Shen Q, Fang C, Serpe MJ. Microgel-based etalon immunoassay for IgG detection. Anal Bioanal Chem 2023; 415:5645-5656. [PMID: 37421438 DOI: 10.1007/s00216-023-04834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023]
Abstract
We developed an immunoassay for mouse immunoglobulin (IgG) quantitation using poly(N-isopropylacrylamide-co-acrylic acid) (pNIPAm-co-AAc) microgel-based etalon devices. To achieve this, a biotinylated primary antibody specific to mouse IgG was immobilized on the top Au layer of an etalon device via its interaction with a streptavidin-modified etalon surface. Mouse IgG captured on the etalon surface from the solution was quantified using an HRP-conjugated secondary antibody. HRP catalyzed the oxidation of 4-chloro-1-naphthol (4CN) to form insoluble 4-chloro-1-naphthon (4CNP), resulting in a concentration change of 4CN in solution. The etalon was able to detect the 4CN concentration change by monitoring the extent of the etalon's reflectance peak shift, which allows the quantitation of mouse IgG. The etalon-based assay can detect mouse IgG down to 0.018 nM with a linear range of 0.02-5 nM.
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Affiliation(s)
- Qiming Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Changhao Fang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Michael J Serpe
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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Zuo L, Ren K, Guo X, Pokhrel P, Pokhrel B, Hossain MA, Chen ZX, Mao H, Shen H. Amalgamation of DNAzymes and Nanozymes in a Coronazyme. J Am Chem Soc 2023; 145:5750-5758. [PMID: 36795472 PMCID: PMC10325850 DOI: 10.1021/jacs.2c12367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Artificial enzymes such as nanozymes and DNAzymes are economical and stable alternatives to natural enzymes. By coating Au nanoparticles (AuNPs) with a DNA corona (AuNP@DNA), we amalgamated nanozymes and DNAzymes into a new artificial enzyme with catalytic efficiency 5 times higher than AuNP nanozymes, 10 times higher than other nanozymes, and significantly greater than most of the DNAzymes on the same oxidation reaction. The AuNP@DNA demonstrates excellent specificity as its reactivity on a reduction reaction does not change with respect to pristine AuNP. Single-molecule fluorescence and force spectroscopies and density functional theory (DFT) simulations indicate a long-range oxidation reaction initiated by radical production on the AuNP surface, followed by radical transport to the DNA corona, where the binding and turnover of substrates take place. The AuNP@DNA is named coronazyme because of its natural enzyme mimicking capability through the well-orchestrated structures and synergetic functions. By incorporating different nanocores and corona materials beyond DNAs, we anticipate that the coronazymes represent generic enzyme mimics to carry out versatile reactions in harsh environments.
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Affiliation(s)
- Li Zuo
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Xianming Guo
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Bishal Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | | | - Zhao-Xu Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44242, USA
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10
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Abstract
Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.
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Abstract
Lytic polysaccharide monooxygenases (LPMOs) are unique redox enzymes capable of disrupting the crystalline surfaces of industry-relevant recalcitrant polysaccharides, such as chitin and cellulose. Historically, LPMOs were thought to be slow enzymes relying on O2 as the co-substrate, but it is now clear that these enzymes prefer H2O2, allowing for fast depolymerization of polysaccharides through a peroxygenase reaction. Thus, quantifying H2O2 in LPMO reaction set-ups is of a great interest. The horseradish peroxidase (HRP)/Amplex Red (AR) assay is one of the most popular and accessible tools for measuring hydrogen peroxide. This assay has been used in various types of biological and biochemical studies, including LPMO research, but suffers from pitfalls that need to be accounted for. In this Chapter, we discuss this method and its use for assessing the often rate-limiting in situ formation of H2O2 in LPMO reactions. We show that, after accounting for multiple potential side reactions, quantitative data on H2O2 production obtained with the HRP/Amplex Red assay provide useful clues for understanding the catalytic activity of LPMOs, including the impact of reductants and transition metal ions.
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Affiliation(s)
- Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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12
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Prüfer M, Wenger C, Bier FF, Laux EM, Hölzel R. Activity of AC electrokinetically immobilized horseradish peroxidase. Electrophoresis 2022; 43:1920-1933. [PMID: 35904497 DOI: 10.1002/elps.202200073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/22/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022]
Abstract
Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2 O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
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Affiliation(s)
- Mareike Prüfer
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
| | - Christian Wenger
- IHP GmbH - Leibniz Institute for Innovative Microelectronics, Frankfurt/Oder, Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Eva-Maria Laux
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
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13
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Noji H, Minagawa Y, Ueno H. Enzyme-based digital bioassay technology - key strategies and future perspectives. LAB ON A CHIP 2022; 22:3092-3109. [PMID: 35861036 DOI: 10.1039/d2lc00223j] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Digital bioassays based on single-molecule enzyme reactions represent a new class of bioanalytical methods that enable the highly sensitive detection of biomolecules in a quantitative manner. Since the first reports of these methods in the 2000s, there has been significant growth in this new bioanalytical strategy. The principal strategy of this method is to compartmentalize target molecules in micron-sized reactors at the single-molecule level and count the number of microreactors showing positive signals originating from the target molecule. A representative application of digital bioassay is the digital enzyme-linked immunosorbent assay (ELISA). Owing to their versatility, various types of digital ELISAs have been actively developed. In addition, some disease markers and viruses possess catalytic activity, and digital bioassays for such enzymes and viruses have, thus, been developed. Currently, with the emergence of new microreactor technologies, the targets of this methodology are expanding from simple enzymes to more complex systems, such as membrane transporters and cell-free gene expression. In addition, multiplex or multiparametric digital bioassays have been developed to assess precisely the heterogeneities in sample molecules/systems that are obscured by ensemble measurements. In this review, we first introduce the basic concepts of digital bioassays and introduce a range of digital bioassays. Finally, we discuss the perspectives of new classes of digital bioassays and emerging fields based on digital bioassay technology.
