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Diamanti E, López-Gallego F. Single-Particle and Single-Molecule Characterization of Immobilized Enzymes: A Multiscale Path toward Optimizing Heterogeneous Biocatalysts. Angew Chem Int Ed Engl 2024; 63:e202319248. [PMID: 38476019 DOI: 10.1002/anie.202319248] [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: 12/13/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Heterogeneous biocatalysis is highly relevant in biotechnology as it offers several benefits and practical uses. To leverage the full potential of heterogeneous biocatalysts, the establishment of well-crafted protocols, and a deeper comprehension of enzyme immobilization on solid substrates are essential. These endeavors seek to optimize immobilized biocatalysts, ensuring maximal enzyme performance within confined spaces. For this aim, multidimensional characterization of heterogeneous biocatalysts is required. In this context, spectroscopic and microscopic methodologies conducted at different space and temporal scales can inform about the intraparticle enzyme kinetics, the enzyme spatial distribution, and the mass transport issues. In this Minireview, we identify enzyme immobilization, enzyme catalysis, and enzyme inactivation as the three main processes for which advanced characterization tools unveil fundamental information. Recent advances in operando characterization of immobilized enzymes at the single-particle (SP) and single-molecule (SM) levels inform about their functional properties, unlocking the full potential of heterogeneous biocatalysis toward biotechnological applications.
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Affiliation(s)
- Eleftheria Diamanti
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain
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2
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Leccese S, Calcinoni A, Wilson A, Kirilovsky D, Carbonera D, Onfroy T, Jolivalt C, Mezzetti A. Orange Carotenoid Protein in Mesoporous Silica: A New System towards the Development of Colorimetric and Fluorescent Sensors for pH and Temperature. MICROMACHINES 2023; 14:1871. [PMID: 37893308 PMCID: PMC10609006 DOI: 10.3390/mi14101871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
Orange carotenoid protein (OCP) is a photochromic carotenoprotein involved in the photoprotection of cyanobacteria. It is activated by blue-green light to a red form OCPR capable of dissipating the excess of energy of the cyanobacterial photosynthetic light-harvesting systems. Activation to OCPR can also be achieved in the dark. In the present work, activation by pH changes of two different OCPs-containing echinenone or canthaxanthin as carotenoids-is investigated in different conditions. A particular emphasis is put on OCP encapsulated in SBA-15 mesoporous silica nanoparticles. It is known that in these hybrid systems, under appropriate conditions, OCP remains photoactive. Here, we show that when immobilised in SBA-15, the OCP visible spectrum is sensitive to pH changes, but such a colorimetric response is very different from the one observed for OCP in solution. In both cases (SBA-15 matrices and solutions), pH-induced colour changes are related either by orange-to-red OCP activation, or by carotenoid loss from the denatured protein. Of particular interest is the response of OCP in SBA-15 matrices, where a sudden change in the Vis absorption spectrum and in colour is observed for pH changing from 2 to 3 (in the case of canthaxanthin-binding OCP in SBA-15: λMAX shifts from 454 to 508 nm) and for pH changing from 3 to 4 (in the case of echinenone-binding OCP in SBA-15: λMAX shifts from 445 to 505 nm). The effect of temperature on OCP absorption spectrum and colour (in SBA-15 matrices) has also been investigated and found to be highly dependent on the properties of the used mesoporous silica matrix. Finally, we also show that simultaneous encapsulation in selected surface-functionalised SBA-15 nanoparticles of appropriate fluorophores makes it possible to develop OCP-based pH-sensitive fluorescent systems. This work therefore represents a proof of principle that OCP immobilised in mesoporous silica is a promising system in the development of colorimetric and fluorometric pH and temperature sensors.
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Affiliation(s)
- Silvia Leccese
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 Place Jussieu, 75005 Paris, France (A.C.); (C.J.)
| | - Andrea Calcinoni
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 Place Jussieu, 75005 Paris, France (A.C.); (C.J.)
