1
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Lee S, Showalter J, Zhang L, Cassin-Ross G, Rouached H, Busch W. Nutrient levels control root growth responses to high ambient temperature in plants. Nat Commun 2024; 15:4689. [PMID: 38824148 PMCID: PMC11144241 DOI: 10.1038/s41467-024-49180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
Global warming will lead to significantly increased temperatures on earth. Plants respond to high ambient temperature with altered developmental and growth programs, termed thermomorphogenesis. Here we show that thermomorphogenesis is conserved in Arabidopsis, soybean, and rice and that it is linked to a decrease in the levels of the two macronutrients nitrogen and phosphorus. We also find that low external levels of these nutrients abolish root growth responses to high ambient temperature. We show that in Arabidopsis, this suppression is due to the function of the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and its transcriptional regulation of the transceptor NITRATE TRANSPORTER 1.1 (NRT1.1). Soybean and Rice homologs of these genes are expressed consistently with a conserved role in regulating temperature responses in a nitrogen and phosphorus level dependent manner. Overall, our data show that root thermomorphogenesis is a conserved feature in species of the two major groups of angiosperms, monocots and dicots, that it leads to a reduction of nutrient levels in the plant, and that it is dependent on environmental nitrogen and phosphorus supply, a regulatory process mediated by the HY5-NRT1.1 module.
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Affiliation(s)
- Sanghwa Lee
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Julia Showalter
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Ling Zhang
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Gaëlle Cassin-Ross
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
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2
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Bittner JP, Smirnova I, Jakobtorweihen S. Investigating Biomolecules in Deep Eutectic Solvents with Molecular Dynamics Simulations: Current State, Challenges and Future Perspectives. Molecules 2024; 29:703. [PMID: 38338447 PMCID: PMC10856712 DOI: 10.3390/molecules29030703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Deep eutectic solvents (DESs) have recently gained increased attention for their potential in biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond acceptor and a hydrogen bond donor, which allows for tailoring their properties for particular applications. If produced from sustainable resources, they can provide a greener alternative to many traditional organic solvents for usage in various applications (e.g., as reaction environment, crystallization agent, or storage medium). To navigate this large design space, it is crucial to comprehend the behavior of biomolecules (e.g., enzymes, proteins, cofactors, and DNA) in DESs and the impact of their individual components. Molecular dynamics (MD) simulations offer a powerful tool for understanding thermodynamic and transport processes at the atomic level and offer insights into their fundamental phenomena, which may not be accessible through experiments. While the experimental investigation of DESs for various biotechnological applications is well progressed, a thorough investigation of biomolecules in DESs via MD simulations has only gained popularity in recent years. Within this work, we aim to provide an overview of the current state of modeling biomolecules with MD simulations in DESs and discuss future directions with a focus for optimizing the molecular simulations and increasing our fundamental knowledge.
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Affiliation(s)
- Jan Philipp Bittner
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Irina Smirnova
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
- Institute of Chemical Reaction Engineering, Hamburg University of Technology, Eißendorfer Straße 38, 21073 Hamburg, Germany
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3
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Lee S, Busch W. Assessing Temperature Responses in Roots. Methods Mol Biol 2024; 2795:37-42. [PMID: 38594525 DOI: 10.1007/978-1-0716-3814-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Due to global warming, it is important to understand how plants respond to high ambient temperature. Plant growth responses to high ambient temperature are termed thermomophogenesis and have been explored for more than a decade. However, this was mostly focused on the above-ground part of plants, the shoot. In this chapter, we describe a simple method to assess root growth phenotype to high ambient temperatures. In principle, this protocol can be applied for any other treatments to test overall seedling growth.
