1
|
Ivanov YD, Shumov ID, Kozlov AF, Valueva AA, Ershova MO, Ivanova IA, Ableev AN, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Atomic Force Microscopy Study of the Long-Term Effect of the Glycerol Flow, Stopped in a Coiled Heat Exchanger, on Horseradish Peroxidase. MICROMACHINES 2024; 15:499. [PMID: 38675310 PMCID: PMC11052087 DOI: 10.3390/mi15040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Glycerol is employed as a functional component of heat-transfer fluids, which are of use in both bioreactors and various biosensor devices. At the same time, flowing glycerol was reported to cause considerable triboelectric effects. Herein, by using atomic force microscopy (AFM), we have revealed the long-term effect of glycerol flow, stopped in a ground-shielded coiled heat exchanger, on horseradish peroxidase (HRP) adsorption on mica. Namely, the solution of HRP was incubated in the vicinity of the side of the cylindrical coil with stopped glycerol flow, and then HRP was adsorbed from this solution onto a mica substrate. This incubation has been found to markedly increase the content of aggregated enzyme on mica-as compared with the control enzyme sample. We explain the phenomenon observed by the influence of triboelectrically induced electromagnetic fields of non-trivial topology. The results reported should be further considered in the development of flow-based heat exchangers of biosensors and bioreactors intended for operation with enzymes.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| |
Collapse
|
2
|
Estiri H, Bhattacharya S, Buitrago JAR, Castagna R, Legzdiņa L, Casucci G, Ricci A, Parisini E, Gautieri A. Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition. Sci Rep 2023; 13:18610. [PMID: 37903872 PMCID: PMC10616090 DOI: 10.1038/s41598-023-45428-1] [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: 07/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Fructosyl peptide oxidases (FPOX) are deglycating enzymes that find application as key enzymatic components in diabetes monitoring devices. Indeed, their use with blood samples can provide a measurement of the concentration of glycated hemoglobin and glycated albumin, two well-known diabetes markers. However, the FPOX currently employed in enzymatic assays cannot directly detect whole glycated proteins, making it necessary to perform a preliminary proteolytic treatment of the target protein to generate small glycated peptides that can act as viable substrates for the enzyme. This is a costly and time consuming step. In this work, we used an in silico protein engineering approach to enhance the overall thermal stability of the enzyme and to improve its catalytic activity toward large substrates. The final design shows a marked improvement in thermal stability relative to the wild type enzyme, a distinct widening of its access tunnel and significant enzymatic activity towards a range of glycated substrates.
Collapse
Affiliation(s)
- Hajar Estiri
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Shapla Bhattacharya
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
- Faculty of Materials Science and Applied Chemistry, Riga Technical University, Paula Valdena 3, Riga, 1048, Latvia
| | | | - Rossella Castagna
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci 32, 20133, Milano, Italy
| | - Linda Legzdiņa
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Giorgia Casucci
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Andrea Ricci
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Emilio Parisini
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia.
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.
| |
Collapse
|
3
|
Gabbrielli S, Colnaghi L, Mazzuoli-Weber G, Redaelli ACL, Gautieri A. In Silico Analysis of Nanoplastics' and β-amyloid Fibrils' Interactions. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010388. [PMID: 36615582 PMCID: PMC9824275 DOI: 10.3390/molecules28010388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 01/04/2023]
Abstract
Plastic pollution has become a global environmental threat, which leads to an increasing concern over the consequences of plastic exposition on global health. Plastic nanoparticles have been shown to influence the folding of proteins and influence the formation of aberrant amyloid proteins, therefore potentially triggering the development of systemic and local amyloidosis. This work aims to study the interaction between nanoplastics and β-amyloid fibrils to better understand the potential role of nanoplastics in the outbreak of neurodegenerative disorders. Using microsecond-long coarse-grained molecular dynamics simulations, we investigated the interactions between neutral and charged nanoparticles made of the most common plastic materials (i.e., polyethylene, polypropylene, and polystyrene) and β-amyloid fibrils. We observe that the occurrence of contacts, region of amyloid fibril involved, and specific amino acids mediating the interaction depend on the type and charge of the nanoparticles.