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Affiliation(s)
- Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Hiroshi Ueno
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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14
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Hipper E, Blech M, Hinderberger D, Garidel P, Kaiser W. Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques. Pharmaceutics 2021; 14:72. [PMID: 35056968 PMCID: PMC8779573 DOI: 10.3390/pharmaceutics14010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.
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Affiliation(s)
- Elena Hipper
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Dariush Hinderberger
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Wolfgang Kaiser
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
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15
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Yang J, Xiao X, Xia L, Li G, Shui L. Microfluidic Magnetic Analyte Delivery Technique for Separation, Enrichment, and Fluorescence Detection of Ultratrace Biomarkers. Anal Chem 2021; 93:8273-8280. [PMID: 34061492 DOI: 10.1021/acs.analchem.1c01130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A microfluidic magnetic analyte delivery (μMAD) technique was developed to realize sample preparation and ultrasensitive biomarker detection. A simply designed microfluidic device was employed to carry out this technique, including a poly(dimethylsiloxane)-glass hybrid microchip having four straight rectangular channels and a permanent magnet. In the μMAD process, functionalized magnetic beads (MBs) were used to recognize and isolate analytes from a complex sample matrix, deliver analytes into tiny microchannels, and preconcentrate analytes in the magnetic trapping/detection region for in situ fluorescence detection. In the feasibility study and sensitivity optimization, horseradish peroxidase-labeled MBs were used, and critical parameters for the signal amplification performance of μMAD were carefully evaluated. At optimized conditions, a sensitivity improvement of at least 2 orders of magnitude was achieved. As a proof of concept, μMAD was combined with the enzyme-linked immunosorbent assay (ELISA), while carcinoembryonic antigen (CEA), prostate-specific antigen (PSA), and interleukin 6 (IL-6) were selected as model biomarkers. The limits of detection (LODs) of μMAD-ELISA were as low as 0.29 pg/mL for CEA, 0.047 pg/mL for PSA, and 0.021 pg/mL for IL-6, which corresponded to an over 200-fold reduction compared to their commercial ELISA results. Meanwhile, μMAD-ELISA revealed high selectivity and reproducibility. In clinical sample analysis, good accuracy was acquired for human serum analysis relative to commercial ELISA kits, and satisfied recoveries of 85.1-102% with RSDs of 1.7-9.8% for IL-6 and 84.7-113% with RSDs of 3.2-8.3% for interferon-γ were obtained. This ultrasensitive and easy operation technique provides a valuable approach for trace-level biomarker detection for practical applications.
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Affiliation(s)
- Jiani Yang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaohua Xiao
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Ling Xia
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Lingling Shui
- School of Information and Optoelectronic Science and Engineering, South China Normal University, Guangzhou 510006, China
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16
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Zhou Y, Yang H, Wang C, Xue Y, Wang X, Bao C, Zhu L. In situ formation of a biomimetic lipid membrane triggered by an aggregation-enhanced photoligation chemistry. Chem Sci 2021; 12:3627-3632. [PMID: 34163636 PMCID: PMC8179432 DOI: 10.1039/d0sc06049f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Nature or synthetic systems that can self-assemble into biomimetic membranes and form compartments in aqueous solution have received extensive attention. However, these systems often have the problems of requiring complex processes or lacking of control in simulating lipid synthesis and membrane formation of cells. This paper demonstrates a conceptually new strategy that uses a photoligation chemistry to convert nonmembrane molecules to yield liposomes. Lysosphingomyelin (Lyso) and 2-nitrobenzyl alcohol derivatives (NBs) are used as precursors and the amphiphilic character of Lyso promotes the formation of mixed aggregates with NBs, bringing the lipid precursors into close proximity. Light irradiation triggers the conversion of NBs into reactive aldehyde intermediates, and the preassembly facilitates the efficient and specific ligation between aldehyde and Lyso amine over other biomolecules, thereby accelerating the synthesis of phospholipids and forming membrane compartments similar to natural lipids. The light-controllable transformation represents the use of an external energy stimulus to form a biomimetic phospholipid membrane, which has a wide range of applications in medicinal chemistry, synthetic biological and abiogenesis.
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Affiliation(s)
- Yaowu Zhou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Huiting Yang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Chenxi Wang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Yuan Xue
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Xuebin Wang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130# Meilong Road Shanghai 200237 China
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130# Meilong Road Shanghai 200237 China
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
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17
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Mishin V, Heck DE, Laskin DL, Laskin JD. The amplex red/horseradish peroxidase assay requires superoxide dismutase to measure hydrogen peroxide in the presence of NAD(P)H. Free Radic Res 2020; 54:620-628. [PMID: 32912004 PMCID: PMC7874521 DOI: 10.1080/10715762.2020.1821883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 01/08/2023]
Abstract
A sensitive fluorescence assay based on Amplex Red (AR) oxidation by horseradish peroxidase (AR/HRP) is described which continuously monitor rates of H2O2 production by microsomal enzymes in the presence of relatively high concentrations of NADPH. NADPH and NADH are known to interact with HRP and generate significant quantities of superoxide anion, a radical that spontaneously dismutates to form H2O2 which interferes with the AR/HRP assay. Microsomal enzymes generate H2O2 as a consequence of electron transfer from NADPH to cytochrome P450 hemoproteins with subsequent oxygen activation. We found that superoxide anion formation via the interaction of NADPH with HRP was inhibited by superoxide dismutase (SOD) without affecting H2O2 generation by microsomal enzymes. Using SOD in enzyme assays, we consistently detected rates of H2O2 production using microgram quantities of microsomal proteins (2.62 ± 0.20 picomol/min/µg protein for liver microsomes from naïve female rats, 12.27 ± 1.29 for liver microsomes from dexamethasone induced male rats, and 2.17 ± 0.25 picomol/min/µg protein for human liver microsomes). This method can also be applied to quantify rates of H2O2 production by oxidases where superoxide anion generation by NADH or NADPH and HRP can interfere with enzyme assays.
