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Kaczor-Kamińska M, Kaszuba K, Bilska-Wilkosz A, Iciek M, Wróbel M, Kamiński K. Dimethyl Sulfoxide (DMSO) as a Potential Source of Interference in Research Related to Sulfur Metabolism-A Preliminary Study. Antioxidants (Basel) 2024; 13:582. [PMID: 38790687 PMCID: PMC11117631 DOI: 10.3390/antiox13050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Dimethyl sulfoxide (DMSO), an organosulfur compound, is widely used as the gold standard solvent in biological research. It is used in cell culture experiments and as a component of formulations in in vivo studies. Unfortunately, parameters related to sulfur metabolism are often not taken into account when using DMSO. Therefore, in this work we aim to show that the addition of DMSO to the culture medium (even in amounts commonly considered acceptable) alters some parameters of sulfur metabolism. For this study, we used three cell lines: a commercially available Caco-2 line (HTB-37, ATCC) and two lines created as part of our early studies (likewise previously described in the literature) to investigate the anomalies of sulfur metabolism in mucopolysaccharidosis. As the negative effects of DMSO on the cell membrane are well known, additional experiments with the partial loading of DMSO into polymerosomes (poly(ethylene glycol) methyl ether-block-poly(lactide-co-glycolide), PEG-PLGA) were performed to eliminate these potentially disruptive effects. The results show that DMSO is a source of interference in studies related to sulfur metabolism and that there are not just simple effects that can be corrected in the final result by subtracting control values, since complex synergisms are also observed.
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Affiliation(s)
- Marta Kaczor-Kamińska
- Chair in Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, Kopernika 7 St., 31-034 Krakow, Poland; (K.K.); (A.B.-W.); (M.I.); (M.W.)
| | - Kinga Kaszuba
- Chair in Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, Kopernika 7 St., 31-034 Krakow, Poland; (K.K.); (A.B.-W.); (M.I.); (M.W.)
| | - Anna Bilska-Wilkosz
- Chair in Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, Kopernika 7 St., 31-034 Krakow, Poland; (K.K.); (A.B.-W.); (M.I.); (M.W.)
| | - Małgorzata Iciek
- Chair in Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, Kopernika 7 St., 31-034 Krakow, Poland; (K.K.); (A.B.-W.); (M.I.); (M.W.)
| | - Maria Wróbel
- Chair in Medical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, Kopernika 7 St., 31-034 Krakow, Poland; (K.K.); (A.B.-W.); (M.I.); (M.W.)
| | - Kamil Kamiński
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 St., 30-387 Krakow, Poland;
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Dick CF, Alcantara CL, Carvalho-Kelly LF, Lacerda-Abreu MA, Cunha-E-Silva NL, Meyer-Fernandes JR, Vieyra A. Iron Uptake Controls Trypanosoma cruzi Metabolic Shift and Cell Proliferation. Antioxidants (Basel) 2023; 12:antiox12050984. [PMID: 37237850 DOI: 10.3390/antiox12050984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: Ionic transport in Trypanosoma cruzi is the object of intense studies. T. cruzi expresses a Fe-reductase (TcFR) and a Fe transporter (TcIT). We investigated the effect of Fe depletion and Fe supplementation on different structures and functions of T. cruzi epimastigotes in culture. (2) Methods: We investigated growth and metacyclogenesis, variations of intracellular Fe, endocytosis of transferrin, hemoglobin, and albumin by cell cytometry, structural changes of organelles by transmission electron microscopy, O2 consumption by oximetry, mitochondrial membrane potential measuring JC-1 fluorescence at different wavelengths, intracellular ATP by bioluminescence, succinate-cytochrome c oxidoreductase following reduction of ferricytochrome c, production of H2O2 following oxidation of the Amplex® red probe, superoxide dismutase (SOD) activity following the reduction of nitroblue tetrazolium, expression of SOD, elements of the protein kinase A (PKA) signaling, TcFR and TcIT by quantitative PCR, PKA activity by luminescence, glyceraldehyde-3-phosphate dehydrogenase abundance and activity by Western blotting and NAD+ reduction, and glucokinase activity recording NADP+ reduction. (3) Results: Fe depletion increased oxidative stress, inhibited mitochondrial function and ATP formation, increased lipid accumulation in the reservosomes, and inhibited differentiation toward trypomastigotes, with the simultaneous metabolic shift from respiration to glycolysis. (4) Conclusion: The processes modulated for ionic Fe provide energy for the T. cruzi life cycle and the propagation of Chagas disease.
