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Korasick DA, Buckley DP, Palpacelli A, Cursio I, Cesaroni E, Cheng J, Tanner JJ. Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1. Chem Biol Interact 2024; 394:110993. [PMID: 38604394 DOI: 10.1016/j.cbi.2024.110993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Aldehyde dehydrogenase 7A1 (ALDH7A1) catalyzes a step of lysine catabolism. Certain missense mutations in the ALDH7A1 gene cause pyridoxine dependent epilepsy (PDE), a rare autosomal neurometabolic disorder with recessive inheritance that affects almost 1:65,000 live births and is classically characterized by recurrent seizures from the neonatal period. We report a biochemical, structural, and computational study of two novel ALDH7A1 missense mutations that were identified in a child with rare recurrent seizures from the third month of life. The mutations affect two residues in the oligomer interfaces of ALDH7A1, Arg134 and Arg441 (Arg162 and Arg469 in the HGVS nomenclature). The corresponding enzyme variants R134S and R441C (p.Arg162Ser and p.Arg469Cys in the HGVS nomenclature) were expressed in Escherichia coli and purified. R134S and R441C have 10,000- and 50-fold lower catalytic efficiency than wild-type ALDH7A1, respectively. Sedimentation velocity analytical ultracentrifugation shows that R134S is defective in tetramerization, remaining locked in a dimeric state even in the presence of the tetramer-inducing coenzyme NAD+. Because the tetramer is the active form of ALDH7A1, the defect in oligomerization explains the very low catalytic activity of R134S. In contrast, R441C exhibits wild-type oligomerization behavior, and the 2.0 Å resolution crystal structure of R441C complexed with NAD+ revealed no obvious structural perturbations when compared to the wild-type enzyme structure. Molecular dynamics simulations suggest that the mutation of Arg441 to Cys may increase intersubunit ion pairs and alter the dynamics of the active site gate. Our biochemical, structural, and computational data on two novel clinical variants of ALDH7A1 add to the complexity of the molecular determinants underlying pyridoxine dependent epilepsy.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - David P Buckley
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | | | - Ida Cursio
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Elisabetta Cesaroni
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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2
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Srivastava S, Dafale NA. Tailored microbial consortium producing hydrolytic enzyme cocktail for maximum saccharification of wheat straw. Bioresour Technol 2024; 399:130560. [PMID: 38460563 DOI: 10.1016/j.biortech.2024.130560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
The potential of hydrolytic enzyme cocktail obtained from designed bacterial consortium WSh-1 comprising Bacillus subtilis CRN 16, Paenibacillus dendritiformis CRN 18, Niallia circulans CRN 24, Serratia marscens CRN 29, and Streptomyces sp. CRN 30, was investigated for maximum saccharification. Activity was further enhanced to 1.01 U/ml from 0.82 U/ml by supplementing growth medium with biotin and cellobiose as a cofactor and inducer. Through kinetic analysis, the enzyme cocktail showed a high wheat straw affinity with Michaelis-Menten constant (Km) of 0.68 µmol/L and a deconstruction rate (Vmax) of 4.5 U/ml/min. The statistical optimization of critical parameters increased saccharification to 89 %. The optimized process in a 5-L lab-scale bioreactor yielded 501 mg/g of reducing sugar from NaOH-pretreated wheat straw. Lastly, genomic insights revealed unique abundant oligosaccharide deconstruction enzymes with the most diverse CAZyme profile. The consortium-mediated enzyme cocktails offer broader versatility with efficiency for the economical and sustainable valorization of lignocellulosic waste.
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Affiliation(s)
- Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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Ali EAA, Hussein NA, El-Hakim AE, Amer MA, Shahein YE. Cloning and catalytic profile of Hyalomma dromedarii leucine aminopeptidase. Int J Biol Macromol 2024; 268:131778. [PMID: 38657929 DOI: 10.1016/j.ijbiomac.2024.131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Ticks have harmful impacts on both human and animal health and cause considerable economic losses. Leucine aminopeptidase enzymes (LAP) play important roles during tick infestation to liberate vital amino acids necessary for growth. The aim of the current study is to identify, express and characterize the LAP from the hard tick Hyalomma dromedarii and elucidate its biochemical characteristics. We cloned an open reading frame of 1560 bp encoding a protein of 519 amino acids. The LAP full-length was expressed in Escherichia coli BL21 (DE3) and purified. The recombinant enzyme (H.d rLAP- 6×His) had a predicted molecular mass of approximately 55 kDa. Purification and the enzymatic characteristics of H.d rLAP- 6×His were studied. The purified enzyme showed maximum activity at 37 °C and pH 8.0-8.5 using Leu-p-nitroanilide as a substrate. The activity of H.d rLAP- 6×His was sensitive to β-mercaptoethanol, dl-dithiothreitol, 1,10- phenanthroline, bestatin HCl, and EDTA and completely abolished by 0.05 % SDS. In parallel, the enzymatic activity was enhanced by Ni2+, Mn2+ and Mg2+, partially inhibited by Na+, Cu2+, Ca2+ and completely inhibited by Zn2+.
