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Perillo MA, Burgos I, Clop EM, Sanchez JM, Nolan V. The role of water in reactions catalysed by hydrolases under conditions of molecular crowding. Biophys Rev 2023; 15:639-660. [PMID: 37681097 PMCID: PMC10480385 DOI: 10.1007/s12551-023-01104-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023] Open
Abstract
Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.
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Affiliation(s)
- Maria A. Perillo
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Inés Burgos
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química Industrial y Aplicada, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
| | - Eduardo M. Clop
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Julieta M. Sanchez
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08193 Barcelona, Spain
| | - Verónica Nolan
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
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2
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Pota G, Gallucci N, Cavasso D, Krauss IR, Vitiello G, López-Gallego F, Costantini A, Paduano L, Califano V. Controlling the Adsorption of β-Glucosidase onto Wrinkled SiO 2 Nanoparticles To Boost the Yield of Immobilization of an Efficient Biocatalyst. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1482-1494. [PMID: 36651862 PMCID: PMC9893809 DOI: 10.1021/acs.langmuir.2c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Indexed: 06/17/2023]
Abstract
β-Glucosidase (BG) catalyzes the hydrolysis of cellobiose to glucose, a substrate for fermentation to produce the carbon-neutral fuel bioethanol. Enzyme thermal stability and reusability can be improved through immobilization onto insoluble supports. Moreover, nanoscaled matrixes allow for preserving high reaction rates. In this work, BG was physically immobilized onto wrinkled SiO2 nanoparticles (WSNs). The adsorption procedure was tuned by varying the BG:WSNs weight ratio to achieve the maximum controllability and maximize the yield of immobilization, while different times of immobilization were monitored. Results show that a BG:WSNs ratio equal to 1:6 wt/wt provides for the highest colloidal stability, whereas an immobilization time of 24 h results in the highest enzyme loading (135 mg/g of support) corresponding to 80% yield of immobilization. An enzyme corona is formed in 2 h, which gradually disappears as the protein diffuses within the pores. The adsorption into the silica structure causes little change in the protein secondary structure. Furthermore, supported enzyme exhibits a remarkable gain in thermal stability, retaining complete folding up to 90 °C. Catalytic tests assessed that immobilized BG achieves 100% cellobiose conversion. The improved adsorption protocol provides simultaneously high glucose production, enhanced yield of immobilization, and good reusability, resulting in considerable reduction of enzyme waste in the immobilization stage.
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Affiliation(s)
- Giulio Pota
- University
of Naples Federico II, Department of Chemical,
Materials and Production Engineering, 80125Naples, Italy
| | - Noemi Gallucci
- University
of Naples Federico II, Department of Chemical
Sciences, 80125Naples, Italy
- CSGI, Center for Colloid and Surface Science, 50019Sesto Fiorentino(FI), Italy
| | - Domenico Cavasso
- University
of Naples Federico II, Department of Chemical
Sciences, 80125Naples, Italy
| | - Irene Russo Krauss
- University
of Naples Federico II, Department of Chemical
Sciences, 80125Naples, Italy
- CSGI, Center for Colloid and Surface Science, 50019Sesto Fiorentino(FI), Italy
| | - Giuseppe Vitiello
- University
of Naples Federico II, Department of Chemical,
Materials and Production Engineering, 80125Naples, Italy
- CSGI, Center for Colloid and Surface Science, 50019Sesto Fiorentino(FI), Italy
| | - Fernando López-Gallego
- Center
for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), 20850Donostia-San
Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 948009Bilbao, Spain
| | - Aniello Costantini
- University
of Naples Federico II, Department of Chemical,
Materials and Production Engineering, 80125Naples, Italy
| | - Luigi Paduano
- University
of Naples Federico II, Department of Chemical
Sciences, 80125Naples, Italy
- CSGI, Center for Colloid and Surface Science, 50019Sesto Fiorentino(FI), Italy
| | - Valeria Califano
- Institute