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Affiliation(s)
- Vladimir Mishin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey 08854
| | - Diane E Heck
- Department of Environmental Health Science, School of Health Sciences and Practice, New York Medical College, Valhalla, New York 10595
| | - Debra L Laskin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey 08854
| | - Jeffrey D Laskin
- Department of Environmental and Occupational Health, Rutgers University School of Public Health, Piscataway, New Jersey 08854
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18
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Moreno S, Sharan P, Engelke J, Gumz H, Boye S, Oertel U, Wang P, Banerjee S, Klajn R, Voit B, Lederer A, Appelhans D. Light-Driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002135. [PMID: 32783385 DOI: 10.1002/smll.202002135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling-contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand.
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Affiliation(s)
- Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
| | - Priyanka Sharan
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
- Materials Science Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Johanna Engelke
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
| | - Hannes Gumz
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden, 01062, Germany
| | - Susanne Boye
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
| | - Ulrich Oertel
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
| | - Peng Wang
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
| | - Susanta Banerjee
- Materials Science Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
- Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden, 01062, Germany
| | - Albena Lederer
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
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19
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Measurement of Oxidative Stress Markers In Vitro Using Commercially Available Kits. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-47318-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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20
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Dong B, Mansour N, Pei Y, Wang Z, Huang T, Filbrun SL, Chen M, Cheng X, Pruski M, Huang W, Fang N. Single Molecule Investigation of Nanoconfinement Hydrophobicity in Heterogeneous Catalysis. J Am Chem Soc 2020; 142:13305-13309. [PMID: 32687344 DOI: 10.1021/jacs.0c05905] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanoconfinement imposes physical constraints and chemical effects on reactivity in nanoporous catalyst systems. In the present study, we lay the groundwork for quantitative single-molecule measurements of the effects of chemical environment on heterogeneous catalysis in nanoconfinement. Choosing hydrophobicity as an exemplary chemical environmental factor, we compared a range of essential parameters for an oxidation reaction on platinum nanoparticles (NPs) confined in hydrophilic and hydrophobic nanopores. Single-molecule experimental measurements at the single particle level showed higher catalytic activity, stronger adsorption strength, and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores. Interestingly, different dissociation kinetic behaviors of the product molecules in the two types of nanopores were deduced from the single-molecule imaging data.
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Affiliation(s)
- Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Nourhan Mansour
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuchen Pei
- Department of Chemistry, Iowa State University Ames, Iowa 50011, United States.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Zhuoran Wang
- Department of Chemistry, Iowa State University Ames, Iowa 50011, United States.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Tengxiang Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Minda Chen
- Department of Chemistry, Iowa State University Ames, Iowa 50011, United States.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Xiaodong Cheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Marek Pruski
- Department of Chemistry, Iowa State University Ames, Iowa 50011, United States.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Wenyu Huang
- Department of Chemistry, Iowa State University Ames, Iowa 50011, United States.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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21
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Montaser A, Lehtonen M, Gynther M, Huttunen KM. L-Type Amino Acid Transporter 1-Utilizing Prodrugs of Ketoprofen Can Efficiently Reduce Brain Prostaglandin Levels. Pharmaceutics 2020; 12:pharmaceutics12040344. [PMID: 32290494 PMCID: PMC7238114 DOI: 10.3390/pharmaceutics12040344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
In order to efficiently combat neuroinflammation, it is essential to deliver the anti-inflammatory drugs to their target sites in the brain. Pro-drugs utilizing the L-type amino acid transporter 1 (LAT1) can be transported across the blood-brain barrier (BBB) and the cellular barriers of the brain’s parenchymal cells. In this study, we evaluated, for the first time, the efficacy of LAT1-utilizing prodrugs of ketoprofen (KPF) on cyclooxygenase (COX) enzymes in vitro and prostaglandin E2 production in vivo by using an enzymatic assay and liquid chromatography- tandem mass spectrometry method, respectively. Aliphatic amino acid-conjugated pro-drugs inhibited the peroxidase activity of COX in vitro in their intact form (85% inhibition, IC50 ≈ 1.1 µM and 79%, IC50 ≈ 2.3 µM), which was comparable to KPF (90%, IC50 ≈ 0.9). Thus, these compounds acted more as KPF derivatives rather than pro-drugs. In turn, aromatic amino acid-conjugated pro-drugs behaved differently. The ester pro-drug inhibited the COX peroxidase activity in vitro (90%, IC50 ≈ 0.6 µM) due to its bioconversion to KPF, whereas the amide pro-drug was inactive toward COX enzymes in vitro. However, the amide pro-drug released KPF in the mouse brain in sufficient and effective amounts measured as reduced PGE2 levels.
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22
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Wang L, Chen Y. Luminescence-Sensing Tb-MOF Nanozyme for the Detection and Degradation of Estrogen Endocrine Disruptors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:8351-8358. [PMID: 31965786 DOI: 10.1021/acsami.9b22537] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using flexible structures and components of metal-organic framework (MOF) materials, we designed and developed an artificial nanozyme with dual functions of a catalyst and luminescent sensor specifically for the determination and degradation of hormone 17β-estradiol (E2) and its derivatives (E1, E3, and EE2), a class of disruptors with strong effect on the human endocrine system. This nanozyme composed of the luminescent Tb3+ ion, catalytic coenzyme factor hemin, and light-harvesting ligand can be used to both degrade E2 like natural horseradish peroxidase (HRP) and sense E2 as low as 50 pM by its luminescence. The nanozyme catalyzes the decomposition of E2 and its derivatives through a mechanism of active hydroxyl radicals and oxidative high-valent iron-oxo intermediates. The prepared nanozyme is pluripotent, stable, and cheap and can replace the widely used combination of natural enzyme and chromogenic substrate. The present strategy of constructing artificial enzymes directly from functional units provides a new way for the design and development of smart, multifunctional artificial enzymes.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , P. R. China
| | - Yang Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , P. R. China
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23
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Yadav AK, Reinhardt CJ, Arango AS, Huff HC, Dong L, Malkowski MG, Das A, Tajkhorshid E, Chan J. An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells. Angew Chem Int Ed Engl 2020; 59:3307-3314. [PMID: 31854058 PMCID: PMC7416425 DOI: 10.1002/anie.201914845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 01/05/2023]
Abstract
Cyclooxygenase-2 (COX-2) overexpression is prominent in inflammatory diseases, neurodegenerative disorders, and cancer. Directly monitoring COX-2 activity within its native environment poses an exciting approach to account for and illuminate the effect of the local environments on protein activity. Herein, we report the development of CoxFluor, the first activity-based sensing approach for monitoring COX-2 within live cells with confocal microscopy and flow cytometry. CoxFluor strategically links a natural substrate with a dye precursor to engage both the cyclooxygenase and peroxidase activities of COX-2. This catalyzes the release of resorufin and the natural product, as supported by molecular dynamics and ensemble docking. CoxFluor enabled the detection of oxygen-dependent changes in COX-2 activity that are independent of protein expression within live macrophage cells.