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy;
| | - Adjélé Wilson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France (D.K.)
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France (D.K.)
| | | | - Thomas Onfroy
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 Place Jussieu, 75005 Paris, France (A.C.); (C.J.)
| | - Claude Jolivalt
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 Place Jussieu, 75005 Paris, France (A.C.); (C.J.)
| | - Alberto Mezzetti
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 Place Jussieu, 75005 Paris, France (A.C.); (C.J.)
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3
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Bolivar JM, Woodley JM, Fernandez-Lafuente R. Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization. Chem Soc Rev 2022; 51:6251-6290. [PMID: 35838107 DOI: 10.1039/d2cs00083k] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.
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Affiliation(s)
- Juan M Bolivar
- FQPIMA group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, 28040, Spain
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC, C/Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid 28049, Spain. .,Center of Excellence in Bionanoscience Research, External Scientific Advisory Academic, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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4
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Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials. Molecules 2021; 26:molecules26102952. [PMID: 34065629 PMCID: PMC8156760 DOI: 10.3390/molecules26102952] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors are gaining widespread attention as non-destructive tools, visible to the human eye, that are capable of a real-time and in-situ response. Optical “visual” sensors are expanding researchers’ interests in many chemical contexts and are routinely used for biological, environmental, and medical applications. In this review we provide an overview of trending colorimetric, fluorescent, or dual-mode responsive visual pH sensors. These sensors include molecular synthetic organic sensors, metal organic frameworks (MOF), engineered sensing nanomaterials, and bioengineered sensors. We review different typological chemical entities of visual pH sensors, three-dimensional structures, and signaling mechanisms for pH sensing and applications; developed in the past five years. The progression of this review from simple organic molecules to biological macromolecules seeks to benefit beginners and scientists embarking on a project of pH sensing development, who needs background information and a quick update on advances in the field. Lessons learned from these tools will aid pH determination projects and provide new ways of thinking for cell bioimaging or other cutting-edge in vivo applications.
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5
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Steinegger A, Wolfbeis OS, Borisov SM. Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications. Chem Rev 2020; 120:12357-12489. [PMID: 33147405 PMCID: PMC7705895 DOI: 10.1021/acs.chemrev.0c00451] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 12/13/2022]
Abstract
This is the first comprehensive review on methods and materials for use in optical sensing of pH values and on applications of such sensors. The Review starts with an introduction that contains subsections on the definition of the pH value, a brief look back on optical methods for sensing of pH, on the effects of ionic strength on pH values and pKa values, on the selectivity, sensitivity, precision, dynamic ranges, and temperature dependence of such sensors. Commonly used optical sensing schemes are covered in a next main chapter, with subsections on methods based on absorptiometry, reflectometry, luminescence, refractive index, surface plasmon resonance, photonic crystals, turbidity, mechanical displacement, interferometry, and solvatochromism. This is followed by sections on absorptiometric and luminescent molecular probes for use pH in sensors. Further large sections cover polymeric hosts and supports, and methods for immobilization of indicator dyes. Further and more specific sections summarize the state of the art in materials with dual functionality (indicator and host), nanomaterials, sensors based on upconversion and 2-photon absorption, multiparameter sensors, imaging, and sensors for extreme pH values. A chapter on the many sensing formats has subsections on planar, fiber optic, evanescent wave, refractive index, surface plasmon resonance and holography based sensor designs, and on distributed sensing. Another section summarizes selected applications in areas, such as medicine, biology, oceanography, bioprocess monitoring, corrosion studies, on the use of pH sensors as transducers in biosensors and chemical sensors, and their integration into flow-injection analyzers, microfluidic devices, and lab-on-a-chip systems. An extra section is devoted to current challenges, with subsections on challenges of general nature and those of specific nature. A concluding section gives an outlook on potential future trends and perspectives.