of Sciences and Technologies for Sustainable Energy and Mobility (STEMS), National Research Council of Italy (CNR), Viale Marconi 4, 80125Naples, Italy
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JIANG H, LV XF, ZHAO KX. Progress of Aptamer Screening Techniques Based on Microfluidic Chips. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60015-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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4
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β-sheet to α-helix conversion and thermal stability of β-Galactosidase encapsulated in a nanoporous silica gel. Biochem Biophys Res Commun 2019; 508:270-274. [DOI: 10.1016/j.bbrc.2018.11.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/03/2018] [Accepted: 11/12/2018] [Indexed: 11/19/2022]
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Bhowal AC, Kundu S. A comparative study on intrinsic fluorescence of BSA and lysozyme proteins in presence of different divalent ions from their solution and thin film conformations. LUMINESCENCE 2017; 33:267-276. [PMID: 29052335 DOI: 10.1002/bio.3409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/21/2017] [Accepted: 08/24/2017] [Indexed: 01/04/2023]
Abstract
Optical emission behaviours of lysozyme and bovine serum albumin, from bulk and thin film geometry, were studied in the presence of three different divalent ions (Mg2+ , Ca2+ or Ba2+ ) using different spectroscopic [steady-state fluorescence, UV-Vis and Fourier transform infra-red (FTIR)] techniques. Additionally, protein thin films on silicon surfaces were prepared and morphological studies were carried out using atomic force microscopy. Dynamic quenching was mainly identified for both proteins in the presence of Mg2+ , Ca2+ and Ba2+ ions. The molecular conformation of the proteins was modified in thin films compared with that in solution, consequently quenching efficiencies also varied. ATR-FTIR studies confirmed the conformational changes of proteins in the presence of all divalent ions. All metal ions used were divalent in nature and belonged to the same group of the periodic table but, depending on their individual characteristics such as electron affinity, ionic radius, etc., the magnitude of the protein and hydrated ion interaction varied and accordingly the quenching efficiency was modified. Quenching was maximum for Ca2+ ions, followed by the other two ions. Our study clearly illustrates the geometry-dependent physical and biological functions of proteins.
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Affiliation(s)
- Ashim Chandra Bhowal
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam, India
| | - Sarathi Kundu
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam, India
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Zhao B, Zhou L, Ma L, He Y, Gao J, Li D, Jiang Y. Co-immobilization of glucose oxidase and catalase in silica inverse opals for glucose removal from commercial isomaltooligosaccharide. Int J Biol Macromol 2017; 107:2034-2043. [PMID: 29051100 DOI: 10.1016/j.ijbiomac.2017.10.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
In this work, glucose oxidase (GOD) and catalase (CAT) were co-immobilized on novel silica inverse opals (IO-SiO2) through sol-gel process. The immobilized bi-enzyme system named GOD/CAT@IO-SiO2 was successfully fabricated and characterized. Morphology characterization indicated that GOD/CAT@IO-SiO2 had hierarchical porous structure, and the pore diameter of macroporous and mesoporous were 500±50nm and 6.8nm, respectively. The macrospores were connected through windows of 100±30nm. The results of stability tests indicated that both acid (or base) resistance and thermal tolerance of GOD/CAT@IO-SiO2 were improved. When GOD/CAT@IO-SiO2 was used to remove glucose from commercial isomaltooligosaccharide (IMO), the immobilized bi-enzyme system exhibited the good performance. The removal efficiency of glucose reached up to 98.97% under the conditions of GOD/CAT activity ratio of 1:30, the amount of enzyme of 68.8mg, reaction time of 9.39h, reaction temperature of 35.2°C and pH of 7.05. After reused 6 times, 79.19% of removal efficiency could be still retained. The present work demonstrates that the immobilized bi-enzyme (GOD/CAT@IO-SiO2) is not only a very promising system for glucose removal but also has great potential for applications in production of gluconic acid, preparation of biosensors, enzyme bioreactors, etc.