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Affiliation(s)
- Claudia F Dick
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - Carolina L Alcantara
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - Luiz F Carvalho-Kelly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Marco Antonio Lacerda-Abreu
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Narcisa L Cunha-E-Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - José R Meyer-Fernandes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Adalberto Vieyra
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
- Programa de Pós-Graduação em Biomedicina Translacional /BIOTRANS, Universidade do Grande Rio, Duque de Caxias 25071-202, RJ, Brazil
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An HPLC-based assay for improved measurement of glutamate decarboxylase inhibition/activation. Neurochem Int 2022; 161:105433. [PMID: 36273705 DOI: 10.1016/j.neuint.2022.105433] [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: 08/18/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
L-Glutamic acid decarboxylase (GAD) is an enzyme that ensures the balance between the levels of two neurotransmitters, γ-aminobutyric acid (GABA) and L-glutamic acid (L-Glu), necessary for proper brain functioning. A reduction in the concentrations of GABA and/or GAD activity has been implicated in the symptoms associated with epilepsy, which could be plausibly alleviated by the application of GAD activators. As any unnecessary interference in GAD catalytic activity could be detrimental, it is important to study whether CNS (or other) drug candidates act on GAD or not. The ability to identify and reduce this risk early could significantly improve the process of drug development. Although many methods for measuring GAD activity in various biological samples have been described, only few (such as manometric and radiometric) were adopted as in vitro assays for the screening of potential GAD inhibitors/activators. However, these methods require specialized equipment and/or an expensive radiolabeled substrate, and may have sensitivity and/or reliability issues. Therefore, this study aimed to develop an HPLC-DAD-based assay that would allow a simple and more accurate measurement of GAD inhibition or activation using unpurified mice or rat brain homogenates. This assay is based on the quantification of GABA, formed during the enzymatic reaction, after its derivatization with dansyl chloride. Various parameters were evaluated to optimize the assay procedure (e.g. homogenate volume, incubation time, DMSO content, GAD, GABA, and dansyl-GABA stabilities). This assay was validated for pharmacological screenings using 3-mercaptopropionic acid and gallic acid and GAD obtained from different experimental animals.
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Kaspar F, Neubauer P, Kurreck A. The Peculiar Case of the Hyper-thermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus*. Chembiochem 2021; 22:1385-1390. [PMID: 33258231 PMCID: PMC8247850 DOI: 10.1002/cbic.202000679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/22/2020] [Indexed: 12/16/2022]
Abstract
The poor solubility of many nucleosides and nucleobases in aqueous solution demands harsh reaction conditions (base, heat, cosolvent) in nucleoside phosphorylase-catalyzed processes to facilitate substrate loading beyond the low millimolar range. This, in turn, requires enzymes that can withstand these conditions. Herein, we report that the pyrimidine nucleoside phosphorylase from Thermus thermophilus is active over an exceptionally broad pH (4-10), temperature (up to 100 °C) and cosolvent space (up to 80 % (v/v) nonaqueous medium), and displays tremendous stability under harsh reaction conditions with predicted total turnover numbers of more than 106 for various pyrimidine nucleosides. However, its use as a biocatalyst for preparative applications is critically limited due to its inhibition by nucleobases at low concentrations, which is unprecedented among nonspecific pyrimidine nucleoside phosphorylases.
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Affiliation(s)
- Felix Kaspar
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Peter Neubauer
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
| | - Anke Kurreck
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
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de Albuquerque S, Cianni L, de Vita D, Duque C, Gomes ASM, Gomes P, Laughton C, Leitão A, Montanari CA, Montanari R, Ribeiro JFR, da Silva JS, Teixeira C. Molecular design aided by random forests and synthesis of potent trypanocidal agents as cruzain inhibitors for Chagas disease treatment. Chem Biol Drug Des 2020; 96:948-960. [PMID: 33058457 DOI: 10.1111/cbdd.13663] [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: 09/30/2019] [Revised: 12/13/2019] [Accepted: 12/23/2019] [Indexed: 11/30/2022]
Abstract
Cruzain is an established target for the identification of novel trypanocidal agents, but how good are in vitro/in vivo correlations? This work describes the development of a random forests model for the prediction of the bioavailability of cruzain inhibitors that are Trypanosoma cruzi killers. Some common properties that characterize drug-likeness are poorly represented in many established cruzain inhibitors. This correlates with the evidence that many high-affinity cruzain inhibitors are not trypanocidal agents against T. cruzi. On the other hand, T. cruzi killers that present typical drug-like characteristics are likely to show better trypanocidal action than those without such features. The random forests model was not outperformed by other machine learning methods (such as artificial neural networks and support vector machines), and it was validated with the synthesis of two new trypanocidal agents. Specifically, we report a new lead compound, Neq0565, which was tested on T. cruzi Tulahuen (β-galactosidase) with a pEC50 of 4.9. It is inactive in the host cell line showing a selectivity index (SI = EC50 cyto /EC50 T. cruzi ) higher than 50.