Collapse
Affiliation(s)
- Silvia Gabbrielli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milano, Italy
| | - Gemma Mazzuoli-Weber
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany
| | - Alberto Cesare Luigi Redaelli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Correspondence:
| |
Collapse
|
4
|
Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy. Int J Mol Sci 2022; 23:ijms231911319. [PMID: 36232620 PMCID: PMC9570233 DOI: 10.3390/ijms231911319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/11/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t1/2 at 35 °C and a 5.7 °C increase in melting temperature (Tm). Unexpectedly, its specific activity and catalytic efficiency (kcat/Km) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.
Collapse
|
5
|
Suzuki M, Date M, Kashiwagi T, Suzuki E, Yokoyama K. Rational design of a disulfide bridge increases the thermostability of microbial transglutaminase. Appl Microbiol Biotechnol 2022; 106:4553-4562. [PMID: 35729274 DOI: 10.1007/s00253-022-12024-8] [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: 02/19/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/02/2022]
Abstract
Microbial transglutaminase (MTG) has numerous industrial applications in the food and pharmaceutical sectors. Unfortunately, the thermostability of MTG is too low to tolerate the desired conditions used in many of these commercial processes. In a previous study, we used protein engineering to improve the thermostability of MTG. Specifically, we generated a T7C/E58C mutant of MTG from Streptomyces mobaraensis that displayed enhanced resistance to thermal inactivation. In this study, a rational structure-based approach was adopted to introduce a disulfide bridge to further increase the thermostability of MTG. In all, four new mutants, each containing a novel disulfide bond, were engineered. Of these four mutants, D3C/G283C showed the most promising thermostability with a significantly higher ∆T50 (defined as the temperature of incubation at which 50% of the initial activity remains) of + 9 °C by comparison to wild-type MTG. Indeed, D3C/G283C combined enhanced thermostability with a 2.1-fold increased half-life at 65 °C compared with the wild-type enzyme. By structure-based rational design, we were able to create an MTG variant which might be useful for expanding the scope of application in food. KEY POINTS: • Microbial transglutaminase (MTG) is an enzyme used in many food applications • The applicability of MTG to various industrial processes other than the food sector is being investigated • Improvement of thermostability was confirmed for the disulfide bridge mutant D3C/G283C.
Collapse
Affiliation(s)
- Mototaka Suzuki
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Masayo Date
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Tatsuki Kashiwagi
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Eiichiro Suzuki
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan.,Kihara Memorial Yokohama Foundation for the Advancement of Life Sciences Yokohama, Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Keiichi Yokoyama
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan. .,R&B Planning Department, Ajinomoto Co., Inc, Tokyo, 104-8315, Japan.
| |
Collapse
|
6
|
Wang S, Meng K, Su X, Hakulinen N, Wang Y, Zhang J, Luo H, Yao B, Huang H, Tu T. Cysteine Engineering of an Endo-polygalacturonase from Talaromyces leycettanus JCM 12802 to Improve Its Thermostability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6351-6359. [PMID: 34043362 DOI: 10.1021/acs.jafc.1c01618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thermostable enzymes have many advantages for industrial applications. Therefore, in this study, computer-aided design technology was used to improve the thermostability of a highly active endo-polygalacturonase from Talaromyces leycettanus JCM12802 at an optimal temperature of 70 °C. The melting temperature and specific activity of the obtained mutant T316C/G344C were increased by 10 °C and 36.5%, respectively, compared with the wild-type enzyme. The crystal structure of the T316C/G344C mutant showed no formation of a disulfide bond between the introduced cysteines, indicating a different mechanism than the conventional mechanism underlying improved enzyme thermostability. The cysteine substitutions directly formed a new alkyl hydrophobic interaction and caused conformational changes in the side chains of the adjacent residues Asn315 and Thr343, which in turn caused a local reconstruction of hydrogen bonds. This method greatly improved the thermostability of the enzyme without affecting its activity; thus, our findings are of great significance for both theoretical research and practical applications.