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Affiliation(s)
- Bin Zhao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Liya Zhou
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China.
| | - Li Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Ying He
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Jing Gao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Dan Li
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China
| | - Yanjun Jiang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300130, China; National-Local Joint Engineering Laboratory for Energy Conservation of Chemical Process Integration and Resources Utilization, Hebei University of Technology, Tianjin 300130, China.
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7
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Bouaziz Z, Soussan L, Janot JM, Lepoitevin M, Bechelany M, Djebbi MA, Amara ABH, Balme S. Structure and antibacterial activity relationships of native and amyloid fibril lysozyme loaded on layered double hydroxide. Colloids Surf B Biointerfaces 2017; 157:10-17. [DOI: 10.1016/j.colsurfb.2017.05.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 11/29/2022]
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Kahveci Z, Martínez-Tomé MJ, Mallavia R, Mateo CR. Fluorescent Biosensor for Phosphate Determination Based on Immobilized Polyfluorene-Liposomal Nanoparticles Coupled with Alkaline Phosphatase. ACS APPLIED MATERIALS & INTERFACES 2017; 9:136-144. [PMID: 27966351 DOI: 10.1021/acsami.6b12434] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This work describes the development of a novel fluorescent biosensor based on the inhibition of alkaline phosphatase (ALP). The biosensor is composed of the enzyme ALP and the conjugated cationic polyfluorene HTMA-PFP. The working principle of the biosensor is based on the fluorescence quenching of this polyelectrolyte by p-nitrophenol (PNP), a product of the hydrolysis reaction of p-nitrophenyl phosphate (PNPP) catalyzed by ALP. Because HTMA-PFP forms unstable aggregates in buffer, with low fluorescence efficiency, previous stabilization of the polyelectrolyte was required before the development of the biosensor. HTMA-PFP was stabilized through its interaction with lipid vesicles to obtain stable blue-emitting nanoparticles (NPs). Fluorescent NPs were characterized, and the ability to be quenched by PNP was evaluated. These nanoparticles were coupled to ALP and entrapped in a sol-gel matrix to produce a biosensor that can serve as a screening platform to identify ALP inhibitors. The components of the biosensor were examined before and after sol-gel entrapment, and the biosensor was optimized to allow the determination of phosphate ion in aqueous medium.
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Affiliation(s)
- Zehra Kahveci
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202, Elche, Alicante, Spain
| | - Maria José Martínez-Tomé
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202, Elche, Alicante, Spain
| | - Ricardo Mallavia
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202, Elche, Alicante, Spain
| | - C Reyes Mateo
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202, Elche, Alicante, Spain
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9
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Gospodarczyk W, Kozak M. The severe impact of in vivo-like microfluidic flow and the influence of gemini surfactants on amyloid aggregation of hen egg white lysozyme. RSC Adv 2017. [DOI: 10.1039/c6ra26675d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The formation of amyloid plaques is being intensively studied, as this process underlies severe human diseases, including Alzheimer's disease, and the exact mechanism of this specific aggregation has not been resolved yet.
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Affiliation(s)
- W. Gospodarczyk
- Department of Macromolecular Physics
- Faculty of Physics
- Adam Mickiewicz University
- Poznań
- Poland
| | - M. Kozak
- Department of Macromolecular Physics
- Faculty of Physics
- Adam Mickiewicz University
- Poznań
- Poland
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10
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Burgos MI, Velasco MI, Acosta RH, Perillo MA. Environmental Topology and Water Availability Modulates the Catalytic Activity of β-Galactosidase Entrapped in a Nanosporous Silicate Matrix. Sci Rep 2016; 6:36593. [PMID: 27811995 PMCID: PMC5095660 DOI: 10.1038/srep36593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/17/2016] [Indexed: 02/02/2023] Open
Abstract
In the present work we studied the catalytic activity of E. coli β-Gal confined in a nanoporous silicate matrix (Eβ-Gal) at different times after the beginning of the sol-gel polymerization process. Enzyme kinetic experiments with two substrates (ONPG and PNPG) that differed in the rate-limiting steps of the reaction mechanism for their β-Gal-catalyzed hydrolysis, measurements of transverse relaxation times (T2) of water protons through 1H-NMR, and scanning electron microscopy analysis of the gel nanostructure, were performed. In conjunction, results provided evidence that water availability is crucial for the modulation observed in the catalytic activity of β-Gal as long as water participate in the rate limiting step of the reaction (only with ONPG). In this case, a biphasic rate vs. substrate concentration was obtained exhibiting one phase with catalytic rate constant (kcA), similar to that observed in solution, and another phase with a higher and aging-dependent catalytic rate constant (kcB). More structured water populations (lower T2) correlates with higher catalytic rate constants (kcB). The T2-kcB negative correlation observed along the aging of gels within the 15-days period assayed reinforces the coupling between water structure and the hydrolysis catalysis inside gels.
