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Iijima K, Kaji N, Tokeshi M, Baba Y. Micro- and nanochamber array system for single enzyme assays. Sci Rep 2023; 13:13322. [PMID: 37587179 PMCID: PMC10432523 DOI: 10.1038/s41598-023-40544-4] [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: 02/22/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023] Open
Abstract
Arrays of small reaction containers, ranging from 624 femtoliters (10-15 L) to 270 attoliters (10-18 L), for capturing a single enzyme molecule and measuring the activity were developed along with a new reversible sealing system based on a pneumatic valve actuator made of polydimethylsiloxane (PDMS). The valve was actuated by PBS solution, effectively preventing evaporation of the solution from the micro- and nanochambers and allowing the assay to be performed over a long period of time. The hydrolysis rates of β-D-galactosidase (β-gal), kcat, were decreased according to the decrease of the chamber size, and the overall tendency seems to be symmetrically related to the specific surface area of the chambers even under the prevented condition of non-specific adsorption. The spatial localization of the protons in the chambers, which might could affect the dissociation state of the proteins, was also investigated to explain the decrease in the hydrolysis rate. The developed chamber system developed here may be useful for artificially reproducing the confined intracellular environment and molecular crowding conditions.
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Affiliation(s)
- Kazuki Iijima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Manabu Tokeshi
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita-13, Nishi-8, Kita-Ku, Sapporo, 060-8628, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, 263-8555, Japan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 807, Taiwan, ROC
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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: 1.5] [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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Videira-Quintela D, Guillén F, Prazeres SF, Montalvo G. Immobilization of Kluyveromyces lactis β-Galactosidase on Meso-macroporous Silica: Use of Infrared Spectroscopy to Rationalize the Catalytic Efficiency. Chempluschem 2022; 87:e202200340. [PMID: 36515233 PMCID: PMC10369856 DOI: 10.1002/cplu.202200340] [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: 10/04/2022] [Revised: 11/16/2022] [Indexed: 11/20/2022]
Abstract
Enzyme immobilization on adequate carriers is a challenging strategy. Understanding the enzyme-carrier interactions and their effects on enzyme conformation and bioactivity is critical. In this study, a meso-macropores silica (MMS) was used to immobilize β-galactosidase from the yeast Kluyveromyces lactis (β-gal-KL) by physical adsorption. The bioactivity of the immobilized β-gal-KL was altered, evidenced by the increased Km , decreased Vmax and kcat , and increased activity at alkaline values. By performing infrared spectroscopy analysis and subsequent secondary structure assessment from the amide I band, the immobilized β-gal-KL suffered a β-sheet (∼31-35 %) to α-helix (∼15-19 %) transition with increased turns (∼21-22 %) with respect to the free β-gal-KL having ∼12 % α-helix, ∼42 % β-sheet, and ∼17 % turns. These findings led us to correlate the observed bioactivity performance to structural alterations to a non-native conformation. The presented line of thought can lead to a better understanding of the reasons causing bioactivity alterations upon enzyme immobilization.
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Affiliation(s)
- Diogo Videira-Quintela
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Francisco Guillén
- Facultad de Farmacia, Departamento de Biomedicina y Biotecnología, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Sofia F Prazeres
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Gemma Montalvo
- Facultad de Farmacia, Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona km 33.6, 28871 Alcalá de Henares, Madrid, Spain.,Instituto Universitario de Investigación en Ciencias Policiales, Universidad de Alcalá, Libreros 27, 28801, Madrid, Spain
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Nolan V, Collin A, Rodriguez C, Perillo MA. Effect of Polyethylene Glycol-Induced Molecular Crowding on the Enzymatic Activity and Thermal Stability of β-Galactosidase from Kluyveromyces lactis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8875-8882. [PMID: 32686401 DOI: 10.1021/acs.jafc.0c02316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, we report the effect of polyethylene glycol (PEG6000)-induced molecular crowding (MC) on the catalytic activity and thermal stability of Kluyveromyces lactis β-galactosidase (β-Gal). The β-Gal-catalyzed hydrolysis of o-nitrophenyl-β-d-galactopyranoside followed a Michaelian kinetics at [PEG6000] ≤ 25% w/v and positive cooperativity at higher concentrations (35% w/v PEG6000). Compared with dilute solutions, in the MC media, β-Gal exhibited stronger thermal stability, as shown by the increase in the residual activity recovered after preincubation at high temperatures (e.g., 45 °C) and by the slower inactivation kinetics. Considering the effects of water thermodynamic activity on the reaction kinetics and protein structure and the effect of the exclusion volume on protein conformation, we suggest that changes in the protein oligomerization state and hydration could be the responsible for the behavior observed at the highest MC levels assayed. These results could be relevant and should be taken into account in industrial food processes applying β-Gal from K. lactis.
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Affiliation(s)
- Verónica Nolan
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Fı́sicas y Naturales. ICTA and Departamento de Quı́mica, Cátedra de Quı́mica Biológica, Avenue Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), 5016 Córdoba, Argentina
| | - Alejandro Collin
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Fı́sicas y Naturales. ICTA and Departamento de Quı́mica, Cátedra de Quı́mica Biológica, Avenue Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), 5016 Córdoba, Argentina
| | - Carolina Rodriguez
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Fı́sicas y Naturales. ICTA and Departamento de Quı́mica, Cátedra de Quı́mica Biológica, Avenue Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), 5016 Córdoba, Argentina
| | - María A Perillo
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Fı́sicas y Naturales. ICTA and Departamento de Quı́mica, Cátedra de Quı́mica Biológica, Avenue Vélez Sársfield 1611, 5016 Córdoba, Argentina
- CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), 5016 Córdoba, Argentina
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Nolan V, Clop PD, Burgos MI, Perillo MA. Dual substrate/solvent- roles of water and mixed reaction-diffusion control of β-Galactosidase catalyzed reactions in PEG-induced macromolecular crowding conditions. Biochem Biophys Res Commun 2019; 515:190-195. [DOI: 10.1016/j.bbrc.2019.05.081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
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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: 1.7] [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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Estevinho BN, Samaniego N, Talens-Perales D, Fabra MJ, López-Rubio A, Polaina J, Marín-Navarro J. Development of enzymatically-active bacterial cellulose membranes through stable immobilization of an engineered β-galactosidase. Int J Biol Macromol 2018; 115:476-482. [DOI: 10.1016/j.ijbiomac.2018.04.081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/06/2018] [Accepted: 04/14/2018] [Indexed: 01/25/2023]
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