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Affiliation(s)
- Sérgio de Albuquerque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Lorenzo Cianni
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Daniela de Vita
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Carla Duque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ana S M Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Andrei Leitão
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Carlos A Montanari
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Raphael Montanari
- Centro de Robótica de São Carlos, EESC-ICMC, Universidade de São Paulo, São Paulo, Brazil
| | - Jean F R Ribeiro
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - João Santana da Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Deutch CE. Inhibition of urease activity in the urinary tract pathogens Staphylococcus saprophyticus and Proteus mirabilis by dimethylsulfoxide (DMSO). J Appl Microbiol 2019; 128:1514-1523. [PMID: 31860153 DOI: 10.1111/jam.14560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/15/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022]
Abstract
AIMS Urease is a virulence factor for the urinary tract pathogens Staphylococcus saprophyticus and Proteus mirabilis. Dimethylsulfoxide (DMSO) is structurally similar to urea, used as a solvent for urease inhibitors, and an effective treatment for interstitial cystitis/bladder pain syndrome (IC/BPS). The aims of this study were to test DMSO as a urease inhibitor and determine its physiological effects on S. saprophyticus and P. mirabilis. METHODS AND RESULTS Urease activity in extracts and whole cells was measured by the formation of ammonium ions. Urease was highly sensitive to noncompetitive inhibition by DMSO (Ki about 6 mmol l-1 ). DMSO inhibited urease activity in whole cells, limited bacterial growth in media containing urea, and slowed the increase in pH which occurred in artificial urine medium. CONCLUSIONS DMSO should be used with caution as a solvent when testing plant extracts or other potential urease inhibitors. Because it can inhibit bacterial growth and delay an increase in pH, it may be an effective treatment for urinary tract infections. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first detailed study of the inhibition of urease by DMSO. Dimethylsulfoxide may be used to treat urinary tract infections that are resistant to antibiotics or herbal remedies.
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Devi S, Sharma B, Kumar R, Singh Kanwar S. Purification, characterization, and biological cytotoxic activity of the extracellular cholesterol oxidase produced by Castellaniella sp. COX. J Basic Microbiol 2019; 60:253-267. [PMID: 31750957 DOI: 10.1002/jobm.201900365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 01/19/2023]
Abstract
A new bacterial strain producing extracellular cholesterol oxidase (ChOx) was isolated and identified as Castellaniella sp. COX. The ChOx was purified by salting-out and ion-exchange chromatography up to 10.4-fold, with a specific activity of 15 U/mg with a molecular mass of 59 kDa. The purified ChOx exhibited pH 8.0 and temperature 40°C for its optimum activity. The enzyme showed stability over a wide pH range and was most stable at pH value 7.0, and at pH 8.0, it retained almost 86% of its initial activity after 3 h of incubation at 37°C. The enzyme possessed a half-life of 8 h at 37°C, 7 h at 40°C, and 3 h at 50°C. A Lineweaver-Burk plot was calibrated to determine its Km (0.16 mM) and Vmax (18.7 μmol·mg-1 ·min-1 ). The ChOx activity was enhanced with Ca2+ , Mg2+ , and Mn2+ while it was inhibited by Hg2+ , Ba2+ , Fe2+ , Cu2+ , and Zn2+ ions. Organic solvents like acetone, n-butanol, toluene, dimethyl sulfoxide, chloroform, benzene, and methanol were well tolerated by the enzyme while iso-propanol and ethanol were found to enhance the activity of purified ChOx. ChOx induced cytotoxicity with an IC50 value of 1.78 and 1.88 U/ml against human RD and U87MG established cell lines, respectively, while broadly sparing the normal human cells.
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Affiliation(s)
- Sunita Devi
- Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
| | - Bhupender Sharma
- Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
| | - Rakesh Kumar
- Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Shimla, Himachal Pradesh, India
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Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W. β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 2018; 122:11895-11905. [DOI: 10.1021/acs.jpcb.8b08308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sylwia Berbeć
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | | | - Agnieszka Hernik-Magoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | - Grzegorz Ścibisz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
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Wang TF, Chi MC, Lai KL, Lin MG, Chen YY, Lo HF, Lin LL. High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue. PeerJ 2018; 6:e5863. [PMID: 30402354 PMCID: PMC6215446 DOI: 10.7717/peerj.5863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
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Affiliation(s)
- Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Kuan-Ling Lai
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan.,Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
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Liu GJ, Wang B, Zhang Y, Xing GW, Yang X, Wang S. A tetravalent sialic acid-coated tetraphenylethene luminogen with aggregation-induced emission characteristics: design, synthesis and application for sialidase activity assay, high-throughput screening of sialidase inhibitors and diagnosis of bacterial vaginosis. Chem Commun (Camb) 2018; 54:10691-10694. [PMID: 30187046 DOI: 10.1039/c8cc06300a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report a turn-on tetravalent sialic acid-coated tetraphenylethene luminogen (TPE4S) with excellent hydrophilicity, good stability, high sensitivity and unique selectivity towards sialidases, and the maximum fluorescence enhancement was ∼40 fold. More importantly, TPE4S was successfully utilized for the screening of sialidase inhibitors and diagnosis of bacterial vaginosis.