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Affiliation(s)
- M Ines Burgos
- IIByT-UNC CONICET. Cátedra de Química Biológica, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba. Av. Vélez Sársfield 1611, X5016GCA Córdoba, Argentina
| | - Manuel I Velasco
- IFEG-UNC CONICET. FaMAF-Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - Rodolfo H Acosta
- IFEG-UNC CONICET. FaMAF-Universidad Nacional de Córdoba, 5000 Córdoba, Argentina
| | - María A Perillo
- IIByT-UNC CONICET. Cátedra de Química Biológica, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba. Av. Vélez Sársfield 1611, X5016GCA Córdoba, Argentina
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Interaction of two imidazolium gemini surfactants with two model proteins BSA and HEWL. Colloid Polym Sci 2015; 293:2855-2866. [PMID: 26412930 PMCID: PMC4575695 DOI: 10.1007/s00396-015-3671-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/26/2015] [Accepted: 06/14/2015] [Indexed: 02/06/2023]
Abstract
Gemini surfactants and their interactions with proteins have gained considerable scientific interest, especially when amyloidogenic proteins are taken into account. In this work, the influence of two selected dicationic (gemini) surfactants (3,3′-[1,8-(2,7-dioxaoctane)]bis(1-dodecylimidazolium) chloride and 3,3′-[1,12-(2,11-dioxadodecane)]bis(1-dodecylimidazolium) chloride) on two model proteins, bovine serum albumin (BSA) and hen egg white lysozyme (HEWL), have been investigated. A pronounced and sophisticated influence on BSA structure has been revealed, including a considerable change of protein radius of gyration as well as substantial alteration of its secondary structure. Radius of gyration has been found to rise significantly with addition of surfactants and to fall down for high surfactants concentration. Similarly, a remarkable fall of secondary structure (α-helix content) has been observed, followed by its partial retrieval for high surfactants concentration. A strong aggregation of BSA has been observed for a confined range of surfactants concentrations as well. In case of HEWL-gemini system, on the other hand, the protein-surfactant interaction was found to be weak. Molecular mechanisms explaining such behaviour of protein-surfactant systems have been proposed. The differences of properties of both studied surfactants have also been discussed.