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Affiliation(s)
- Sanghwa Lee
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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4
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Gupta S, Elliott JR, Anderko A, Crosthwaite J, Chapman WG, Lira CT. Current Practices and Continuing Needs in Thermophysical Properties for the Chemical Industry. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Sumnesh Gupta
- The Dow Chemical Company, 1254 Enclave Parkway, Houston, Texas 77077, United States
| | - J. Richard Elliott
- Chemical, Biomolecular, and Corrosion Engineering Department, University of Akron, Akron, Ohio 44325-3906, United States
| | - Andrzej Anderko
- OLI Systems, Inc., 2 Gatehall Drive, Suite 1D, Parsippany, New Jersey 07054, United States
| | - Jacob Crosthwaite
- The Dow Chemical Company, 1897 Building, Midland, Michigan 48667, United States
| | - Walter G. Chapman
- Chemical and Biomolecular Engineering Department, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Carl T. Lira
- Chemical Engineering & Materials Science, Michigan State University, East Lansing, Michigan 48824-2288, United States
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5
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Keppler M, Moser S, Jessen HJ, Held C, Andexer JN. Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions. Beilstein J Org Chem 2022; 18:1278-1288. [PMID: 36225726 PMCID: PMC9520863 DOI: 10.3762/bjoc.18.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Polyphosphate kinases (PPKs) have become popular biocatalysts for nucleotide 5'-triphosphate (NTP) synthesis and regeneration. Two unrelated families are described: PPK1 and PPK2. They are structurally unrelated and use different catalytic mechanisms. PPK1 enzymes prefer the usage of adenosine 5'-triphosphate (ATP) for polyphosphate (polyP) synthesis while PPK2 enzymes favour the reverse reaction. With the emerging use of PPK enzymes in biosynthesis, a deeper understanding of the enzymes and their thermodynamic reaction course is of need, especially in comparison to other kinases. Here, we tested four PPKs from different organisms under the same conditions without any coupling reactions. In comparison to other kinases using phosphate donors with comparably higher phosphate transfer potentials that are characterised by reaction yields close to full conversion, the PPK-catalysed reaction reaches an equilibrium in which about 30% ADP is left. These results were obtained for PPK1 and PPK2 enzymes, and are supported by theoretical data on the basic reaction. At high concentrations of substrate, the different kinetic preferences of PPK1 and PPK2 can be observed. The implications of these results for the application of PPKs in chemical synthesis and as enzymes for ATP regeneration systems are discussed.
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Affiliation(s)
- Michael Keppler
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Sandra Moser
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Christoph Held
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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6
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Tao X, Yang R, Xiao Y, Liao L, Xiao X, Nie C. Complexation and enantioselectivity of novel bridge-like uranyl- 2-((1Z,9Z)-9-(2-Hydroxyphenyl)-3,5,6,8-tetrahydrobenzo[ h][1,4,7,10] dioxadiazacyclododecin-2-yl)-5-methoxyphenol with chiral organophosphorus pesticide enantiomers of R/S-malathions. ENVIRONMENTAL TECHNOLOGY 2022; 43:3378-3389. [PMID: 33886435 DOI: 10.1080/09593330.2021.1921055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Designing new uranyl complexes with enantioselectivity is of great significance for the identification and separation of enantiomers of chiral pesticides. In this paper, a new asymmetric rigid uranyl-2-((1Z,9Z)-9-(2-Hydroxyphenyl)-3,5,6,8-tetrahydrobenzo[h][1,4,7,10] dioxadiaza-cyclododecin-2-yl)-5-methoxyphenol(Uranyl-HTDM) was designed, we used Uranyl-HTDM as a receptor to selectively coordinate with the guests of the chiral organophosphorus pesticide R/S-malathions(R/S-MLTs) to explore the receptor's enatioselectivity recognition of the chiral guests of R/S-MLTs. Density functional theory (DFT) method was used to comprehensively study the complexation mode of the receptor with enantiomers. The results showed that the U of Uranyl-HTDM could coordinate with both the thiophosphoryl sulfur and carbonyl oxygens of R/S-MLTs in different environments, respectively. The thermodynamics calculations further indicated that the receptor could selectively recognize the thiophosphoryl sulfur and carbonyl oxygen atoms of R/S-malathions, and the complexation abilities of Uranyl-HTDM to the R/S-malathions under different solvents were not the same. The smaller the polarity of solvents, the stronger the complexation ability of Uranyl-HTDM with R-malathion, toluene was an ideal solvent with large △G change and enatioselectivity coefficient of 99.55%. The study provides useful references for the design of new uranyl-salophens and for the experimental study on the molecular recognition of chiral organophosphorus pesticides.