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Affiliation(s)
- Andreas Steinegger
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Otto S. Wolfbeis
- Institute
of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany
| | - Sergey M. Borisov
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
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6
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Liu J, Tong S, Sun H, Chang Y, Luo H, Yu H, Shen Z. Effect of shaking speed on immobilization of cephalosporin C acylase: Correlation between protein distribution and properties of the immobilized enzymes. Biotechnol Prog 2020; 37:e3063. [PMID: 32776709 DOI: 10.1002/btpr.3063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/06/2022]
Abstract
During enzyme immobilization, enzyme activity and protein distribution are affected by various factors such as enzyme load, temperature, and pH. In general, two types of protein distribution patterns (heterogeneous or homogeneous) are observed inside a porous carrier, owing to differences in preparation parameters. During the immobilization of a fusion protein (CCApH) of cephalosporin C acylase (CCA) and pHluorin (a pH-sensitive mutant of green fluorescent protein), different shaking speeds induced obvious differences in protein distribution on an epoxy carrier, LX-1000EPC. Enzyme immobilization with a homogeneous distribution pattern was observed at a low shaking speed (120 rpm) with an operational stability of 10 batches at 37°C. The operational stability of an immobilisate with heterogeneous protein distribution prepared at a high shaking speed (200 rpm) was six batches. Given the pH-sensitive characteristics of pHluorin in the fusion protein, the intraparticle pH of CCApH immobilisates during catalysis was monitored using confocal laser scanning microscopy. The microenvironmental pH of the immobilisate with heterogeneous protein distribution sharply decreased by about 2 units; this decrease in the pH may be detrimental to the life-span of immobilized CCA. Thus, this work demonstrates the good operational stability of pH-sensitive proton-forming immobilized enzymes with homogeneous protein distribution.
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Affiliation(s)
- Jingran Liu
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, China.,Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Shuangming Tong
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, China.,Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Hongxu Sun
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yanhong Chang
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Hui Luo
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Zhongyao Shen
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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7
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Okkelman IA, McGarrigle R, O’Carroll S, Berrio DC, Schenke-Layland K, Hynes J, Dmitriev RI. Extracellular Ca2+-Sensing Fluorescent Protein Biosensor Based on a Collagen-Binding Domain. ACS APPLIED BIO MATERIALS 2020; 3:5310-5321. [DOI: 10.1021/acsabm.0c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Irina A. Okkelman
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Ryan McGarrigle
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Shane O’Carroll
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Daniel Carvajal Berrio
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
| | - Katja Schenke-Layland
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen 72770, Germany
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles 90095, California, United States
| | - James Hynes
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Ruslan I. Dmitriev
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
- I.M. Sechenov First Moscow State University, Institute for Regenerative Medicine, Moscow 119992, Russian Federation
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
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8
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Consolati T, Bolivar JM, Petrasek Z, Berenguer J, Hidalgo A, Guisan JM, Nidetzky B. Intraparticle pH Sensing Within Immobilized Enzymes: Immobilized Yellow Fluorescent Protein as Optical Sensor for Spatiotemporal Mapping of pH Inside Porous Particles. Methods Mol Biol 2020; 2100:319-333. [PMID: 31939133 DOI: 10.1007/978-1-0716-0215-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
pH is a fundamental variable in enzyme catalysis and its measurement therefore is crucial for understanding and optimizing enzyme-catalyzed reactions. Whereas measurements within homogeneous bulk liquid solution are prominently used, enzymes immobilized inside porous particles often suffer from pH gradients due to partition effects and heterogeneously catalyzed biochemical reactions. Unfortunately, the measurements of intraparticle pH are not available due to the lack of useful suitable methodologies; as a consequence the biocatalyst characterization is hampered. Here, a fully biocompatible methodology for real-time optical sensing of pH within porous materials is described. A genetically encoded ratiometric pH indicator, the superfolder yellow fluorescent protein (sYFP), is used to functionalize the internal surface of enzyme carrier supports. By using controlled, tailor-made immobilization, sYFP is homogeneously distributed within these materials, and so enables, via self-referenced imaging analysis, pH measurements in high accuracy and with useful spatiotemporal resolution. The hydrolysis of penicillin by a penicillin acylase, taking place in solution or confined to the solid surface of the porous matrix is used to show the monitoring of evolution of internal pH. Thus, pH sensing based on immobilized sYFP represents a broadly applicable technique to the study of the internally heterogeneous environment of immobilized enzymes into solid particles.