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Affiliation(s)
- Anuj K Yadav
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Reinhardt
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hannah C Huff
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Liang Dong
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Michael G Malkowski
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Aditi Das
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Emad Tajkhorshid
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jefferson Chan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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24
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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25
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Yadav AK, Reinhardt CJ, Arango AS, Huff HC, Dong L, Malkowski MG, Das A, Tajkhorshid E, Chan J. An Activity‐Based Sensing Approach for the Detection of Cyclooxygenase‐2 in Live Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914845] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Anuj K. Yadav
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Christopher J. Reinhardt
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Andres S. Arango
- Center for Biophysics and Quantitative Biology Department of Biochemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Hannah C. Huff
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Liang Dong
- Department of Structural Biology Jacobs School of Medicine and Biomedical Sciences University at Buffalo Buffalo NY 14203 USA
| | - Michael G. Malkowski
- Department of Structural Biology Jacobs School of Medicine and Biomedical Sciences University at Buffalo Buffalo NY 14203 USA
| | - Aditi Das
- Center for Biophysics and Quantitative Biology Department of Biochemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Comparative Biosciences University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Center for Biophysics and Quantitative Biology Department of Biochemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Jefferson Chan
- Department of Chemistry Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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26
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Beltran-Torres M, Sugich-Miranda R, Santacruz-Ortega H, Machi L, Inoue M, Velázquez-Contreras EF, Soberanes Y, Höpfl H, Pérez-González R, Navarro RE, Salazar-Medina AJ, Sotelo Mundo RR. Comparative Studies of Structures and Peroxidase-like Activities of Copper(II) and Iron(III) Complexes with an EDTA-Based Phenylene-Macrocycle and Its Acyclic Analogue. ACS OMEGA 2019; 4:22487-22496. [PMID: 31909331 PMCID: PMC6941385 DOI: 10.1021/acsomega.9b03164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
With the objective of studying the conformational and macrocyclic effects of selected metal chelates on their peroxidase activities, Cu2+ and Fe3+ complexes were synthesized with a macrocyclic derivative of ethylenediaminetetraacetic acid and o-phenylenediamine (abbreviated as edtaodH2) and its new open-chain analogue (edtabzH2). The Fe3+ complex of edtaodH2 has a peroxidase-like activity, whereas the complex of edtabzH2 does not. The X-ray study of the former shows the formation of a dimeric molecule {[Fe(edtaod)]2O} in which each metal with an octahedral coordination is overposed over the macrocyclic cavity, as a result of rigid macrocyclic frame, to form an Fe-O-Fe bridge; the exposure of the central metal to the environment facilitates the capture of oxygen to drive the biomimetic activity. The peroxidase-inactive Fe3+ complex consists of a mononuclear complex ion [Fe(edtabz)(H2O)]+, the metal ion of which is suited in a distorted pentagonal bipyramid to be protected from environmental oxygen. The copper(II) complexes, which have mononuclear structures with high thermodynamic stability compared with the iron(III) complexes, show no peroxidase activity. The steric effects play a fundamental role in the biomimetic activity.
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Affiliation(s)
- Melissa Beltran-Torres
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Rocío Sugich-Miranda
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Hisila Santacruz-Ortega
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Lorena Machi
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Motomichi Inoue
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Enrique F. Velázquez-Contreras
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Yedith Soberanes
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
- Centro de Investigación en Alimentación
y Desarrollo A.C. (CIAD), Carretera Gustavo Enrique Astiazarán Rosas Num. 46 Col. La
Victoria, Hermosillo, Sonora 83304, Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas, Instituto de Investigación
en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
| | - Refugio Pérez-González
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Rosa Elena Navarro
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Alex J. Salazar-Medina
- Departamento
de Investigación en Polímeros y Materiales and Departamento
de Ciencias Químico Biológicas, Universidad de Sonora, Blvd. Luis Encinas y Calle Rosales S/N, Hermosillo, Sonora 83000, Mexico
| | - Rogerio R. Sotelo Mundo
- Centro de Investigación en Alimentación
y Desarrollo A.C. (CIAD), Carretera Gustavo Enrique Astiazarán Rosas Num. 46 Col. La
Victoria, Hermosillo, Sonora 83304, Mexico
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27
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Wu C, Maley AM, Walt DR. Single-molecule measurements in microwells for clinical applications. Crit Rev Clin Lab Sci 2019:1-21. [PMID: 31865834 DOI: 10.1080/10408363.2019.1700903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to detect and analyze proteins, nucleic acids, and other biomolecules is critical for clinical diagnostics and for understanding the underlying mechanisms of disease. Current detection methods in clinical and research laboratories rely upon bulk measurement techniques such as immunoassays, polymerase chain reaction, and mass spectrometry to detect these biomarkers. However, many potentially useful protein or nucleic acid biomarkers in blood, saliva, or other biofluids exist at concentrations well below the detection limits of current methods, necessitating the development of more sensitive technologies. Single-molecule measurements are poised to address this challenge, vastly improving sensitivity for detecting low abundance biomarkers and rare events within a population. Microwell arrays have emerged as a powerful tool for single-molecule measurements, enabling ultrasensitive detection of disease-relevant biomolecules in easily accessible biofluids. This review discusses the development, fundamentals, and clinical applications of microwell-based single-molecule methods, as well as challenges and future directions for translating these methods to the clinic.