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Affiliation(s)
- Xuebing Tao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
- Key Laboratory of Hunan Province for Design and Application of Natural Actinide Complexes, Hengyang, People's Republic of China
| | - Rong Yang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
- Key Laboratory of Hunan Province for Design and Application of Natural Actinide Complexes, Hengyang, People's Republic of China
| | - Yang Xiao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
- Key Laboratory of Hunan Province for Design and Application of Natural Actinide Complexes, Hengyang, People's Republic of China
| | - Lifu Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
| | - Xilin Xiao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
| | - Changming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, People's Republic of China
- Key Laboratory of Hunan Province for Design and Application of Natural Actinide Complexes, Hengyang, People's Republic of China
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7
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Moosavi F, Ahrari F, Ahmadian G, Mohammadi M. Sortase-mediated immobilization of Candida antarctica lipase B (CalB) on graphene oxide; comparison with chemical approach. BIOTECHNOLOGY REPORTS 2022; 34:e00733. [PMID: 35686009 PMCID: PMC9171452 DOI: 10.1016/j.btre.2022.e00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022]
Abstract
Sortase A was used for the oriented immobilization of CalB on graphene oxide nanosheets Random attachment of CalB on GO nanosheets were performed by chemical immobilization The immobilized CalB were used for the enrichment of omega-3 fatty acids in fish oil The derivative obtained from oriented immobilization showed improved selectivity
In this study, Candida antarctica lipase B (CalB) was covalently immobilized on the surface of graphene oxide (GO) nanoparticles by sortase-mediated immobilization as well as a chemical attachment approach. Sortase is a transpeptidase that provides one-step purification and targeted immobilization of CalB from one specific site, presenting oriented attachment of the enzyme to a solid support. Chemical immobilization, on the other hand, is considered as a random immobilization, in which the protein can bind to the support from different regions of the protein surface. In this approach, amine-functionalized GO was further modified with glutaraldehyde to facilitate the covalent binding of CalB via its amine residues. The applied methods produced 60% and 100% immobilization yields and presented 0.106 U/mg and 0.085 U/mg of specific activities for the oriented and random immobilization, respectively. The stabilized enzyme with the sortase-mediated approach retained approximately 80% of its initial activity at 50°C.
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8
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Zahed MA, Movahed E, Khodayari A, Zanganeh S, Badamaki M. Biotechnology for carbon capture and fixation: Critical review and future directions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112830. [PMID: 34051533 DOI: 10.1016/j.jenvman.2021.112830] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
To mitigate the growing threat of climate change and develop novel technologies that can eliminate carbon dioxide, the most abundant greenhouse gas derived from the flue gas stream of the fossil fuel-fired power stations, is momentous. The development of carbon capture and sequestration-based technologies may play a significant role in this regard. Carbon fixation mostly occurs by photosynthesizing plants as well as photo and chemoautotrophic microbes that turn the atmospheric carbon dioxide into organic materials via their enzymes. Biofuel can offer a sustainable solution for carbon mitigation. The pragmatic implementation of biofuel production processes is neither cost-effective nor has been proven safe over the long term. Searching for ways to enhance biofuel generation by the employment of genetic engineering is vital. Carbon biosequestration can help to curb the greenhouse effect. In addition, new genomic approaches, which are able to use gene-splicing biotechnology techniques and recombinant DNA technology to produce genetically modified organisms, can contribute to improvement in sustainable and renewable biofuel and biomaterial production from microorganisms. Biopolymers, Biosurfactants, and Biochars are suggested as sustainable future trends. This study aims to pave the way for implementing biotechnology methods to capture carbon and decrease the demand and consumption of fossil fuels as well as the emissions of greenhouse gases. Having a better image of microorganisms' potential role in carbon capture and storage can be prolific in developing powerful techniques to reduce CO2 emissions.
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Affiliation(s)
- Mohammad Ali Zahed
- Faculty of Biological Sciences, Kharazmi University, 14911 - 15719, Tehran, Iran.
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Arezoo Khodayari
- Department of Civil and Environmental Engineering, California State University, Los Angeles, USA
| | - Saba Zanganeh
- Faculty of Biological Sciences, Kharazmi University, 14911 - 15719, Tehran, Iran
| | - Maryam Badamaki
- Faculty of Biological Sciences, Kharazmi University, 14911 - 15719, Tehran, Iran
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9
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Sabatini A, Borsari M, Moss GP, Iotti S. Chemical and biochemical thermodynamics reunification (IUPAC Technical Report). PURE APPL CHEM 2020. [DOI: 10.1515/pac-2019-0908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
According to the 1994 IUBMB-IUPAC Joint Commission on Biochemical Nomenclature (JCBN) on chemical and biochemical reactions, two categories of thermodynamics, based on different concepts and different formalisms, are established: (i) chemical thermodynamics, which employ conventional thermodynamic potentials to deal with chemical reactions [1], [2], [3]; and (ii) biochemical thermodynamics, which employ transformed thermodynamic quantities to deal with biochemical reactions based on the formalism proposed by Alberty [4], [5], [6], [7]. We showed that the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately, can be reunified within the same thermodynamic framework. The thermodynamics of chemical reactions, in which all species are explicitly considered with their atoms and charge balanced, are compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by a mathematical transformation of the usual thermodynamic quantities. The present analysis demonstrates that the transformed values for Δr
G′0 and Δr
H′0 can be obtained directly, without performing any transformation, by simply writing the chemical reactions with all the pseudoisomers explicitly included and the elements and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis reunifies the “two separate worlds” of conventional thermodynamics and transformed thermodynamics.