Collapse
Affiliation(s)
- Sheng Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun Meng
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu 80130, Finland
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
7
|
Esser-Skala W, Wohlschlager T, Regl C, Huber CG. A Simple Strategy to Eliminate Hexosylation Bias in the Relative Quantification of N-Glycosylation in Biopharmaceuticals. Angew Chem Int Ed Engl 2020; 59:16225-16232. [PMID: 32496655 PMCID: PMC7539909 DOI: 10.1002/anie.202002147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 01/04/2023]
Abstract
N‐glycosylation may affect the safety and efficacy of biopharmaceuticals and is thus monitored during manufacturing. Mass spectrometry of the intact protein is increasingly used to reveal co‐existing glycosylation variants. However, quantification of N‐glycoforms via this approach may be biased by single hexose residues as introduced by glycation or O‐glycosylation. Herein, we describe a simple strategy to reveal actual N‐glycoform abundances of therapeutic antibodies, involving experimental determination of glycation levels followed by computational elimination of the “hexosylation bias”. We show that actual N‐glycoform abundances may significantly deviate from initially determined values. Indeed, glycation may even obscure considerable differences in N‐glycosylation patterns of drug product batches. Our observations may thus have implications for biopharmaceutical quality control. Moreover, we solve an instance of the problem of isobaricity, which is fundamental to mass spectrometry.
Collapse
Affiliation(s)
- Wolfgang Esser-Skala
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Therese Wohlschlager
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| |
Collapse
|
8
|
Esser‐Skala W, Wohlschlager T, Regl C, Huber CG. Eine einfache Strategie zur Korrektur des Fehlers aufgrund von Hexosylierung bei relativer Quantifizierung der N‐Glykosylierungsvarianten von Biopharmazeutika. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Esser‐Skala
- Fachbereich Biowissenschaften Bioanalytical Research Labs Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
- Christian-Doppler-Labor für Innovative Werkzeuge zur Charakterisierung von Biosimilars Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
| | - Therese Wohlschlager
- Fachbereich Biowissenschaften Bioanalytical Research Labs Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
- Christian-Doppler-Labor für Innovative Werkzeuge zur Charakterisierung von Biosimilars Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
| | - Christof Regl
- Fachbereich Biowissenschaften Bioanalytical Research Labs Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
- Christian-Doppler-Labor für Innovative Werkzeuge zur Charakterisierung von Biosimilars Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
| | - Christian G. Huber
- Fachbereich Biowissenschaften Bioanalytical Research Labs Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
- Christian-Doppler-Labor für Innovative Werkzeuge zur Charakterisierung von Biosimilars Universität Salzburg Hellbrunner Straße 34 5020 Salzburg Österreich
| |
Collapse
|
9
|
Rigoldi F, Donini S, Torretta A, Carbone A, Redaelli A, Bandiera T, Parisini E, Gautieri A. Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel. Biotechnol Bioeng 2020; 117:3688-3698. [PMID: 32797625 DOI: 10.1002/bit.27535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Fructosyl peptide oxidases (FPOXs) are enzymes currently used in enzymatic assays to measure the concentration of glycated hemoglobin and albumin in blood samples, which serve as biomarkers of diabetes. However, since FPOX are unable to work directly on glycated proteins, current enzymatic assays are based on a preliminary proteolytic digestion of the target proteins. Herein, to improve the speed and costs of the enzymatic assays for diabetes testing, we applied a rational design approach to engineer a novel enzyme with a wider access tunnel to the catalytic site, using a combination of Rosetta design and molecular dynamics simulations. Our final design, L3_35A, shows a significantly wider and shorter access tunnel, resulting from the deletion of five-amino acids lining the gate structures and from a total of 35 point mutations relative to the wild-type (WT) enzyme. Indeed, upon experimental testing, our engineered enzyme shows good structural stability and maintains significant activity relative to the WT.