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Affiliation(s)
- Guang-Jian Liu
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
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Sondhi S, Kaur R, Kaur S, Kaur PS. Immobilization of laccase-ABTS system for the development of a continuous flow packed bed bioreactor for decolorization of textile effluent. Int J Biol Macromol 2018; 117:1093-1100. [DOI: 10.1016/j.ijbiomac.2018.06.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 11/27/2022]
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Yu HT, Chen BY, Li BY, Tseng MC, Han CC, Shyu SG. Efficient pretreatment of lignocellulosic biomass with high recovery of solid lignin and fermentable sugars using Fenton reaction in a mixed solvent. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:287. [PMID: 30377446 PMCID: PMC6195684 DOI: 10.1186/s13068-018-1288-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/09/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Pretreatment of biomass to maximize the recovery of fermentable sugars as well as to minimize the amount of enzyme inhibitors formed during the pretreatment is a challenge in biofuel process. We develop a modified Fenton pretreatment in a mixed solvent (water/DMSO) to combine the advantages of organosolv and Fenton pretreatments. The hemicellulose and cellulose in corncob were effectively degraded into xylose, glucose, and soluble glucose oligomers in a few hours. This saccharide solution, separated from the solid lignin simply by filtration, can be directly applied to the subsequent enzymatic hydrolysis and ethanol fermentation. RESULTS After the pretreatment, 94% carbohydrates were recovered as soluble monosaccharide (xylose and glucose) and glucose oligomers in the filtrates, and 87% of solid lignin was recovered as the filter residue. The filtrates were directly applied to enzymatic hydrolysis, and 92% of raw corncob glucose was recovered. The hydrolysates containing the glucose and xylose from the enzymatic hydrolysis were directly applied to ethanol fermentation with ethanol yield equals 79% of theoretical yield. The pretreatment conditions (130 °C, 1.5 bar; 30 min to 4 h) are mild, and the pretreatment reagents (H2O2, FeCl3, and solvent) had low impact to environment. Using ferrimagnetic Fe3O4 resulted in similar pretreatment efficiency and Fe3O4 could be removed by filtration. CONCLUSIONS A modified Fenton pretreatment of corncob in DMSO/water was developed. Up to 94% of the carbohydrate content of corncob was recovered as a saccharide solution simply by filtration. Such filtrate was directly applied to the subsequent enzymatic hydrolysis and where 92% of the corncob glucose content was obtained. The hydrolysate so obtained was directly applied to ethanol fermentation with good fermentability. The pretreatment method is simple, and the additives and solvents used have a low impact to the environment. This method provides the opportunity to substantially maximize the carbohydrate and solid lignin recovery of biomass with a comparatively green process, such that the efficiency of biorefinery as well as the bioethanol production process can be improved. The pretreatment is still relatively energy intensive and expensive, and further optimization of the process is required in large-scale operation.
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Affiliation(s)
- Hui-Tse Yu
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013 Taiwan
| | - Bo-Yu Chen
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Bing-Yi Li
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Chien-Chung Han
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013 Taiwan
| | - Shin-Guang Shyu
- Institute of Chemistry, Academia Sinica, Taipei, 11529 Taiwan
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13
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Kumar A, Darreh-Shori T. DMSO: A Mixed-Competitive Inhibitor of Human Acetylcholinesterase. ACS Chem Neurosci 2017; 8:2618-2625. [PMID: 29017007 DOI: 10.1021/acschemneuro.7b00344] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Dimethyl sulfoxide (DMSO) is the most common organic solvent used in biochemical and cellular assays during drug discovery programs. Despite its wide use, the effect of DMSO on several enzyme classes, which are crucial targets of the new therapeutic agents, are still unexplored. Here, we report the detailed biochemical analysis of the effects of DMSO on the human acetylcholine-degrading enzyme, acetylcholinesterase (AChE), the primary target of current Alzheimer's therapeutics. Our analysis showed that DMSO is a considerably potent and highly selective irreversible mixed-competitive inhibitor of human AChE with IC50 values in the lower millimolar range, corresponding to 0.88% to 2.6% DMSO (v/v). Most importantly, 1-4% (v/v) DMSO, the commonly used experimental concentrations, showed ∼37-80% inhibition of human AChE activity. We believe that our results will assist in developing stringent protocols and help in the better interpretation of experimental outcomes during screening and biological evaluation of new drugs.