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Affiliation(s)
- Tanja Consolati
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Zdenek Petrasek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Jose Berenguer
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology 'Severo-Ochoa' (UAM-CSIC), Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology 'Severo-Ochoa' (UAM-CSIC), Madrid, Spain
| | - Jose M Guisan
- Institute of Catalysis and Petroleum Chemistry (ICP-CSIC), Madrid, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
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9
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Deciphering the Effect of Microbead Size Distribution on the Kinetics of Heterogeneous Biocatalysts through Single-Particle Analysis Based on Fluorescence Microscopy. Catalysts 2019. [DOI: 10.3390/catal9110896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Understanding the functionality of immobilized enzymes with spatiotemporal resolution and under operando conditions is an unmet need in applied biocatalysis, as well as priceless information to guide the optimization of heterogeneous biocatalysts for industrial purposes. Unfortunately, enzyme immobilization still relies on trial-and-error approximations that prevail over rational designs. Hence, a modern fabrication process to achieve efficient and robust heterogeneous biocatalysts demands comprehensive characterization techniques to track and understand the immobilization process at the protein–material interface. Recently, our group has developed a new generation of self-sufficient heterogeneous biocatalysts based on alcohol dehydrogenases co-immobilized with nicotinamide cofactors on agarose porous microbeads. Harnessing the autofluorescence of NAD+(P)H and using time-lapse fluorescence microscopy, enzyme activity toward the redox cofactors can be monitored inside the beads. To analyze these data, herein we present an image analytical tool to quantify the apparent Michaelis–Menten parameters of alcohol dehydrogenases co-immobilized with NAD(P)+/H at the single-particle level. Using this tool, we found a strong negative correlation between the apparent catalytic performance of the immobilized enzymes and the bead radius when using exogenous bulky substrates in reduction reactions. Therefore, applying image analytics routines to microscopy studies, we can directly unravel the functional heterogeneity of different heterogeneous biocatalyst samples tested under different reaction conditions.
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10
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Bolivar JM, Nidetzky B. The Microenvironment in Immobilized Enzymes: Methods of Characterization and Its Role in Determining Enzyme Performance. Molecules 2019; 24:molecules24193460. [PMID: 31554193 PMCID: PMC6803829 DOI: 10.3390/molecules24193460] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 12/11/2022] Open
Abstract
The liquid milieu in which enzymes operate when they are immobilized in solid materials can be quite different from the milieu in bulk solution. Important differences are in the substrate and product concentration but also in pH and ionic strength. The internal milieu for immobilized enzymes is affected by the chemical properties of the solid material and by the interplay of reaction and diffusion. Enzyme performance is influenced by the internal milieu in terms of catalytic rate (“activity”) and stability. Elucidation, through direct measurement of differences in the internal as compared to the bulk milieu is, therefore, fundamentally important in the mechanistic characterization of immobilized enzymes. The deepened understanding thus acquired is critical for the rational development of immobilized enzyme preparations with optimized properties. Herein we review approaches by opto-chemical sensing to determine the internal milieu of enzymes immobilized in porous particles. We describe analytical principles applied to immobilized enzymes and focus on the determination of pH and the O2 concentration. We show measurements of pH and [O2] with spatiotemporal resolution, using in operando analysis for immobilized preparations of industrially important enzymes. The effect of concentration gradients between solid particle and liquid bulk on enzyme performance is made evident and quantified. Besides its use in enzyme characterization, the method can be applied to the development of process control strategies.
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Affiliation(s)
- Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria.
- Chemical and Materials Engineering Department, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, A-8010 Graz, Austria.