Collapse
Affiliation(s)
- Federica Rigoldi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy
| | - Archimede Torretta
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy
| | - Anna Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,D3-PharmaChemistry, Istituto Italiano di Tecnologia, Genova, Italy
| | - Alberto Redaelli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
| | - Tiziano Bandiera
- D3-PharmaChemistry, Istituto Italiano di Tecnologia, Genova, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy.,Biotechnology Group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Alfonso Gautieri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
| |
Collapse
|
10
|
Investigation of the Influence of Liquid Motion in a Flow-Based System on an Enzyme Aggregation State with an Atomic Force Microscopy Sensor: The Effect of Glycerol Flow. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10144825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Atomic force microscopy is employed to study the influence of the motion of a glycerol solution through a coiled (spiral-wound) polymeric communication pipe on the aggregation state of a protein, with the example of a horseradish peroxidase (HRP) enzyme. The measuring cell with the buffered solution of the protein was placed within the experimental setup over the pipe coil, through which glycerol was pumped. It is demonstrated that, in such a system, the flow of a non-aqueous liquid (glycerol) leads to a change in the physicochemical properties of a protein, whose solution was incubated in the measuring cell placed over the coil. Namely, changes in both the adsorbability onto mica and the aggregation state of the model HRP protein were observed. As glycerol-containing liquids are commonly used in biosensor operations, the results reported herein can be useful to the development of biosensor systems, in which polymeric communications are employed in sample delivery and thermal stabilization systems. The data obtained herein can also be of use for the development of specified hydrodynamic models.
Collapse
|
11
|
Wang F, Zhang G, Peng J, Ji X, Hai J, Deng X, Lin L. High cell-density fermentation, expression and purification of bacteriophage lysin TSPphg, a thermostable antimicrobial protein from extremophilic Thermus bacteriophage TSP4. Protein Expr Purif 2020; 174:105676. [PMID: 32442498 DOI: 10.1016/j.pep.2020.105676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/28/2022]
Abstract
Recently, high cell-density (HCD) cultivation has become an important tool for production of many microbial products. However, to the best of our knowledge, no study regarding HCD fermentation, overproduction and purification of thermostable bacteriophage lysin has been reported. Here, by employing a glucose-limited fed-batch strategy, we performed high density fermentation of the host Escherichia coli BL21(DE3) cells, compared the efficiency of high pressure homogenization, ultrasonication and thermolysis in bacterial cell disruption after HCD cultivation, and purified TSPphg, a thermostable lysin derived from extremophilic bacteriophage TSP4. On the 20-L scale, the overproduction level of TSPphg was up to 67.8 ± 0.7%. In total, we obtained a broth titer of 3322.8 ± 26 mg/L TSPphg with a purity of 95.5 ± 0.7% from a bacterial cell mass of 86.3 ± 4.9 g/L after 26 h of fermentation. The overall productivity of TSPphg was 127.8 ± 1 mg/L/h. Additionally, the antimicrobial activity of purified TSPphg against both Gram-negative (Escherichia coli O157) and Gram-positive (Staphylococcus aureus) pathogenic bacteria was further confirmed by scanning electron microscope analysis. Summarily, for the first time, we have established a relatively stable and efficient HCD cultivation and purification process for recovery of thermostable lysins from extremophilic Thermus bacteriophages. Our results provide insights into the strategies for time-saving and cost-effective production of antimicrobial proteins to replace or supplement antibiotics in the current age of mounting antibiotic resistance.
Collapse
Affiliation(s)
- Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Guanling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Jiani Peng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xinyu Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Jun Hai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Xianyu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Lianbing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China; Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.