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Affiliation(s)
- Amit Kumar
- Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology,
Care Sciences, and Society, Division of Translational Alzheimer Neurobiology, NOVUM, 4th Floor, 141 86 Stockholm, Sweden
| | - Taher Darreh-Shori
- Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology,
Care Sciences, and Society, Division of Translational Alzheimer Neurobiology, NOVUM, 4th Floor, 141 86 Stockholm, Sweden
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14
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Uliassi E, Fiorani G, Krauth-Siegel RL, Bergamini C, Fato R, Bianchini G, Carlos Menéndez J, Molina MT, López-Montero E, Falchi F, Cavalli A, Gul S, Kuzikov M, Ellinger B, Witt G, Moraes CB, Freitas-Junior LH, Borsari C, Costi MP, Bolognesi ML. Crassiflorone derivatives that inhibit Trypanosoma brucei glyceraldehyde-3-phosphate dehydrogenase ( Tb GAPDH) and Trypanosoma cruzi trypanothione reductase ( Tc TR) and display trypanocidal activity. Eur J Med Chem 2017; 141:138-148. [DOI: 10.1016/j.ejmech.2017.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/18/2017] [Accepted: 10/02/2017] [Indexed: 01/23/2023]
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15
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Misuri L, Cappiello M, Balestri F, Moschini R, Barracco V, Mura U, Del-Corso A. The use of dimethylsulfoxide as a solvent in enzyme inhibition studies: the case of aldose reductase. J Enzyme Inhib Med Chem 2017; 32:1152-1158. [PMID: 28856935 PMCID: PMC6009938 DOI: 10.1080/14756366.2017.1363744] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/21/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Aldose reductase (AR) is an enzyme devoted to cell detoxification and at the same time is strongly involved in the aetiology of secondary diabetic complications and the amplification of inflammatory phenomena. AR is subjected to intense inhibition studies and dimethyl sulfoxide (DMSO) is often present in the assay mixture to keep the inhibitors in solution. DMSO was revealed to act as a weak but well detectable AR differential inhibitor, acting as a competitive inhibitor of the L-idose reduction, as a mixed type of non-competitive inhibitor of HNE reduction and being inactive towards 3-glutathionyl-4-hydroxynonanal transformation. A kinetic model of DMSO action with respect to differently acting inhibitors was analysed. Three AR inhibitors, namely the flavonoids neohesperidin dihydrochalcone, rutin and phloretin, were used to evaluate the effects of DMSO on the inhibition studies on the reduction of L-idose and HNE.
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Affiliation(s)
- Livia Misuri
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Tuscany Region PhD School in Biochemistry and Molecular Biology, Italy
| | - Mario Cappiello
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Francesco Balestri
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Roberta Moschini
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Vito Barracco
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Tuscany Region PhD School in Biochemistry and Molecular Biology, Italy
| | - Umberto Mura
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
| | - Antonella Del-Corso
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Pisa, Italy
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16
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ElBaz FN, Gamal RF, ElBaz AF, Ibrahim NE, ElMekawy A. Biochemical and biotechnological studies on a novel purified bacillus cholesterol oxidase tolerant to solvent and thermal stress. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1306742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Fathy N. ElBaz
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City (USC), Sadat City, Egypt
| | - Rawia F. Gamal
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ashraf F. ElBaz
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City (USC), Sadat City, Egypt
| | - Nasser E. Ibrahim
- Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute, University of Sadat City (USC), Sadat City, Egypt
| | - Ahmed ElMekawy
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City (USC), Sadat City, Egypt
- Faculty of Engineering, Computer and Mathematical Sciences, School of Chemical Engineering, University of Adelaide, Adelaide, Australia
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17
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Naughton BS, Reich NO. Mechanisms of Protein Translocation on DNA Are Differentially Responsive to Water Activity. Biochemistry 2016; 55:6957-6960. [PMID: 27992993 DOI: 10.1021/acs.biochem.6b00872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water plays important but poorly understood roles in the functions of most biomolecules. We are interested in understanding how proteins use diverse search mechanisms to locate specific sites on DNA; here we present a study of the role of closely associated waters in diverse translocation mechanisms. The bacterial DNA adenine methyltransferase, Dam, moves across large segments of DNA using an intersegmental hopping mechanism, relying in part on movement through bulk water. In contrast, other proteins, such as the bacterial restriction endonuclease EcoRI, rely on a sliding mechanism, requiring the protein to stay closely associated with DNA. Here we probed how these two mechanistically distinct proteins respond to well-characterized osmolytes, dimethyl sulfoxide (DMSO), and glycerol. The ability of Dam to move over large segments of DNA is not impacted by either osmolyte, consistent with its minimal reliance on a sliding mechanism. In contrast, EcoRI endonuclease translocation is significantly enhanced by DMSO and inhibited by glycerol, providing further corroboration that these proteins rely on distinct translocation mechanisms. The well-established similar effects of these osmolytes on bulk water, and their differential effects on macromolecule-associated waters, support our results and provide further evidence of the importance of water in interactions between macromolecules and their ligands.