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Melo AM, Fedorov A, Prieto M, Coutinho A. Exploring homo-FRET to quantify the oligomer stoichiometry of membrane-bound proteins involved in a cooperative partition equilibrium. Phys Chem Chem Phys 2015; 16:18105-17. [PMID: 24722583 DOI: 10.1039/c4cp00060a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The establishment of protein-protein interactions between membrane-bound proteins is associated with several biological functions and dysfunctions. Here, an analytical framework that uses energy homo transfer to directly probe quantitatively the oligomerization state of membrane-bound proteins engaged in a three-state cooperative partition is presented. Briefly, this model assumes that monomeric protein molecules partition into the bilayer surface and reversibly assemble into oligomers with k subunits. A general equation relating the overall steady-state fluorescence anisotropy of the sample to its fractional labeling was derived by considering explicitly that the anisotropy of mixed oligomers containing i-labeled monomers is inversely proportional to the number of labeled subunits per oligomer (Runnels and Scarlata limit). This method was very robust in describing the electrostatic interaction of Alexa Fluor 488 fluorescently labeled lysozyme (Lz-A488) with phosphatidylserine-containing membranes. The pronounced decrease detected in the fluorescence anisotropy of Lz-A488 always correlated with the system reaching a high membrane surface density of the protein (at a low lipid-to-protein (L/P) molar ratio). The occurrence of energy homo transfer-induced fluorescence depolarization was further confirmed by measuring the anisotropy decays of Lz-A488 under these conditions. A global analysis of the steady-state anisotropy data obtained under a wide range of experimental conditions (variable anionic lipid content of the liposomes, L/P molar ratios and protein fractional labeling) confirmed that membrane-bound Lz-A488 assembled into oligomeric complexes, possibly with a stoichiometry of k = 6 ± 1. This study illustrates that even in the presence of a coupled partition-oligomerization equilibrium, steady-state anisotropy measurements provide a simple and reliable tool to monitor the self-assembly of membrane-bound proteins.
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Affiliation(s)
- Ana M Melo
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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13
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Lin H, Zhang W, Jia S, Guan Z, Yang CJ, Zhu Z. Microfluidic approaches to rapid and efficient aptamer selection. BIOMICROFLUIDICS 2014; 8:041501. [PMID: 25379085 PMCID: PMC4189129 DOI: 10.1063/1.4890542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/07/2014] [Indexed: 05/04/2023]
Abstract
With their advantages as molecular recognition elements, aptamers have been extensively studied and used for bioanalytical and biomedical applications. However, the process of enrichment and screening of aptamers remains a bottleneck for aptamer development. Recently, microfluidic methods have been increasingly used for rapid and efficient aptamer selection, showing their remarkable advantages over conventional methods. This review briefly introduces aptamers and their advantages. The conventional process of generating aptamers is discussed, followed by the analysis of the key obstacles to efficient aptamer selection. Microfluidic methods for highly efficient enrichment and screening of aptamers are reviewed in detail.
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Affiliation(s)
- Hui Lin
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Weiting Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Shasha Jia
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
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14
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Song X, Jiang Z, Li L, Wu H. Immobilization of β-glucuronidase in lysozyme-induced biosilica particles to improve its stability. Front Chem Sci Eng 2014. [DOI: 10.1007/s11705-014-1421-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Mallavia R, Martínez-Tomé MJ, Vázquez-Guilló R, Kahveci Z, Estepa A, Mateo CR. Stabilization of neutral polyfluorene in aqueous solution through their interaction with phospholipids and sol-gel encapsulation. ACS APPLIED MATERIALS & INTERFACES 2013; 5:2952-2958. [PMID: 23537131 DOI: 10.1021/am400570t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Interaction between poly[9,9-bis(6'-bromohexyl)-2,7-fluorene-co-alt-1,4-phenylene] (PFPBr2), a neutral conjugated polyfluorene which is completely insoluble in water, and zwitterionic phospholipids has been investigated in order to generate new fluorescent structures which are stable in aqueous media as a means of extending the biological applications of these kinds of polymers. Two types of differently shaped and composed fluorescent structures were identified and then isolated and characterized separately using different biophysical techniques. The first structure type, corresponding to liposomal complexes, showed a fluorescence band centered around 405 nm and maximum absorption at 345 nm, while the second, corresponding to polymer-phospholipid aggregates of variable sizes with lower lipid content, absorbed at longer wavelengths and displayed a well resolved fluorescence spectrum with a maximum centered at 424 nm. Both structures were stable in a large range of pH, and their fluorescence intensity remained practically unaltered for 10 days; it then began to decrease, which was probably because of aggregation. Encapsulation of these structures within the pores of a sol-gel matrix did not affect their fluorescent properties but increased their stability, avoiding further aggregation and subsequent precipitation.
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Affiliation(s)
- Ricardo Mallavia
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández de Elche, Edificio Torregaitán. Avda. de la Universidad s/n, Alicante 03202, Elche, Spain.