| |
Collapse
|
12
|
López-Chávez E, Pérez-Hernández G, Aparicio F, Alas SJ. On the Thermal Stability of O 6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:2138-2154. [PMID: 32250621 DOI: 10.1021/acs.jcim.0c00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed molecular dynamics simulations to analyze the thermal stability of the O6-methylguanine-DNA methyltransferase (MGMT) protein, both hyperthermophilic archaeon Pyrococcus kodakaraensis (Pk-MGMT) and its mesophilic homologue pair, obtained from enterobacterium Escherichia coli (AdaC). This theoretical study was done at three different temperatures: 302, 371, and 450 K. The molecular dynamics has been performed in explicit aqueous solvent during a period of time of 95 ns, including periodic boundary conditions and constant pressure. The same procedure has been used for both proteins, and each simulation has been carried out by triplicate. Hence, we performed 18 simulations. In this way, we have done different analyses to explore the factors that may affect the thermal stability of Pk-MGMT. The structural behavior was analyzed using indicators such as root-mean-square deviation, radius of gyration, solvent-accessible surface area, hydrogen bonds, native contacts, secondary structure, and salt bridge formation. The results showed that when the temperature increases, the global atomic fluctuations increase too, which suggests that both proteins lose thermal stability, but as expected, this fact is highlighted in AdaC. Moreover, the contacts of the native state in AdaC are considerably lower than those found in Pk-MGMT at 450 K. Also, the structural studies showed that conserved and nonconserved salt bridges kept close contacts with the Pk-MGMT protein at high temperatures. These interaction types act as molecular staples and are mainly responsible to provide thermostability to the hyperthermophilic protein.
Collapse
Affiliation(s)
- Erick López-Chávez
- Posgrado en Ciencias Naturales e Ingeniería, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Felipe Aparicio
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Salomón J Alas
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico.,Departamento de Química, Unidad Iztapalapa, Universidad Autónoma Metropolitana, Ciudad de México 09340, Mexico
| |
Collapse
|
13
|
The Anti-Amyloidogenic Action of Doxycycline: A Molecular Dynamics Study on the Interaction with Aβ42. Int J Mol Sci 2019; 20:ijms20184641. [PMID: 31546787 PMCID: PMC6769662 DOI: 10.3390/ijms20184641] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
The pathological aggregation of amyloidogenic proteins is a hallmark of many neurological diseases, including Alzheimer’s disease and prion diseases. We have shown both in vitro and in vivo that doxycycline can inhibit the aggregation of Aβ42 amyloid fibrils and disassemble mature amyloid fibrils. However, the molecular mechanisms of the drug’s anti-amyloidogenic property are not understood. In this study, a series of molecular dynamics simulations were performed to explain the molecular mechanism of the destabilization of Aβ42 fibrils by doxycycline and to compare the action of doxycycline with those of iododoxorubicin (a toxic structural homolog of tetracyclines), curcumin (known to have anti-amyloidogenic activity) and gentamicin (an antibiotic with no experimental evidence of anti-amyloidogenic properties). We found that doxycycline tightly binds the exposed hydrophobic amino acids of the Aβ42 amyloid fibrils, partly leading to destabilization of the fibrillar structure. Clarifying the molecular determinants of doxycycline binding to Aβ42 may help devise further strategies for structure-based drug design for Alzheimer’s disease.
Collapse
|
14
|
Ts2631 Endolysin from the Extremophilic Thermus scotoductus Bacteriophage vB_Tsc2631 as an Antimicrobial Agent against Gram-Negative Multidrug-Resistant Bacteria. Viruses 2019; 11:v11070657. [PMID: 31323845 PMCID: PMC6669862 DOI: 10.3390/v11070657] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/27/2022] Open
Abstract
Bacteria that thrive in extreme conditions and the bacteriophages that infect them are sources of valuable enzymes resistant to denaturation at high temperatures. Many of these heat-stable proteins are useful for biotechnological applications; nevertheless, none have been utilized as antibacterial agents. Here, we demonstrate the bactericidal potential of Ts2631 endolysin from the extremophilic bacteriophage vB_Tsc2631, which infects Thermus scotoductus, against the alarming multidrug-resistant clinical strains of Acinetobacter baumannii, Pseudomonas aeruginosa and pathogens from the Enterobacteriaceae family. A 2–3.7 log reduction in the bacterial load was observed in antibacterial tests against A. baumannii and P. aeruginosa after 1.5 h. The Ts2631 activity was further enhanced by ethylenediaminetetraacetic acid (EDTA), a metal ion chelator (4.2 log reduction in carbapenem-resistant A. baumannii) and, to a lesser extent, by malic acid and citric acid (2.9 and 3.3 log reductions, respectively). The EDTA/Ts2631 combination reduced all pathogens of the Enterobacteriaceae family, particularly multidrug-resistant Citrobacter braakii, to levels below the detection limit (>6 log); these results indicate that Ts2631 endolysin could be useful to combat Gram-negative pathogens. The investigation of A. baumannii cells treated with Ts2631 endolysin variants under transmission electron and fluorescence microscopy demonstrates that the intrinsic antibacterial activity of Ts2631 endolysin is dependent on the presence of its N-terminal tail.