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Affiliation(s)
- Brigitte S Naughton
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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18
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Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers 2016; 105:864-72. [PMID: 27463323 DOI: 10.1002/bip.22924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/05/2022]
Abstract
Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity.
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Affiliation(s)
- Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996.,Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830
| | - Quentin R Johnson
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, 37996
| | - Wilfredo Evangelista
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830. .,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996.
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19
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Machado ATP, Silva M, Iulek J. Expression, purification, enzymatic characterization and crystallization of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa. Protein Expr Purif 2016; 127:125-130. [PMID: 27426132 DOI: 10.1016/j.pep.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/28/2016] [Accepted: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Naegleria gruberi had its genome sequenced by Fritz-Laylin and collaborators in 2010. It is not pathogenic, but has characteristics similar to those of Naegleria fowleri, opportunistic pathogen that can cause fatal encephalitis in humans. N. gruberi genome has contributed to a better understanding of the primitive eukaryotic metabolism and revealed the complexity of several metabolic pathways. In this paper we describe the expression, purification, enzyme characterization and crystallization of N. gruberi GAPDH, the first one for an organism belonging to phylum Percolozoa. The results indicated that 10 mM, 8.0 and 25 °C are the optimum arsenate concentration, pH and temperature, respectively. The enzyme presents allosteric positive cooperativity for substrates NAD(+) and G3P as indicated by the Hill coefficients. The phylogenetic proximity between N. fowleri and N. gruberi suggests that contributions from the study of the latter might provide information to assist the search for treatments of Primary Amebic Meningoencephalitis, especially, in this work, taking into account that GAPDH is identified as a therapeutic target.
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Affiliation(s)
| | - Marcio Silva
- Department of Education, Federal Technological University of Paraná, 84016-210, Ponta Grossa, PR, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, 84030-900, Ponta Grossa, PR, Brazil.
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20
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An D, Ye Z. Synthesis and surface activity of novel glucose ester surfactants containing carbohydrate and hydrocarbon chain. J DISPER SCI TECHNOL 2016. [DOI: 10.1080/01932691.2016.1170609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Dong An
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Zhiwen Ye
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
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21
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Catalytic activity and structural stability of three different Bacillus enzymes in water/organic co-solvent mixtures. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2015.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Characterization of Aspartate Kinase from Corynebacterium pekinense and the Critical Site of Arg169. Int J Mol Sci 2015; 16:28270-84. [PMID: 26633359 PMCID: PMC4691045 DOI: 10.3390/ijms161226098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 11/21/2022] Open
Abstract
Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni2+. Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production.
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23
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Prati F, Bergamini C, Molina MT, Falchi F, Cavalli A, Kaiser M, Brun R, Fato R, Bolognesi ML. 2-Phenoxy-1,4-naphthoquinones: From a Multitarget Antitrypanosomal to a Potential Antitumor Profile. J Med Chem 2015; 58:6422-34. [DOI: 10.1021/acs.jmedchem.5b00748] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Federica Prati
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Christian Bergamini
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Teresa Molina
- Instituto de Química Médica (IQM-CSIC), c/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Federico Falchi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Andrea Cavalli
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Marcel Kaiser
- Swiss Tropical & Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz
1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical & Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz
1, 4003 Basel, Switzerland
| | - Romana Fato
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6/Via Irnerio 48, 40126 Bologna, Italy
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24
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Toward the Development of Dual-Targeted Glyceraldehyde-3-phosphate Dehydrogenase/Trypanothione Reductase Inhibitors againstTrypanosoma bruceiandTrypanosoma cruzi. ChemMedChem 2014; 9:371-82. [DOI: 10.1002/cmdc.201300399] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/05/2013] [Indexed: 12/22/2022]
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25
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Integration of methods in cheminformatics and biocalorimetry for the design of trypanosomatid enzyme inhibitors. Future Med Chem 2014; 6:17-33. [DOI: 10.4155/fmc.13.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The enzyme GAPDH, which acts in the glycolytic pathway, is seen as a potential target for pharmaceutical intervention of Chagas disease. Results: Herein, we report the discovery of new Trypanosoma cruzi GAPDH (TcGAPDH) inhibitors from target- and ligand-based virtual screening protocols using isothermal titration calorimetry (ITC) and molecular dynamics. Molecular dynamics simulations were used to gain insight on the binding poses of newly identified inhibitors acting at the TcGAPDH substrate (G3P) site. Conclusion: Nequimed125, the most potent inhibitor to act upon TcGAPDH so far, which sits on the G3P site without any contact with the co-factor (NAD+) site, underpins the result obtained by ITC that it is a G3P-competitive inhibitor. Molecular dynamics simulation provides biding poses of TcGAPDH inhibitors that correlate with mechanisms of inhibition observed by ITC. Overall, a new class of dihydroindole compounds that act upon TcGAPDH through a competitive mechanism of inhibition as proven by ITC measurements also kills T. cruzi.