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Affiliation(s)
| | - Marco Borsari
- Dipartimento di Scienze Chimiche e Geologiche , Università degli Studi di Modena e Reggio Emilia , via Campi 103 , 41125 Modena , Italy
| | - Gerard P. Moss
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road , London E1 4NS, UK
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology (FaBit) , Università di Bologna ; via San Donato 15 , 40127 Bologna , Italy
- National Institute of Biostructures and Biosystems (NIBB) , 00136 Rome , Italy
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10
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Standard Gibbs energy of metabolic reactions: V. Enolase reaction. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140365. [DOI: 10.1016/j.bbapap.2020.140365] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 11/17/2022]
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11
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Greinert T, Baumhove K, Sadowski G, Held C. Standard Gibbs energy of metabolic reactions: IV. Triosephosphate isomerase reaction. Biophys Chem 2020; 258:106330. [PMID: 31981743 DOI: 10.1016/j.bpc.2020.106330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/07/2020] [Accepted: 01/11/2020] [Indexed: 12/27/2022]
Abstract
The glycolytic pathway is present in most organisms and represents a central part of the energy production mechanism in a cell. For a general understanding of glycolysis, the investigation from a thermodynamic point of view is essential and allows realising thermodynamic feasibility analyses under in vivo conditions. However, available literature standard Gibbs energies of reaction, ΔRg'0, are calculated using equilibrium-molality ratios Km', which might lead to a misinterpretation of the glycolytic pathway. It was the aim of this work to thermodynamically investigate the triosephosphate isomerase (TPI) reaction to provide new activity-based reaction data. In vitro equilibrium experiments were performed, and activity coefficients were predicted with the equation of state electrolyte PC-SAFT (ePC-SAFT). The combination of experimental concentrations and predicted activity coefficients yielded the thermodynamic equilibrium constant Ka and a new value for ΔRg'0(298.15 K, pH 7) = 7.1 ± 0.3 kJ mol‑1. The availability of the new ΔRg'0 value allowed predicting influences of the reaction medium on the reaction equilibrium of the TPI reaction. In this work, influences of the initial substrate concentration, pH and Mg2+ concentration on the reaction equilibrium were investigated and a method is presented to predict these influences. The higher the substrate concentration and the higher the temperature, the stronger the reaction equilibrium is shifted on the product side. While the pH did not have a significant influence on the reaction equilibrium, Mg2+ yielded a shift of the reaction equilibrium to the substrate side. All these effects were predicted correctly with ePC-SAFT. Based on the ePC-SAFT predictions we concluded that a charge-reduction of the product by complexation of the product with Mg2+ was responsible for the strong influence of Mg2+ on the reaction equilibrium. Finally, the standard enthalpy of reaction of ΔRh'0(pH 7) = 18 ± 7 kJ mol‑1 was determined with the equilibrium constants Ka at 298.15 K, 304.15 K and 310.15 K using the van 't Hoff equation.
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Affiliation(s)
- Thorsten Greinert
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Kristina Baumhove
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
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12
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Bülow M, Schmitz A, Mahmoudi T, Schmidt D, Junglas F, Janiak C, Held C. Odd–even effect for efficient bioreactions of chiral alcohols and boosted stability of the enzyme. RSC Adv 2020; 10:28351-28354. [PMID: 35519137 PMCID: PMC9055634 DOI: 10.1039/d0ra05406b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022] Open
Abstract
We describe a holistic approach for achieving a nearly quantitative conversion for an enzymatic reaction while simultaneously increasing the long-term stability of the enzyme. The approach provided chemical control of bioreactions by utilizing newly synthesized tetrahydrothiophene-based ionic liquids (THT ILs). We showcased its power by using THT-ILs as additives at a low concentration (only 10 mmol L−1) in the alcohol dehydrogenase (ADH)-catalyzed synthesis of methylated 1-phenylethanol (Me-PE). We discovered an “odd–even” effect of the IL-cation chain length: Me-PE displayed beneficial interactions with THT ILs having odd-numbered chain lengths and deleterious interactions with those having even-numbered chain lengths. An intermolecular thermodynamic simulation of the bulk phase and critical micelle concentration investigations of the local surroundings of the THT-ILs proved the occurrence of these interactions, and these two methods confirmed the odd–even effect from different perspectives. Additionally, storing the ADH enzyme in pure THT IL at room temperature allowed for a boosted long-term stability of the enzyme (500 times greater than that in aqueous buffer) without the need for freezing. We describe a holistic approach for achieving a nearly quantitative conversion for an enzymatic reaction while simultaneously increasing the long-term stability of the enzyme.![]()