Collapse
|
15
|
Bilal M, Cui J, Iqbal HMN. Tailoring enzyme microenvironment: State-of-the-art strategy to fulfill the quest for efficient bio-catalysis. Int J Biol Macromol 2019; 130:186-196. [PMID: 30817963 DOI: 10.1016/j.ijbiomac.2019.02.141] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 02/08/2023]
Abstract
Enzymes as green industrial biocatalysts have become a powerful norm that offers several advantages over traditional catalytic agents with regard to process efficiency, reusability, sustainability, and overall cost-effective ratio. However, enzymes obtained from natural origins are often engineered/tailored since their native forms do not fulfill the acute need for the industrial application. Revolutionary developments in protein engineering provide excellent opportunities for designing and constructing novel industrial biocatalysts with improved functional properties including catalytic activity, stability, substrate specificity, and reaction product inhibition. Momentum in enzyme immobilization has enabled robustness and optimal functions in extreme industrial environments, such as high temperature or organic solvents. The emergence of multi-enzyme catalytic cascade based on a combination of biocatalysts presents multifarious opportunities in biosynthesis, biocatalysis, and biotransformation. This review focuses on the emerging and state-of-the-art enzyme engineering trends and approaches to constructing innovative nano- and microstructured biocatalysts with enhanced catalytic activity and stability features requisite for industrial exploitation. Continuous key developments in this direction together with protein engineering in unique ways might offer ever-increasing opportunities for future biocatalysis-based industrial bioprocesses.
Collapse
Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No 29, 13th, Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
| |
Collapse
|
16
|
Molecular dynamics investigation of halogenated amyloidogenic peptides. J Mol Model 2019; 25:124. [PMID: 31020417 DOI: 10.1007/s00894-019-4012-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.
Collapse
|
17
|
Bashirova A, Pramanik S, Volkov P, Rozhkova A, Nemashkalov V, Zorov I, Gusakov A, Sinitsyn A, Schwaneberg U, Davari MD. Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability. Int J Mol Sci 2019; 20:E1602. [PMID: 30935060 PMCID: PMC6479618 DOI: 10.3390/ijms20071602] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/29/2023] Open
Abstract
Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15⁻21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52⁻58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15⁻22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
Collapse
Affiliation(s)
- Anna Bashirova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| | - Pavel Volkov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Vitaly Nemashkalov
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142292, Moscow region, Russia.
| | - Ivan Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexander Gusakov
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Arkady Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstrasse 50, Aachen 52056, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| |
Collapse
|
18
|
Danchin A. Bacteria in the ageing gut: did the taming of fire promote a long human lifespan? Environ Microbiol 2018; 20:1966-1987. [PMID: 29727052 DOI: 10.1111/1462-2920.14255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Unique among animals as they evolved towards Homo sapiens, hominins progressively cooked their food on a routine basis. Cooked products are characterized by singular chemical compounds, derived from the pervasive Maillard reaction. This same reaction is omnipresent in normal metabolism involving carbonyls and amines, and its products accumulate with age. The gut microbiota acts as a first line of defence against the toxicity of cooked Maillard compounds, that also selectively shape the microbial flora, letting specific metabolites to reach the blood stream. Positive selection of metabolic functions allowed the body of hominins who tamed fire to use and dispose of these age-related compounds. I propose here that, as a hopeful accidental consequence, this resulted in extending human lifespan far beyond that of our great ape cousins. The limited data exploring the role of taming fire on the human genetic setup and on its microbiota is discussed in relation with ageing.
Collapse
Affiliation(s)
- Antoine Danchin
- Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, Paris, 75013, France.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong
| |
Collapse
|