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26
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Soares FA, Sesti-Costa R, da Silva JS, de Souza MCB, Ferreira VF, da C. Santos F, Monteiro PA, Leitão A, Montanari CA. Molecular design, synthesis and biological evaluation of 1,4-dihydro-4-oxoquinoline ribonucleosides as TcGAPDH inhibitors with trypanocidal activity. Bioorg Med Chem Lett 2013; 23:4597-601. [DOI: 10.1016/j.bmcl.2013.06.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/05/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
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27
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Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J. Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. Chembiochem 2013; 14:890-7. [DOI: 10.1002/cbic.201200733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Indexed: 11/11/2022]
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28
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Stepankova V, Damborsky J, Chaloupkova R. Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases. Biotechnol J 2013; 8:719-29. [PMID: 23420811 DOI: 10.1002/biot.201200378] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/21/2013] [Accepted: 02/12/2013] [Indexed: 01/12/2023]
Abstract
Haloalkane dehalogenases are microbial enzymes with a wide range of biotechnological applications, including biocatalysis. The use of organic co-solvents to solubilize their hydrophobic substrates is often necessary. In order to choose the most compatible co-solvent, the effects of 14 co-solvents on activity, stability and enantioselectivity of three model enzymes, DbjA, DhaA, and LinB, were evaluated. All co-solvents caused at high concentration loss of activity and conformational changes. The highest inactivation was induced by tetrahydrofuran, while more hydrophilic co-solvents, such as ethylene glycol and dimethyl sulfoxide, were better tolerated. The effects of co-solvents at low concentration were different for each enzyme-solvent pair. An increase in DbjA activity was induced by the majority of organic co-solvents tested, while activities of DhaA and LinB decreased at comparable concentrations of the same co-solvent. Moreover, a high increase of DbjA enantioselectivity was observed. Ethylene glycol and 1,4-dioxane were shown to have the most positive impact on the enantioselectivity. The favorable influence of these co-solvents on both activity and enantioselectivity makes DbjA suitable for biocatalytic applications. This study represents the first investigation of the effects of organic co-solvents on the biocatalytic performance of haloalkane dehalogenases and will pave the way for their broader use in industrial processes.
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Affiliation(s)
- Veronika Stepankova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Masaryk University, Brno, Czech Republic
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29
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Immobilization of β-galactosidase on modified polypropilene membranes. Int J Biol Macromol 2012; 51:710-9. [DOI: 10.1016/j.ijbiomac.2012.07.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/28/2012] [Accepted: 07/31/2012] [Indexed: 11/24/2022]
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30
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Roy S, Jana B, Bagchi B. Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme. J Chem Phys 2012; 136:115103. [PMID: 22443797 DOI: 10.1063/1.3694268] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations.
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Affiliation(s)
- Susmita Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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31
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Shao Q, He Y, White AD, Jiang S. Different effects of zwitterion and ethylene glycol on proteins. J Chem Phys 2012; 136:225101. [DOI: 10.1063/1.4726135] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Cheleski J, Freitas RF, Wiggers HJ, Rocha JR, de Araújo APU, Montanari CA. Expression, purification and kinetic characterization of His-tagged glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi. Protein Expr Purif 2010; 76:190-6. [PMID: 21138769 DOI: 10.1016/j.pep.2010.11.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 11/22/2010] [Accepted: 11/22/2010] [Indexed: 11/17/2022]
Abstract
Trypanosomes are flagellated protozoa responsible for serious parasitic diseases that have been classified by the World Health Organization as tropical sicknesses of major importance. One important drug target receiving considerable attention is the enzyme glyceraldehyde-3-phosphate dehydrogenase from the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (T. cruzi Glyceraldehyde-3-phosphate dehydrogenase (TcGAPDH); EC 1.2.1.12). TcGAPDH is a key enzyme in the glycolytic pathway of T. cruzi and catalyzes the oxidative phosphorylation of D-glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate (1,3-BPG) coupled to the reduction of oxidized nicotinamide adenine dinucleotide, (NAD(+)) to NADH, the reduced form. Herein, we describe the cloning of the T. cruzi gene for TcGAPDH into the pET-28a(+) vector, its expression as a tagged protein in Escherichia coli, purification and kinetic characterization. The His(6)-tagged TcGAPDH was purified by affinity chromatography. Enzyme activity assays for the recombinant His(6)-TcGAPDH were carried out spectrophotometrically to determine the kinetic parameters. The apparent Michaelis-Menten constant (K(M)(app)) determined for D-glyceraldehyde-3-phosphate and NAD(+) were 352±21 and 272±25 μM, respectively, which were consistent with the values for the untagged enzyme reported in the literature. We have demonstrated by the use of Isothermal Titration Calorimetry (ITC) that this vector modification resulted in activity preserved for a higher period. We also report here the use of response surface methodology (RSM) to determine the region of optimal conditions for enzyme activity. A quadratic model was developed by RSM to describe the enzyme activity in terms of pH and temperature as independent variables. According to the RMS contour plots and variance analysis, the maximum enzyme activity was at 29.1°C and pH 8.6. Above 37°C, the enzyme activity starts to fall, which may be related to previous reports that the quaternary structure begins a process of disassembly.