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Affiliation(s)
- Mark Bülow
- Laboratory of Thermodynamics
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Alexa Schmitz
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
| | - Termeh Mahmoudi
- Laboratory of Thermodynamics
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Dana Schmidt
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
| | - Fabian Junglas
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
| | - Christoph Janiak
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine-Universität Düsseldorf
- 40204 Düsseldorf
- Germany
| | - Christoph Held
- Laboratory of Thermodynamics
- Technical University Dortmund
- 44227 Dortmund
- Germany
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13
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Phosphorylation Dynamics of JNK Signaling: Effects of Dual-Specificity Phosphatases (DUSPs) on the JNK Pathway. Int J Mol Sci 2019; 20:ijms20246157. [PMID: 31817617 PMCID: PMC6941053 DOI: 10.3390/ijms20246157] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023] Open
Abstract
Protein phosphorylation affects conformational change, interaction, catalytic activity, and subcellular localization of proteins. Because the post-modification of proteins regulates diverse cellular signaling pathways, the precise control of phosphorylation states is essential for maintaining cellular homeostasis. Kinases function as phosphorylating enzymes, and phosphatases dephosphorylate their target substrates, typically in a much shorter time. The c-Jun N-terminal kinase (JNK) signaling pathway, a mitogen-activated protein kinase pathway, is regulated by a cascade of kinases and in turn regulates other physiological processes, such as cell differentiation, apoptosis, neuronal functions, and embryonic development. However, the activation of the JNK pathway is also implicated in human pathologies such as cancer, neurodegenerative diseases, and inflammatory diseases. Therefore, the proper balance between activation and inactivation of the JNK pathway needs to be tightly regulated. Dual specificity phosphatases (DUSPs) regulate the magnitude and duration of signal transduction of the JNK pathway by dephosphorylating their substrates. In this review, we will discuss the dynamics of phosphorylation/dephosphorylation, the mechanism of JNK pathway regulation by DUSPs, and the new possibilities of targeting DUSPs in JNK-related diseases elucidated in recent studies.
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14
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Mestrom L, Przypis M, Kowalczykiewicz D, Pollender A, Kumpf A, Marsden SR, Bento I, Jarzębski AB, Szymańska K, Chruściel A, Tischler D, Schoevaart R, Hanefeld U, Hagedoorn PL. Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach. Int J Mol Sci 2019; 20:ijms20215263. [PMID: 31652818 PMCID: PMC6861944 DOI: 10.3390/ijms20215263] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/13/2023] Open
Abstract
Enzymes are nature’s catalyst of choice for the highly selective and efficient coupling of carbohydrates. Enzymatic sugar coupling is a competitive technology for industrial glycosylation reactions, since chemical synthetic routes require extensive use of laborious protection group manipulations and often lack regio- and stereoselectivity. The application of Leloir glycosyltransferases has received considerable attention in recent years and offers excellent control over the reactivity and selectivity of glycosylation reactions with unprotected carbohydrates, paving the way for previously inaccessible synthetic routes. The development of nucleotide recycling cascades has allowed for the efficient production and reuse of nucleotide sugar donors in robust one-pot multi-enzyme glycosylation cascades. In this way, large glycans and glycoconjugates with complex stereochemistry can be constructed. With recent advances, LeLoir glycosyltransferases are close to being applied industrially in multi-enzyme, programmable cascade glycosylations.
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Affiliation(s)
- Luuk Mestrom
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Marta Przypis
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
- Biotechnology Center, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Daria Kowalczykiewicz
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
- Biotechnology Center, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - André Pollender
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Antje Kumpf
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
| | - Stefan R Marsden
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Isabel Bento
- EMBL Hamburg, Notkestraβe 85, 22607 Hamburg, Germany.
| | - Andrzej B Jarzębski
- Institute of Chemical Engineering, Polish Academy of Sciences, Bałtycka 5, 44-100 Gliwice, Poland.
| | - Katarzyna Szymańska
- Department of Chemical and Process Engineering, Silesian University of Technology, Ks. M. Strzody 7, 44-100 Gliwice, Poland.