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Affiliation(s)
- Connie Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Adam M Maley
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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28
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Tobos CI, Kim S, Rissin DM, Johnson JM, Douglas S, Yan S, Nie S, Rice B, Sung KJ, Sikes HD, Duffy DC. Sensitivity and binding kinetics of an ultra-sensitive chemiluminescent enzyme-linked immunosorbent assay at arrays of antibodies. J Immunol Methods 2019; 474:112643. [PMID: 31401067 DOI: 10.1016/j.jim.2019.112643] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022]
Abstract
We have characterized the sensitivity and kinetics of a multiplex immunoassay system based on detection of chemiluminescence (CL) at arrays of antibodies. This enzyme-linked immunosorbent assay (ELISA) was based on the spotting of different antibodies in a circular pattern at the bottom of a well of a microtiter plate. Sandwich immunocomplexes within each spot were labeled with horse radish peroxidase, and CL was generated locally to each spot in the array from turnover of luminol substrate. CL from the arrays across the plate was collected in single images; long exposure times were used to maximize sensitivity, and short exposure times were used to extend the dynamic range at higher signals. Image analysis was used to determine the intensity of light from each spot in the array, and intensity was converted to concentration of protein via comparison to a calibration curve. To determine the intrinsic sensitivity of the CL ELISA array, streptavidin horseradish peroxidase (SA-HRP) was captured on an array spotted with biotinylated detection antibodies. The limit of detection (LOD) of SA-HRP was 105 aM, or 3200 enzymes per 50 μL. A single-plex assay for prostate specific antigen (PSA) was developed that had an LOD of 79 aM when the microtiter plate was shaken orbitally, comparable to the most sensitive immunoassays reported to date. Normalization of CL signals in the PSA assay to signal per molecule of SA-HRP showed that the efficiency of the shaken assay was ~40%. When the plates were not shaken, the efficiency was ~4.5%, i.e., ~9-fold lower than when shaken. To better understand the theoretical basis of the sensitivity of these assays, we developed COMSOL numerical models of the binding kinetics at the array for plates that were shaken orbitally and those not shaken. Experimental data from the orbitally shaken PSA assay were best modeled by inertial mixing in a three-layer system that included a 8-μm-thick concentration boundary layer. Experimental data from the unshaken PSA assay were well modeled by diffusion-limited kinetics. A single-plex assay for IL-10 was developed with an LOD of 69 aM or 1.5 fg/mL, and used to measure this cytokine in plasma and serum of 10 healthy individuals. A 5-plex assay for IL-5, IL-6, IL-10, IL-22, and TNF-α was developed with LODs of 56 aM, 237 aM, 69 aM, 88 aM, and 373 aM, respectively. The assay was used to measure these 5 cytokines in the plasma and serum of the same individuals. The correlation in concentration of IL-10 measured in single-plex and multiplex assays was good (r2 = 0.89; bias = 14.5%). The factors that result in the high sensitivity of CL ELISA arrays-mostly high signal to noise ratio of extended chemiluminescent imaging-are discussed. This multiplex CL ELISA could be used for sensitive profiling of multiple proteins for in vitro diagnostics and biomarker detection in the development of therapeutics.
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Affiliation(s)
- Carmen I Tobos
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Seunghyeon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Rissin
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Joseph M Johnson
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Scott Douglas
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Susan Yan
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Shuai Nie
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Bradley Rice
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David C Duffy
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA.
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29
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Jiang Y, Li X, Morrow BR, Pothukuchy A, Gollihar J, Novak R, Reilly CB, Ellington AD, Walt DR. Single-Molecule Mechanistic Study of Enzyme Hysteresis. ACS CENTRAL SCIENCE 2019; 5:1691-1698. [PMID: 31660437 PMCID: PMC6813718 DOI: 10.1021/acscentsci.9b00718] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 05/04/2023]
Abstract
Hysteresis is an important feature of enzyme-catalyzed reactions, as it reflects the influence of enzyme regulation in the presence of ligands such as substrates or allosteric molecules. In typical kinetic studies of enzyme activity, hysteretic behavior is observed as a "lag" or "burst" in the time course of the catalyzed reaction. These lags and bursts are due to the relatively slow transition from one state to another state of the enzyme molecule, with different states having different kinetic properties. However, it is difficult to understand the underlying mechanism of hysteresis by observing bulk reactions because the different enzyme molecules in the population behave stochastically. In this work, we studied the hysteretic behavior of mutant β-glucuronidase (GUS) using a high-throughput single-molecule array platform and investigated the effect of thermal treatment on the hysteresis.
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Affiliation(s)
- Yu Jiang
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Barrett R. Morrow
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Arti Pothukuchy
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Richard Novak
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Charles B. Reilly
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
| | - Andrew D. Ellington
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- E-mail:
| | - David R. Walt
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute, Harvard University, Boston, Massachusetts 02115, United States
- E-mail:
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30
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Dong B, Pei Y, Mansour N, Lu X, Yang K, Huang W, Fang N. Deciphering nanoconfinement effects on molecular orientation and reaction intermediate by single molecule imaging. Nat Commun 2019; 10:4815. [PMID: 31645571 PMCID: PMC6811571 DOI: 10.1038/s41467-019-12799-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
Nanoconfinement could dramatically change molecular transport and reaction kinetics in heterogeneous catalysis. Here we specifically design a core-shell nanocatalyst with aligned linear nanopores for single-molecule studies of the nanoconfinement effects. The quantitative single-molecule measurements reveal unusual lower adsorption strength and higher catalytic activity on the confined metal reaction centres within the nanoporous structure. More surprisingly, the nanoconfinement effects on enhanced catalytic activity are larger for catalysts with longer and narrower nanopores. Experimental evidences, including molecular orientation, activation energy, and intermediate reactive species, have been gathered to provide a molecular level explanation on how the nanoconfinement effects enhance the catalyst activity, which is essential for the rational design of highly-efficient catalysts.