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Affiliation(s)
- Juliana Cheleski
- Grupo de Estudos em Química Medicinal de Produtos Naturais-NEQUIMED-PN, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
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Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. Eur J Med Chem 2010; 45:5899-909. [DOI: 10.1016/j.ejmech.2010.09.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 11/22/2022]
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Cuypers R, Murali S, Marcelis ATM, Sudhölter EJR, Zuilhof H. Complexation of Phenol and Thiophenol by Amine N-Oxides: Isothermal Titration Calorimetry and ab Initio Calculations. Chemphyschem 2010; 11:3465-73. [DOI: 10.1002/cphc.201000482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kinetic mechanism and catalysis of Trypanosoma cruzi dihydroorotate dehydrogenase enzyme evaluated by isothermal titration calorimetry. Anal Biochem 2010; 399:13-22. [DOI: 10.1016/j.ab.2009.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 11/14/2009] [Accepted: 11/15/2009] [Indexed: 11/20/2022]
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Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
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Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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Cuypers R, Burghoff B, Marcelis ATM, Sudhölter EJR, de Haan AB, Zuilhof H. Complexation of Phenols and Thiophenol by Phosphine Oxides and Phosphates. Extraction, Isothermal Titration Calorimetry, and ab Initio Calculations. J Phys Chem A 2008; 112:11714-23. [DOI: 10.1021/jp801605y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruud Cuypers
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bernhard Burghoff
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Antonius T. M. Marcelis
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ernst J. R. Sudhölter
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - André B. de Haan
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands, Department of DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Chemical Engineering and Chemistry Process Systems Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Quesada-Soriano I, Leal I, Casas-Solvas JM, Vargas-Berenguel A, Barón C, Ruiz-Pérez LM, González-Pacanowska D, García-Fuentes L. Kinetic and thermodynamic characterization of dUTP hydrolysis by Plasmodium falciparum dUTPase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1347-55. [PMID: 18586121 DOI: 10.1016/j.bbapap.2008.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/27/2022]
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and plays an important role in nucleotide metabolism and DNA replication controlling relative cellular levels of dTTP/dUTP, both of which can be incorporated into DNA. Isothermal titration calorimetry has been applied to the determination of the kinetic and thermodynamic parameters of the trimeric Plasmodium falciparum dUTPase, a potential drug target against malaria. The role of divalent ions in binding, and inhibition by different uridine derivatives has been assessed. When dUTP hydrolysis in the presence of EDTA was evaluated, a 105-fold decrease and a 12-fold increase of the k(cat) and Km values, respectively, were observed when compared with the dUTP.Mg2+ complex. Calculation of the activation energy, E(a), and the thermodynamic activation parameters showed that the energetic barrier was approximately 4-fold higher when Mg2+ was depleted. Other divalent ions such as Co2+ or Mn2+ can substitute the physiological cofactor, however the k(cat) was significantly reduced compared to dUTP.Mg2+. Binding and inhibition by dU, dUMP, dUDP, and alpha,beta-imido-dUTP were analysed by ITC and compared with data obtained by spectrophotometric methods and binding equilibrium studies. Product inhibition (Kip dUMP: 99.34 microM) was insignificant yet Ki values for dUDP and alpha,beta-imido-dUTP were in the low micromolar range. The effect of ionic strength on protein stability was also monitored. DSC analysis evidenced a slight increase in the unfolding temperature, Tm, with increasing salt concentrations. Moreover, the thermal unfolding pathway in the presence of salt fits adequately to an irreversible two-state model (N3-->3D).
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Affiliation(s)
- Indalecio Quesada-Soriano
- Area de Química Física, Facultad de Ciencias Experimentales, Universidad de Almería, La Cañada de San Urbano, 04120 Almería, Spain
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