| | | | - Dirk Tischler
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
| | - Rob Schoevaart
- ChiralVision, J.H. Oortweg 21, 2333 CH Leiden, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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15
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Held C, Stolzke T, Knierbein M, Jaworek MW, Luong TQ, Winter R, Sadowski G. Cosolvent and pressure effects on enzyme-catalysed hydrolysis reactions. Biophys Chem 2019; 252:106209. [DOI: 10.1016/j.bpc.2019.106209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
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16
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Alazmi M, Kuwahara H, Soufan O, Ding L, Gao X. Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinformatics 2019; 35:2634-2643. [PMID: 30590445 PMCID: PMC6662295 DOI: 10.1093/bioinformatics/bty1035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/26/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. RESULTS Here, we introduce a machine learning method with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. Since a manual selection of 2D structure-based features can be a tedious and time-consuming task, requiring expert knowledge about the structure-activity relationship of chemical compounds, the systematic feature selection step in our method offers a convenient means to identify relevant 2D fingerprint-based features. By comparing our method with state-of-the-art linear regression-based methods for the standard Gibbs free energy prediction, we demonstrated that its prediction accuracy and prediction coverage are most favorable. Our results show direct evidence that a number of 2D fingerprints collectively provide useful information about the Gibbs free energy of biochemical reactions and that our systematic feature selection procedure provides a convenient way to identify them. AVAILABILITY AND IMPLEMENTATION Our software is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Meshari Alazmi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Othman Soufan
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Lizhong Ding
- Inception Institute of Artificial Intelligence (IIAI), Abu Dhabi, UAE
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
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17
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Tonin F, Otten LG, Arends IWCE. NAD + -Dependent Enzymatic Route for the Epimerization of Hydroxysteroids. CHEMSUSCHEM 2019; 12:3192-3203. [PMID: 30265441 PMCID: PMC6681466 DOI: 10.1002/cssc.201801862] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/28/2018] [Indexed: 05/12/2023]
Abstract
Epimerization of cholic and chenodeoxycholic acid (CA and CDCA, respectively) is a notable conversion for the production of ursodeoxycholic acid (UDCA). Two enantiocomplementary hydroxysteroid dehydrogenases (7α- and 7β-HSDHs) can carry out this transformation fully selectively by specific oxidation of the 7α-OH group of the substrate and subsequent reduction of the keto intermediate to the final product (7β-OH). With a view to developing robust and active biocatalysts, novel NADH-active 7β-HSDH species are necessary to enable a solely NAD+ -dependent redox-neutral cascade for UDCA production. A wild-type NADH-dependent 7β-HSDH from Lactobacillus spicheri (Ls7β-HSDH) was identified, recombinantly expressed, purified, and biochemically characterized. Using this novel NAD+ -dependent 7β-HSDH enzyme in combination with 7α-HSDH from Stenotrophomonas maltophilia permitted the biotransformations of CA and CDCA in the presence of catalytic amounts of NAD+ , resulting in high yields (>90 %) of UCA and UDCA.
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Affiliation(s)
- Fabio Tonin
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Linda G. Otten
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Isabel W. C. E. Arends
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
- Present address: Faculty of ScienceUtrecht UniversityBudapestlaan 63584 CDUtrechtThe Netherlands
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18
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Jain K, Clarke SG. PRMT7 as a unique member of the protein arginine methyltransferase family: A review. Arch Biochem Biophys 2019; 665:36-45. [PMID: 30802433 PMCID: PMC6461449 DOI: 10.1016/j.abb.2019.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are found in a wide variety of eukaryotic organisms and can regulate gene expression, DNA repair, RNA splicing, and stem cell biology. In mammalian cells, nine genes encode a family of sequence-related enzymes; six of these PRMTs catalyze the formation of ω-asymmetric dimethyl derivatives, two catalyze ω-symmetric dimethyl derivatives, and only one (PRMT7) solely catalyzes ω-monomethylarginine formation. Purified recombinant PRMT7 displays a number of unique enzymatic properties including a substrate preference for arginine residues in R-X-R motifs with additional flanking basic amino acid residues and a temperature optimum well below 37 °C. Evidence has been presented for crosstalk between PRMT7 and PRMT5, where methylation of a histone H4 peptide at R17, a PRMT7 substrate, may activate PRMT5 for methylation of R3. Defects in muscle stem cells (satellite cells) and immune cells are found in mouse Prmt7 homozygous knockouts, while humans lacking PRMT7 are characterized by significant intellectual developmental delays, hypotonia, and facial dysmorphisms. The overexpression of the PRMT7 gene has been correlated with cancer metastasis in humans. Current research challenges include identifying cellular factors that control PRMT7 expression and activity, identifying the physiological substrates of PRMT7, and determining the effect of methylation on these substrates.