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Affiliation(s)
- Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Yuchen Pei
- Department of Chemistry, Iowa State University, and Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA
| | - Nourhan Mansour
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Xuemei Lu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, 215006, Suzhou, P. R. China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, 215006, Suzhou, P. R. China
| | - Wenyu Huang
- Department of Chemistry, Iowa State University, and Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA.
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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31
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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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32
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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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33
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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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Zielonka J, Kalyanaraman B. Small-molecule luminescent probes for the detection of cellular oxidizing and nitrating species. Free Radic Biol Med 2018; 128:3-22. [PMID: 29567392 PMCID: PMC6146080 DOI: 10.1016/j.freeradbiomed.2018.03.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 01/24/2023]
Abstract
Reactive oxygen species (ROS) have been implicated in both pathogenic cellular damage events and physiological cellular redox signaling and regulation. To unravel the biological role of ROS, it is very important to be able to detect and identify the species involved. In this review, we introduce the reader to the methods of detection of ROS using luminescent (fluorescent, chemiluminescent, and bioluminescent) probes and discuss typical limitations of those probes. We review the most widely used probes, state-of-the-art assays, and the new, promising approaches for rigorous detection and identification of superoxide radical anion, hydrogen peroxide, and peroxynitrite. The combination of real-time monitoring of the dynamics of ROS in cells and the identification of the specific products formed from the probes will reveal the role of specific types of ROS in cellular function and dysfunction. Understanding the molecular mechanisms involving ROS may help with the development of new therapeutics for several diseases involving dysregulated cellular redox status.
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Affiliation(s)
- Jacek Zielonka
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States.
| | - Balaraman Kalyanaraman
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States
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Kunding AH, Busk LL, Webb H, Klafki HW, Otto M, Kutter JP, Dufva M. Micro-droplet arrays for micro-compartmentalization using an air/water interface. LAB ON A CHIP 2018; 18:2797-2805. [PMID: 30123911 DOI: 10.1039/c8lc00608c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Here we present a water-in-air droplet platform for micro-compartmentalization for single molecule guided synthesis and analysis consisting of a flow-system hosting dense arrays of aqueous microdroplets on a glass surface surrounded by air. The droplets are formed in a few seconds by passing a waterfront over the array of hydrophilic spots surrounded by a hydrophobic coating, thus forming a micro-droplet array (MDA). The droplet volumes are tunable from approximately 50 femtoliter to 20 picoliter by adjusting the size of the hydrophilic spots. MDAs consisting of femtoliter volume droplets were stable for more than 24 hours in air at 37 °C in a reversibly sealed flow-system, thus allowing us to perform assays that require long incubations in the droplets. Using differently fluorescing liquids, it was further shown that droplets can be reformed on the same MDA several times by passing a new liquid plug over the surface, and that fluorescence from one reaction can be washed away with little to no carry-over, hence allowing for multistep reactions to be carried out on the system. The MDA created by an air/water interface supported digital immunoassays as was demonstrated by measuring the Aβ42 peptide in cerebrospinal fluid of Alzheimers patients and control patients. To demonstrate a two step droplet assay, first, histidine tagged peptides were expressed in the droplets and bound to the droplet-enclosed surface. Subsequently, the his-tagged peptides were detected using enzyme-conjugated antibodies in a second droplet generation step. As such, the chip demonstrates features necessary for library preparations for high throughput screening applications.
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Affiliation(s)
- Andreas H Kunding
- Dept. of research & development, SELMA Diagnostics ApS, Copenhagen Bio-Science Park, 2200 Copenhagen, Denmark
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36
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Kienle DF, Falatach RM, Kaar JL, Schwartz DK. Correlating Structural and Functional Heterogeneity of Immobilized Enzymes. ACS NANO 2018; 12:8091-8103. [PMID: 30067333 DOI: 10.1021/acsnano.8b02956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.
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Affiliation(s)
- Daniel F Kienle
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Rebecca M Falatach
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
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Bottom-up single-molecule strategy for understanding subunit function of tetrameric β-galactosidase. Proc Natl Acad Sci U S A 2018; 115:8346-8351. [PMID: 30061400 DOI: 10.1073/pnas.1805690115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this paper, we report an example of the engineered expression of tetrameric β-galactosidase (β-gal) containing varying numbers of active monomers. Specifically, by combining wild-type and single-nucleotide polymorphism plasmids at varying ratios, tetrameric β-gal was expressed in vitro with one to four active monomers. The kinetics of individual enzyme molecules revealed four distinct populations, corresponding to the number of active monomers in the enzyme. Using single-molecule-level enzyme kinetics, we were able to measure an accurate in vitro mistranslation frequency (5.8 × 10-4 per base). In addition, we studied the kinetics of the mistranslated β-gal at the single-molecule level.