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11
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Chen P, Ilyas I, He S, Xing Y, Jin Z, Huang C. Ratiometric pH Sensing and Imaging in Living Cells with Dual-Emission Semiconductor Polymer Dots. Molecules 2019; 24:molecules24162923. [PMID: 31409040 PMCID: PMC6721214 DOI: 10.3390/molecules24162923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 11/25/2022] Open
Abstract
Polymer dots (Pdots) represent newly developed semiconductor polymer nanoparticles and exhibit excellent characteristics as fluorescent probes. To improve the sensitivity and biocompatibility of Pdots ratiometric pH biosensors, we synthesized 3 types of water-soluble Pdots: Pdots-PF, Pdots-PP, and Pdots-PPF by different combinations of fluorescent dyes poly(9,9-dioctylfluorenyl-2,7-diyl) (PFO), poly[(9,9-dioctyl-fluorenyl-2,7-diyl)-co-(1,4-benzo-{2,1′,3}-thiadazole)] (PFBT), and fluorescein isothiocyanate (FITC). We found that Pdots-PPF exhibits optimal performance on pH sensing. PFO and FITC in Pdots-PPF produce pH-insensitive (λ = 439 nm) and pH-sensitive (λ = 517 nm) fluorescence respectively upon a single excitation at 380 nm wavelength, which enables Pdots-PPF ratiometric pH sensing ability. Förster resonance energy transfer (FRET) together with the use of PFBT amplify the FITC signal, which enables Pdots-PPF robust sensitivity to pH. The emission intensity ratio (I517/I439) of Pdots-PPF changes linearly as a function of pH within the range of pH 3.0 to 8.0. Pdots-PPF also possesses desirable reversibility and stability in pH measurement. More importantly, Pdots-PPF was successfully used for cell imaging in Hela cells, exhibiting effective cellular uptake and low cytotoxicity. Our study suggests the promising potential of Pdots-PPF as an in vivo biomarker.
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Affiliation(s)
- Piaopiao Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Iqra Ilyas
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Su He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yichen Xing
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhigang Jin
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.
| | - Chaobiao Huang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.
- Xingzhi College, Zhejiang Normal University, Jinhua 321004, China.
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12
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Benítez-Mateos AI, Mehravar E, Velasco-Lozano S, Salassa L, López-Gallego F. Selective Immobilization of Fluorescent Proteins for the Fabrication of Photoactive Materials. Molecules 2019; 24:E2775. [PMID: 31366154 PMCID: PMC6696454 DOI: 10.3390/molecules24152775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022] Open
Abstract
The immobilization of fluorescent proteins is a key technology enabling to fabricate a new generation of photoactive materials with potential technological applications. Herein we have exploited superfolder green (sGFP) and red (RFP) fluorescent proteins expressed with different polypeptide tags. We fused these fluorescent proteins to His-tags to immobilize them on graphene 3D hydrogels, and Cys-tags to immobilize them on porous microparticles activated with either epoxy or disulfide groups and with Lys-tags to immobilize them on upconverting nanoparticles functionalized with carboxylic groups. Genetically programming sGFP and RFP with Cys-tag and His-tag, respectively, allowed tuning the protein spatial organization either across the porous structure of two microbeads with different functional groups (agarose-based materials activated with metal chelates and epoxy-methacrylate materials) or across the surface of a single microbead functionalized with both metal-chelates and disulfide groups. By using different polypeptide tags, we can control the attachment chemistry but also the localization of the fluorescent proteins across the material surfaces. The resulting photoactive material formed by His-RFP immobilized on graphene hydrogels has been tested as pH indicator to measure pH changes in the alkaline region, although the immobilized fluorescent protein exhibited a narrower dynamic range to measure pH than the soluble fluorescent protein. Likewise, the immobilization of Lys-sGFP on alginate-coated upconverting nanoparticles enabled the infrared excitation of the fluorescent protein to be used as a green light emitter. These novel photoactive biomaterials open new avenues for innovative technological developments towards the fabrication of biosensors and photonic devices.