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Affiliation(s)
- Kanishk Jain
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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19
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Wangler A, Böttcher D, Hüser A, Sadowski G, Held C. Prediction and Experimental Validation of Co-Solvent Influence on Michaelis Constants: A Thermodynamic Activity-Based Approach. Chemistry 2018; 24:16418-16425. [DOI: 10.1002/chem.201803573] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Anton Wangler
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Dominik Böttcher
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Aline Hüser
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Gabriele Sadowski
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Christoph Held
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
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20
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Chapman MR, Cosgrove SC, Turner NJ, Kapur N, Blacker AJ. Highly Productive Oxidative Biocatalysis in Continuous Flow by Enhancing the Aqueous Equilibrium Solubility of Oxygen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Michael R. Chapman
- School of Chemistry and School of Chemical and Process EngineeringInstitute of Process Research and DevelopmentUniversity of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | | | - Nicholas J. Turner
- Manchester Institute of Biotechnology 131 Princess Street Manchester M1 7DN UK
| | - Nikil Kapur
- School of Mechanical EngineeringUniversity of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - A. John Blacker
- School of Chemistry and School of Chemical and Process EngineeringInstitute of Process Research and DevelopmentUniversity of Leeds Woodhouse Lane Leeds LS2 9JT UK
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21
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Chapman MR, Cosgrove SC, Turner NJ, Kapur N, Blacker AJ. Highly Productive Oxidative Biocatalysis in Continuous Flow by Enhancing the Aqueous Equilibrium Solubility of Oxygen. Angew Chem Int Ed Engl 2018; 57:10535-10539. [PMID: 29741801 DOI: 10.1002/anie.201803675] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/03/2018] [Indexed: 11/10/2022]
Abstract
We report a simple, mild, and synthetically clean approach to accelerate the rate of enzymatic oxidation reactions by a factor of up to 100 when compared to conventional batch gas/liquid systems. Biocatalytic decomposition of H2 O2 is used to produce a soluble source of O2 directly in reaction media, thereby enabling the concentration of aqueous O2 to be increased beyond equilibrium solubility under safe and practical conditions. To best exploit this method, a novel flow reactor was developed to maximize productivity (g product L-1 h-1 ). This scalable benchtop method provides a distinct advantage over conventional bio-oxidation in that no pressurized gas or specialist equipment is employed. The method is general across different oxidase enzymes and compatible with a variety of functional groups. These results culminate in record space-time yields for bio-oxidation.
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Affiliation(s)
- Michael R Chapman
- School of Chemistry and School of Chemical and Process Engineering, Institute of Process Research and Development, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Sebastian C Cosgrove
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nikil Kapur
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - A John Blacker
- School of Chemistry and School of Chemical and Process Engineering, Institute of Process Research and Development, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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22
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Ferrario V, Hansen N, Pleiss J. Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity. J Inorg Biochem 2018. [DOI: 10.1016/j.jinorgbio.2018.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics. Trends Biotechnol 2018; 36:234-238. [DOI: 10.1016/j.tibtech.2017.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022]
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24
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Wangler A, Schmidt C, Sadowski G, Held C. Standard Gibbs Energy of Metabolic Reactions: III The 3-Phosphoglycerate Kinase Reaction. ACS OMEGA 2018; 3:1783-1790. [PMID: 30023815 PMCID: PMC6045398 DOI: 10.1021/acsomega.7b01704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/02/2018] [Indexed: 06/02/2023]
Abstract
The glycolytic pathway is one of the most studied metabolic pathways to date. This work focuses on determining the standard Gibbs energy of reaction (ΔRg0) of the first adenosine triphosphate-yielding reaction step of glycolysis, namely, the 3-phosphoglycerate kinase (PGK) reaction. Trustworthy values of ΔRg0 are required for thermodynamic approaches to determine single reaction conversions or even fluxes of metabolic reactions. In literature, the observed ΔRg0,obs values are usually determined directly from the experimental equilibrium composition data without accounting for the nonideality of the reaction mixture. That is the reason why the observed ΔRg0,obs values do not present consistent standard data as they are a function of the concentration, pH, and pMg. In this work, a combination of experimentally determined equilibrium composition data and activity coefficients of the reacting agents was used to determine ΔRg0 values for the temperatures 303, 313, and 323 K at pH 7. The activity coefficients were predicted with the thermodynamic model electrolyte perturbed-chain statistical associating fluid theory (ePC-SAFT). The ePC-SAFT parameters were taken from literature or fitted to new experimental osmotic coefficients. At 313.15 K, a value for ΔRg0 of -16.2 ± 0.2 kJ/mol was obtained. This value is about 4 kJ/mol less negative than what is usually considered as an accepted standard value. The reason behind this discrepancy was found to be the activity coefficients of the reacting agents, which dramatically influence the equilibrium position of the PGK reaction. On the basis of the temperature-dependent ΔRg0 values, the standard enthalpy of reaction was determined and found to be ΔRh0 = -49 ± 9 kJ/mol.