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Esquembre R, Sanz JM, Wall JG, del Monte F, Mateo CR, Ferrer ML. Thermal unfolding and refolding of lysozyme in deep eutectic solvents and their aqueous dilutions. Phys Chem Chem Phys 2013; 15:11248-56. [DOI: 10.1039/c3cp44299c] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Formation and Characterization of Stable Fluorescent Complexes Between Neutral Conjugated Polymers and Cyclodextrins. J Fluoresc 2012; 23:171-80. [DOI: 10.1007/s10895-012-1130-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/10/2012] [Indexed: 11/27/2022]
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18
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Lee JS, Koehorst RBM, van Amerongen H, Feijen J. Time-resolved fluorescence and fluorescence anisotropy of fluorescein-labeled poly(N-isopropylacrylamide) incorporated in polymersomes. J Phys Chem B 2011; 115:13162-7. [PMID: 21995555 DOI: 10.1021/jp207072q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The phase behavior of fluorescein isothiocyanate (FITC) labeled poly(N-isopropylacrylamide) (PNIPAAm) incorporated in polymersomes (Ps) was studied by monitoring the fluorescence lifetime (FL) and the time-resolved fluorescence anisotropy (TRFA) as a function of temperature at pH 7.4. Ps containing FITC-labeled PNIPAAm with a diameter less than 200 nm were prepared by injecting a THF solution of poly(ethylene glycol)-b-poly(d,l-lactide) (mPEG-PDLLA) and FITC tagged PNIPAAm (FITC-N) into phosphate buffered saline (PBS, pH 7.4). Solutions of free FITC (2 μM) and FITC-N (2 μM) in PBS were used as controls. The polarized fluorescence decay curves of FITC were fitted with one rotational correlation time (θ(1)) and the corresponding amplitude (β(1)), while those for FITC-N were fitted with two rotational correlation times (θ(1,2)) and their corresponding amplitudes (β(1,2)). Short rotational correlation times, θ(1), correspond with the rotation of the FITC molecule itself, whereas θ(2) corresponds to FITC-segmental rotation. FITC-N encapsulated in Ps (FITC-N/Ps) showed a decrease of the rotational motion upon increasing the temperature. The long rotational correlation time (θ(2)) of FITC-N increased 3 fold, going from 15 to 40 °C, reflecting a reduced rotational mobility. The residual anisotropy (β(∞)) of FITC-N/Ps at pH 7.4 showed a gradual increase, going from 15 to 25 °C followed by a gradual decrease at higher temperatures. These results are explained by a transition from coil to globule, a gradual increase of intermolecular aggregation, and possibly phase separation and hydrogel formation.
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Affiliation(s)
- Jung Seok Lee
- Department of Polymer Chemistry and Biomaterials, Institute for Biomedical Technology and Technical Medicine, MIRA, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
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A direct coupling between global and internal motions in a single domain protein? MD investigation of extreme scenarios. Biophys J 2011; 101:196-204. [PMID: 21723830 DOI: 10.1016/j.bpj.2011.05.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 04/25/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022] Open
Abstract
Proteins are not rigid molecules, but exhibit internal motions on timescales ranging from femto- to milliseconds and beyond. In solution, proteins also experience global translational and rotational motions, sometimes on timescales comparable to those of the internal fluctuations. The possibility that internal and global motions may be directly coupled has intriguing implications, given that enzymes and cell signaling proteins typically associate with binding partners and cellular scaffolds. Such processes alter their global motion and may affect protein function. Here, we present molecular dynamics simulations of extreme case scenarios to examine whether a possible relationship exists. In our model protein, a ubiquitin-like RhoGTPase binding domain of plexin-B1, we removed either internal or global motions. Comparisons with unrestrained simulations show that internal and global motions are not appreciably coupled in this single-domain protein. This lack of coupling is consistent with the observation that the dynamics of water around the protein, which is thought to permit, if not stimulate, internal dynamics, is also largely independent of global motion. We discuss implications of these results for the structure and function of proteins.