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Affiliation(s)
- Ana I Benítez-Mateos
- Heterogeneous biocatalysis group, CICbiomaGUNE, Edificio Empresarial "C", Paseo de Miramón, 182, 20014 Donostia-San Sebastián, Spain
| | - Ehsan Mehravar
- POLYMAT and Departamento de Química Aplicada, Facultad de Ciencias Químicas, University of the Basque Country, UPV/EHU, 20018 Donostia-San Sebastián, Spain
| | - Susana Velasco-Lozano
- Heterogeneous biocatalysis laboratory, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Luca Salassa
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous biocatalysis laboratory, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain.
- ARAID, Aragon foundation for Science, 50018 Zaragoza, Spain.
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Fluorescent protein nanoparticles: Synthesis and recognition of cellular oxidation damage. Colloids Surf B Biointerfaces 2019; 177:219-227. [PMID: 30743069 DOI: 10.1016/j.colsurfb.2019.01.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
Abstract
Intracellular reactive oxygen species (ROS) generation are associated with many diseases. Lots of studies focus on the detection of intracellular ROS by small fluorescent molecules. However, ROS recognized by biocompatible nanoparticles are relatively less reported. It is widely known that albumin-based nanomaterials possess unique advantages in biomedical applications because they are biodegradable and biocompatible. Herein, fluorescent protein nanoparticles (PNPs) were prepared using BSA as a starting material without introducing extra fluorescent molecules. The blue fluorescent PNPs were well characterized by FL, FTIR, CD, TEM, DLS, etc. It was revealed that the PNPs exhibited two types of emissive centers through FL spectra and the fluorescence lifetimes. Further mechanism study indicated that the fluorescence of the PNPs was mainly derived from three kinds of aromatic amino acids, namely tryptophan, tyrosine and phenylalanine. Moreover, the fluorescence properties of the PNPs were tightly related to pH. The PNPs displayed excellent stabilities under harsh conditions as well as physiological conditions. In addition, the PNPs (200 μg/mL) were nontoxic to HeLa and GES-1 cell lines, showing good biocompatibility. The cellular uptake of PNPs was occurred only when the cells were stressed with glucose oxidase or H2O2, thereafter the bright blue fluorescence was observed, indicating that it could be utilized for the recognition of cellular oxidation damage. These findings will offer novel clues for the future synthesis of even brighter protein nanoparticles and their biomedical applications.
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14
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Correa S, Puertas S, Gutiérrez L, Asín L, Martínez de la Fuente J, Grazú V, Betancor L. Design of stable magnetic hybrid nanoparticles of Si-entrapped HRP. PLoS One 2019; 14:e0214004. [PMID: 30933987 PMCID: PMC6443235 DOI: 10.1371/journal.pone.0214004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
Hybrid and composite nanoparticles represent an attractive material for enzyme integration due to possible synergic advantages of the structural builders in the properties of the nanobiocatalyst. In this study, we report the synthesis of a new stable hybrid nanobiocatalyst formed by biomimetic silica (Si) nanoparticles entrapping both Horseradish Peroxidase (HRP) (EC 1.11.1.7) and magnetic nanoparticles (MNPs). We have demonstrated that tailoring of the synthetic reagents and post immobilization treatments greatly impacted physical and biocatalytic properties such as an unprecedented ~280 times increase in the half-life time in thermal stability experiments. The optimized nanohybrid biocatalyst that showed superparamagnetic behaviour, was effective in the batch conversion of indole-3-acetic acid, a prodrug used in Direct Enzyme Prodrug Therapy (DEPT). Our system, that was not cytotoxic per se, showed enhanced cytotoxic activity in the presence of the prodrug towards HCT-116, a colorectal cancer cell line. The strategy developed proved to be effective in obtaining a stabilized nanobiocatalyst combining three different organic/inorganic materials with potential in DEPT and other biotechnological applications.