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38
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Hsu CL, Li YJ, Jian HJ, Harroun SG, Wei SC, Ravindranath R, Lai JY, Huang CC, Chang HT. Green synthesis of catalytic gold/bismuth oxyiodide nanocomposites with oxygen vacancies for treatment of bacterial infections. NANOSCALE 2018; 10:11808-11819. [PMID: 29911241 DOI: 10.1039/c8nr00800k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have developed a simple and green solution for the synthesis of catalytic gold-doped bismuth oxyiodide (Au/BiOI) nanocomposites at room temperature from an aqueous mixture of gold ions, bismuth ions, and iodide ions. Au nanoparticles (NPs) were formed in situ and doped into BiOI nanosheets. The oxygen vacancies generated in BiOI give rise to its oxidase-like activity, and Au doping facilitated the reaction leading to a 4-fold higher oxidase-like activity of the Au/BiOI nanocomposite. The Au/BiOI nanocomposites showed wide spectrum antimicrobial activity not only against non-multidrug-resistant E. coli, K. pneumoniae, S. enteritidis, S. aureus, and B. subtilis bacteria, but also against multidrug-resistant bacteria, methicillin-resistant S. aureus (MRSA). The gold doping reduced the minimal inhibitory concentration value by ∼2000-fold for the Au/BiOI nanocomposite, in comparison with only BiOI nanoparticles. The bactericidal property of the Au/BiOI nanocomposite arose from the combined effect of the disruption of the bacterial membrane through a strong interaction of the nanocomposite with the bacteria and the generation of reactive oxygen species. Also, the Au/BiOI nanocomposite is highly biocompatible, which has been demonstrated in vitro by analysis of cytotoxicity and hemolysis, and in vivo by evaluating ocular tissue responses. Furthermore, intrastromal administration of Au/BiOI nanocomposites can effectively alleviate S. aureus-induced bacterial keratitis in rabbits, suggesting a significant disinfectant benefit in preclinical studies. The Au/BiOI nanocomposites show great potential for the inactivation of bacterial pathogens in an aqueous environment and treatment of bacterial infection-induced diseases.
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Affiliation(s)
- Chia-Lun Hsu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
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39
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Longwell CK, Labanieh L, Cochran JR. High-throughput screening technologies for enzyme engineering. Curr Opin Biotechnol 2017. [DOI: 10.1016/j.copbio.2017.05.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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40
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Prieto T, Santana V, Britto AMM, Araujo-Chaves JC, R Nascimento O, L Nantes-Cardoso I. Structure and Catalysis of Fe(III) and Cu(II) Microperoxidase-11 Interacting with the Positively Charged Interfaces of Lipids. Molecules 2017; 22:molecules22081212. [PMID: 28933729 PMCID: PMC6151982 DOI: 10.3390/molecules22081212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 11/24/2022] Open
Abstract
Numerous applications have been described for microperoxidases (MPs) such as in photoreceptors, sensing, drugs, and hydrogen evolution. The last application was obtained by replacing Fe(III), the native central metal, by cobalt ion and inspired part of the present study. Here, the Fe(III) of MP-11 was replaced by Cu(II) that is also a stable redox state in aerated medium, and the structure and activity of both MPs were modulated by the interaction with the positively charged interfaces of lipids. Comparative spectroscopic characterization of Fe(III) and Cu(II)MP-11 in the studied media demonstrated the presence of high and low spin species with axial distortion. The association of the Fe(III)MP-11 with CTAB and Cu(II)MP-11 with DODAB affected the colloidal stability of the surfactants that was recovered by heating. This result is consistent with hydrophobic interactions of MPs with DODAB vesicles and CTAB micelles. The hydrophobic interactions decreased the heme accessibility to substrates and the Fe(III) MP-11catalytic efficiency. Cu(II)MP-11 challenged by peroxides exhibited a cyclic Cu(II)/Cu(I) interconversion mechanism that is suggestive of a mimetic Cu/ZnSOD (superoxide dismutase) activity against peroxides. Hydrogen peroxide-activated Cu(II)MP-11 converted Amplex Red® to dihydroresofurin. This study opens more possibilities for technological applications of MPs.
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Affiliation(s)
- Tatiana Prieto
- Universidade Federal do ABC, Santo André 09210-170, SP, Brazil.
| | - Vinicius Santana
- Universidade de São Paulo, Instituto de Física de São Carlos, São Carlos 13400-970, SP, Brazil.
| | | | | | - Otaciro R Nascimento
- Universidade de São Paulo, Instituto de Física de São Carlos, São Carlos 13400-970, SP, Brazil.
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41
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Quantitative determination of trace hydrogen peroxide in the presence of sulfide using the Amplex Red/horseradish peroxidase assay. Anal Chim Acta 2017; 963:61-67. [DOI: 10.1016/j.aca.2017.02.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 02/08/2017] [Accepted: 02/24/2017] [Indexed: 01/07/2023]
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42
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Chen T, Dong B, Chen K, Zhao F, Cheng X, Ma C, Lee S, Zhang P, Kang SH, Ha JW, Xu W, Fang N. Optical Super-Resolution Imaging of Surface Reactions. Chem Rev 2017; 117:7510-7537. [DOI: 10.1021/acs.chemrev.6b00673] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tao Chen
- State
Key Laboratory of Electroanalytical Chemistry and Jilin Province Key
Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, P.R. China
- University of Chinese Academy of Science, Beijing, 100049, P. R. China
| | - Bin Dong
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kuangcai Chen
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Fei Zhao
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xiaodong Cheng
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Seungah Lee
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Peng Zhang
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seong Ho Kang
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ji Won Ha
- Department
of Chemistry, University of Ulsan, 93 Dahak-Ro, Nam-Gu, Ulsan 44610, Republic of Korea
| | - Weilin Xu
- State
Key Laboratory of Electroanalytical Chemistry and Jilin Province Key
Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, P.R. China
| | - Ning Fang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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43
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Craig DB, King SD, Reinfelds G, Henderson AR, Wood TE. Electrophoretic mobility, catalytic rate, and activation energy of catalysis of single molecules of the enzyme β-glucuronidase from Escherichia coli. Int J Biol Macromol 2017; 96:669-674. [DOI: 10.1016/j.ijbiomac.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 10/12/2016] [Accepted: 12/12/2016] [Indexed: 12/28/2022]
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44
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Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. NANOSCALE 2016; 8:19928-19944. [PMID: 27883140 PMCID: PMC5145784 DOI: 10.1039/c6nr06794h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.