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Ahn JY, Jo M, Dua P, Lee DK, Kim S. A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selection. Oligonucleotides 2011; 21:93-100. [PMID: 21413890 DOI: 10.1089/oli.2010.0263] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX often requiring many rounds of selection and amplification. Recently, we have shown the efficient binding and elution of RNA aptamers against target proteins using a microfluidic chip that incorporates 5 sol-gel binding droplets within which specific target proteins are imbedded. Here, we demonstrate that our microfluidic chip in a SELEX experiment greatly improved selection efficiency of RNA aptamers to TATA-binding protein, reducing the number of selection cycles needed to produce high affinity aptamers by about 80%. Many aptamers were identical or homologous to those isolated previously by conventional filter-binding SELEX. The microfluidic chip SELEX is readily scalable using a sol-gel microarray-based target multiplexing. Additionally, we show that sol-gel embedded protein arrays can be used as a high-throughput assay for quantifying binding affinities of aptamers.
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Affiliation(s)
- Ji-Young Ahn
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York
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Luo G, Zhang Q, Del Castillo AR, Urban V, O'Neill H. Characterization of sol-gel-encapsulated proteins using small-angle neutron scattering. ACS APPLIED MATERIALS & INTERFACES 2009; 1:2262-2268. [PMID: 20355861 DOI: 10.1021/am900430v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Entrapment of biomolecules in silica-derived sol-gels has grown into a vibrant area of research since it was originally demonstrated. However, accessing the consequences of entrapment on biomolecules and the gel structure remains a major challenge in characterizing these biohybrid materials. We present the first demonstration that it is possible with small-angle neutron scattering (SANS) to study the conformation of dilute proteins that are entrapped in transparent and dense sol-gels. Using deuterium-labeled green fluorescent protein (GFP) and SANS with contrast variation, we demonstrate that the scattering signatures of the sol-gel and the protein can be separated. Analysis of the scattering curves of the sol-gels using a mass-fractal model shows that the size of the colloidal silica particles and the fractal dimensions of the gels were similar in the absence and presence of protein, demonstrating that GFP did not influence the reaction pathway for the formation of the gel. The major structural difference in the gels was that the pore size was increased 2-fold in the presence of the protein. At the contrast match point for silica, the scattering signal from GFP inside the gel became distinguishable over a wide q range. Simulated scattering curves representing a monomer, end-to-end dimer, and parallel dimer of the protein were calculated and compared to the experimental data. Our results show that the most likely structure of GFP is that of an end-to-end dimer. This approach can be readily applied and holds great potential for the structural characterization of complex biohybrid and other materials.
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Affiliation(s)
- Guangming Luo
- Center for Structural Molecular Biology, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Reátegui E, Aksan A. Effects of the Low-Temperature Transitions of Confined Water on the Structures of Isolated and Cytoplasmic Proteins. J Phys Chem B 2009; 113:13048-60. [DOI: 10.1021/jp903294q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
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23
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Lee F, Chung JE, Kurisawa M. An injectable hyaluronic acid–tyramine hydrogel system for protein delivery. J Control Release 2009; 134:186-93. [DOI: 10.1016/j.jconrel.2008.11.028] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 11/21/2008] [Accepted: 11/30/2008] [Indexed: 10/21/2022]
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24
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Pastor I, Prieto M, Mateo CR. Effect of Sol−Gel Confinement on the Structural Dynamics of the Enzyme Bovine Cu,Zn Superoxide Dismutase. J Phys Chem B 2008; 112:15021-8. [DOI: 10.1021/jp805368s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Isabel Pastor
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
| | - Manuel Prieto
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
| | - C. Reyes Mateo
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202-Elche, Spain, and Centro de Química-Física Molecular and IN- Institute of Nanosciences and Nanotechnology, Instituto Superior Técnico, Av. Rovisco Pais, P-1049-001, Lisboa, Portugal
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