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Affiliation(s)
- Anton Wangler
- Department for Biochemical & Chemical
Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christina Schmidt
- Department for Biochemical & Chemical
Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Department for Biochemical & Chemical
Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Held
- Department for Biochemical & Chemical
Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
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25
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Lemberg M, Schomäcker R, Sadowski G. Thermodynamic prediction of the solvent effect on a transesterification reaction. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2017.10.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Wangler A, Canales R, Held C, Luong TQ, Winter R, Zaitsau DH, Verevkin SP, Sadowski G. Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis. Phys Chem Chem Phys 2018; 20:11317-11326. [DOI: 10.1039/c7cp07346a] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations.
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Affiliation(s)
- A. Wangler
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - R. Canales
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
- Departamento de Ingeniería Química y Bioprocesos
| | - C. Held
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - T. Q. Luong
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - R. Winter
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - D. H. Zaitsau
- Department of Physical Chemistry
- Institute of Chemistry
- University of Rostock
- 18059 Rostock
- Germany
| | - S. P. Verevkin
- Department of Physical Chemistry
- Institute of Chemistry
- University of Rostock
- 18059 Rostock
- Germany
| | - G. Sadowski
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
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27
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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28
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Capuano E, Oliviero T, van Boekel MA. Modeling food matrix effects on chemical reactivity: Challenges and perspectives. Crit Rev Food Sci Nutr 2017; 58:2814-2828. [DOI: 10.1080/10408398.2017.1342595] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Edoardo Capuano
- Food Quality & Design Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Teresa Oliviero
- Food Quality & Design Group, Wageningen University & Research, Wageningen, The Netherlands
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29
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Voges M, Fischer C, Wolff D, Held C. Influence of Natural Solutes and Ionic Liquids on the Yield of Enzyme-Catalyzed Reactions: Measurements and Predictions. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00178] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Voges
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Charlotte Fischer
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Dominik Wolff
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
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30
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Voges M, Fischer F, Neuhaus M, Sadowski G, Held C. Measuring and Predicting Thermodynamic Limitation of an Alcohol Dehydrogenase Reaction. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b01228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Voges
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Straße 70, 44227 Dortmund, Germany
| | - Florian Fischer
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Straße 70, 44227 Dortmund, Germany
| | - Melanie Neuhaus
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Straße 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Straße 70, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Straße 70, 44227 Dortmund, Germany
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31
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Mohapatra BR. Kinetic and thermodynamic properties of alginate lyase and cellulase co-produced by Exiguobacterium species Alg-S5. Int J Biol Macromol 2017; 98:103-110. [PMID: 28122206 DOI: 10.1016/j.ijbiomac.2017.01.091] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 11/30/2022]
Abstract
In an effort to screen out the alginolytic and cellulolytic bacteria from the putrefying invasive seaweed Sargassum species accumulated off Barbados' coast, a potent bacterial strain was isolated. This bacterium, which simultaneously produced alginate lyase and cellulase, was identified as Exiguobacterium sp. Alg-S5 via the phylogenetic approach targeting the 16S rRNA gene. The co-produced alginate lyase and cellulase exhibited maximal enzymatic activity at pH 7.5 and at 40°C and 45°C, respectively. The Km and Vmax values recorded as 0.91mg/mL and 21.8U/mg-protein, respectively, for alginate lyase, and 10.9mg/mL and 74.6U/mg-protein, respectively, for cellulase. First order kinetic analysis of the thermal denaturation of the co-produced alginate lyase and cellulase in the temperature range from 40°C to 55°C revealed that both the enzymes were thermodynamically efficient by displaying higher activation energy and enthalpy of denaturation. These enzymatic properties indicate the potential industrial importance of this bacterium in algal biomass conversion. This appears to be the first report on assessing the efficacy of a bacterium for the co-production of alginate lyase and cellulase.
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Affiliation(s)
- Bidyut R Mohapatra
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, BB11000, Barbados.
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32
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Thermodynamic Activity-Based Interpretation of Enzyme Kinetics. Trends Biotechnol 2017; 35:379-382. [DOI: 10.1016/j.tibtech.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/07/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022]
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33
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Held C. Erweiterung der Prozessfenster enzymkatalysierter Reaktionen. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201650420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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