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Affiliation(s)
- Dibyendu K Sasmal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura E Pulido
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Shan Kasal
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| | - Jun Huang
- The Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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45
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Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation. Proc Natl Acad Sci U S A 2016; 113:15006-15011. [PMID: 27940917 DOI: 10.1073/pnas.1613404114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unraveling the conformational details of an enzyme during the essential steps of a catalytic reaction (i.e., enzyme-substrate interaction, enzyme-substrate active complex formation, nascent product formation, and product release) is challenging due to the transient nature of intermediate conformational states, conformational fluctuations, and the associated complex dynamics. Here we report our study on the conformational dynamics of horseradish peroxidase using single-molecule multiparameter photon time-stamping spectroscopy with mechanical force manipulation, a newly developed single-molecule fluorescence imaging magnetic tweezers nanoscopic approach. A nascent-formed fluorogenic product molecule serves as a probe, perfectly fitting in the enzymatic reaction active site for probing the enzymatic conformational dynamics. Interestingly, the product releasing dynamics shows the complex conformational behavior with multiple product releasing pathways. However, under magnetic force manipulation, the complex nature of the multiple product releasing pathways disappears and more simplistic conformations of the active site are populated.
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46
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Affiliation(s)
- Yi Zhang
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Japan Science and Technology Agency , Tokyo 102-0076, Japan
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47
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Abstract
Over the last decade, femtoliter arrays have been used as a simple and robust way to encapsulate and monitor the kinetics of single enzyme molecules. Encapsulating individual enzyme molecules within a femtoliter-sized reaction chamber does not require immobilization of the enzyme molecules or fluorescent tagging of the enzyme molecules, which offers the unique advantage of observing unmodified single enzyme molecules free in solution. Several fascinating details about enzyme kinetics have been revealed using these femtoliter arrays, which were unattainable from traditional ensemble experiments. Here, we discuss various considerations to take into account when developing single-molecule enzyme assays in femtoliter arrays and the advantages and disadvantages of various protocols.
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Affiliation(s)
| | - D R Walt
- Tufts University, Medford, MA, United States.
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48
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A novel fluorimetric method for laccase activities measurement using Amplex Red as substrate. Talanta 2016; 162:143-150. [PMID: 27837810 DOI: 10.1016/j.talanta.2016.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/18/2016] [Accepted: 10/02/2016] [Indexed: 11/21/2022]
Abstract
In this paper, a novel fluorescence-based method for laccase assay was presented. The method was based on the transformation of Amplex Red into a highly fluorescent and colored resorufin catalyzed by laccase in the presence of O2. The catalysis and transformation mechanism were investigated in detail. The kinetic parameters of the Amplex Red catalysis by laccase were determined using the Lineweaver-Burk equation. Vmax and Km were estimated to be 15.63μmolmin-1 and 76.88μmolL-1, respectively. Under optimal conditions, a good linear correlation was found between fluorescence intensity and laccase activities within 5.62-702UL-1 (r=0.9992), with a detection limit of 1.76UL-1 (S/N=3). A series of repeatability measurements (351UL-1 laccase) gave reproducible results with a relative standard deviation (RSD) of 1.9% (n=11). The recoveries ranged from 93.7% to 100.0% after standard additions. Common existing species such as Mg2+, Zn2+, Ni2+, Al3+, Co2+, Cd2+, K+, Ca2+, Na+, Fe3+, Li+, Cu2+, Mn2+, Fe2+, l-lysine, glycine, glucose, phenol, humic acid, lignin peroxidase, manganese peroxidase alkaline phosphatase, cellulose, glucose oxidase, urease, catalase, invertase, and horseradish peroxidase did not significantly exhibit interference. The test solution (i.e., Amplex Red stock solution) could stabilize at least three months via storage in dark at 4±0.1°C. These results confirmed that the laccase-Amplex Red system was stable and reproducible with strong anti-interference ability and good selectivity, suggesting that this method can has great potential in practical applications for the assay of laccase activity. The proposed method was further successfully used to detect laccase activities in 38 soil samples. We noticed that the laccase activity significantly correlated with total nitrogen content (r=0.559; p<0.01) of soil, indicating laccase activity assay holds great promise as an index of soil analysis. These findings indicate that this presented method has great perspective in ecological investigation and fundamental research of soil environment.
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49
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Ribou AC. Synthetic Sensors for Reactive Oxygen Species Detection and Quantification: A Critical Review of Current Methods. Antioxid Redox Signal 2016; 25:520-33. [PMID: 27225539 DOI: 10.1089/ars.2016.6741] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
SIGNIFICANCE Redox reactions play important roles in both physiological and pathological processes, highlighting the importance of quantifying and localizing intracellular redox-active components. Most research has focused on direct investigation of reactive oxygen species (ROS). Intensity-based fluorescent methods are very sensitive and easy to use, but they lack specificity and can produce artifacts. In this article, we focus on synthetic sensors, describing experimental pitfalls associated with their use. We also present alternative methods for the detection of free radicals. RECENT ADVANCES New approaches have been developed to overcome the main artifact of intensity-based methods: spurious changes in fluorescence intensity caused by oxidation. These new approaches are based on analytical measurements of the oxidized sensors or techniques that are not susceptible to oxidation, such as electron spin resonance and fluorescence lifetime-based methods. Regardless of the approach, the need for detection of ROS on the subcellular level, especially in the mitochondria, has motivated the development of new probes. CRITICAL ISSUES Flow cytometry systems and confocal microscopes are now available to the majority of biologists, and commercially available probes are, therefore, more widely used. The fact that these new applications are cited in thousands of publications makes these sensors even more attractive. FUTURE DIRECTIONS The field of ROS detection by synthetic sensors continues to expand, bringing needed additional research to the development of robust techniques that are applicable both in vitro and in vivo. Antioxid. Redox Signal. 25, 520-533.
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Affiliation(s)
- Anne-Cécile Ribou
- Institute of Modeling and Analysis in Geo-Environmental and Health (IMAGES_ESPACE-DEV), University of Perpignan Via Domitia , Perpignan, France
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50
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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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