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Affiliation(s)
- Sonali Correa
- Laboratorio de Biotecnología, Universidad ORT Uruguay, Montevideo, Uruguay
| | | | - Lucía Gutiérrez
- Instituto de Nanociencia de Aragón, Universidad de Zaragoza, Campus Río Ebro, Edificio I+D, Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científica, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Laura Asín
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Jesús Martínez de la Fuente
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científica, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Valeria Grazú
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científica, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Lorena Betancor
- Laboratorio de Biotecnología, Universidad ORT Uruguay, Montevideo, Uruguay
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15
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O'Donnell N, Okkelman IA, Timashev P, Gromovykh TI, Papkovsky DB, Dmitriev RI. Cellulose-based scaffolds for fluorescence lifetime imaging-assisted tissue engineering. Acta Biomater 2018; 80:85-96. [PMID: 30261339 DOI: 10.1016/j.actbio.2018.09.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/11/2018] [Accepted: 09/23/2018] [Indexed: 12/12/2022]
Abstract
Quantitative measurement of pH and metabolite gradients by microscopy is one of the challenges in the production of scaffold-grown organoids and multicellular aggregates. Herein, we used the cellulose-binding domain (CBD) of the Cellulomonas fimi CenA protein for designing biosensor scaffolds that allow measurement of pH and Ca2+ gradients by fluorescence intensity and lifetime imaging (FLIM) detection modes. By fusing CBD with pH-sensitive enhanced cyan fluorescent protein (CBD-ECFP), we achieved efficient labeling of cellulose-based scaffolds based on nanofibrillar, bacterial cellulose, and decellularized plant materials. CBD-ECFP bound to the cellulose matrices demonstrated pH sensitivity comparable to untagged ECFP (1.9-2.3 ns for pH 6-8), thus making it compatible with FLIM-based analysis of extracellular pH. By using 3D culture of human colon cancer cells (HCT116) and adult stem cell-derived mouse intestinal organoids, we evaluated the utility of the produced biosensor scaffold. CBD-ECFP was sensitive to increases in extracellular acidification: the results showed a decline in 0.2-0.4 pH units in response to membrane depolarization by the protonophore FCCP. With the intestinal organoid model, we demonstrated multiparametric imaging by combining extracellular acidification (FLIM) with phosphorescent probe-based monitoring of cell oxygenation. The described labeling strategy allows for the design of extracellular pH-sensitive scaffolds for multiparametric FLIM assays and their use in engineered live cancer and stem cell-derived tissues. Collectively, this research can help in achieving the controlled biofabrication of 3D tissue models with known metabolic characteristics. STATEMENT OF SIGNIFICANCE: We designed biosensors consisting of a cellulose-binding domain (CBD) and pH- and Ca2+-sensitive fluorescent proteins. CBD-tagged biosensors efficiently label various types of cellulose matrices including nanofibrillar cellulose and decellularized plant materials. Hybrid biosensing cellulose scaffolds designed in this study were successfully tested by multiparameter FLIM microscopy in 3D cultures of cancer cells and mouse intestinal organoids.
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Affiliation(s)
- Neil O'Donnell
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Irina A Okkelman
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Peter Timashev
- Institute for Regenerative Medicine, I.M. Sechenov First Moscow State University, Moscow, Russian Federation; Institute of Photonic Technologies, Research Center 'Crystallography and Photonics', Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatyana I Gromovykh
- Department of Biotechnology, I.M. Sechenov First Moscow State University, Moscow, Russian Federation
| | - Dmitri B Papkovsky
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ruslan I Dmitriev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; Institute for Regenerative Medicine, I.M. Sechenov First Moscow State University, Moscow, Russian Federation.
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16
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Shi XM, Mei LP, Zhang N, Zhao WW, Xu JJ, Chen HY. A Polymer Dots-Based Photoelectrochemical pH Sensor: Simplicity, High Sensitivity, and Broad-Range pH Measurement. Anal Chem 2018; 90:8300-8303. [DOI: 10.1021/acs.analchem.8b02291] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xiao-Mei Shi
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Li-Ping Mei
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Nan Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
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