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Affiliation(s)
- Esraa A A Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Nahla A Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
| | - Amr E El-Hakim
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Mahmoud A Amer
- Zoology Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622 Cairo, Egypt.
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Lim RC, Gary RK. Kinetic analysis of T4 polynucleotide kinase via isothermal titration calorimetry. Arch Biochem Biophys 2024; 756:109995. [PMID: 38621448 DOI: 10.1016/j.abb.2024.109995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
T4 polynucleotide kinase (T4 PNK) phosphorylates the 5'-terminus of DNA and RNA substrates. It is widely used in molecular biology. Single nucleotides can serve as substrates if a 3'-phosphate group is present. In this study, the T4 PNK-catalyzed conversion of adenosine 3'-monophosphate (3'-AMP) to adenosine-3',5'-bisphosphate was characterized using isothermal titration calorimetry (ITC). Although ITC is typically used to study ligand binding, in this case the instrument was used to evaluate enzyme kinetics by monitoring the heat production due to reaction enthalpy. The reaction was initiated with a single injection of 3'-AMP substrate into the sample cell containing T4 PNK and ATP at pH 7.6 and 30 °C, and Michaelis-Menten analysis was performed on the reaction rates derived from the plot of differential power versus time. The Michaelis-Menten constant, KM, was 13 μM, and the turnover number, kcat, was 8 s-1. The effect of inhibitors was investigated using pyrophosphate (PPi). PPi caused a dose-dependent decrease in the apparent kcat and increase in the apparent KM under the conditions tested. Additionally, the intrinsic reaction enthalpy and the activation energy of the T4 PNK-catalyzed phosphorylation of 3'-AMP were determined to be -25 kJ/mol and 43 kJ/mol, respectively. ITC is seldom used as a tool to study enzyme kinetics, particularly for technically-challenging enzymes such as kinases. This study demonstrates that quantitative analysis of kinase activity can be amenable to the ITC single injection approach.
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Affiliation(s)
- Rebecca C Lim
- Department of Chemistry & Biochemistry, University of Nevada, Las Vegas, USA
| | - Ronald K Gary
- Department of Chemistry & Biochemistry, University of Nevada, Las Vegas, USA.
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Punia P, Singh L. Evaluation of free and immobilized cellulase on chitosan-modified magnetic nanoparticles for saccharification of sorghum residue. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03010-7. [PMID: 38607415 DOI: 10.1007/s00449-024-03010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Enzymatic hydrolysis plays a pivotal role in transforming lignocellulosic biomass. Addressing alternate techniques to optimize the utilization of cellulolytic enzymes is one strategy to improve its efficiency and lower process costs. Cellulases are highly specific and environmentally benign biocatalysts that break down intricate polysaccharides into simple forms of sugars. In contrast to the most difficult and time-consuming enzyme immobilization processes, in this research, we studied simple, mild, and successful techniques for immobilization of pure cellulase on magnetic nanocomposites using glutaraldehyde as a linker and used in the application of sorghum residue biomass. Fe3O4 nanoparticles were coated with chitosan from the co-precipitation method, which served as an enzyme carrier. The nanoparticles were observed under XRD, Zeta Potential, FESEM, VSM, and FTIR. The size morphology results presented that the Cs@Fe3O4 have 42.2 nm, while bare nanoparticles (Fe3O4) have 31.2 nm in size. The pure cellulase reaches to 98.07% of loading efficiency and 71.67% of recovery activity at optimal conditions. Moreover, immobilized enzyme's pH stability, thermostability, and temperature tolerance were investigated at suitable conditions. The kinetic parameters of free and immobilized enzyme were estimated as Vmax; 29 ± 1.51 and 27.03 ± 2.02 µmol min-1 mg-1, Km; 4.7 ± 0.49 mM and 2.569 ± 0.522 mM and Kcat; 0.13 s-1, and 0.89 s-1. Sorghum residue was subjected to 2% NaOH pre-treatment at 50 ℃. Pre-treated biomass contains cellulose of 64.8%, used as a raw material to evaluate the efficiency of reducing sugar during hydrolysis and saccharification of free and immobilized cellulase, which found maximum concentration of glucose 5.42 g/L and 5.12 g/L on 72 h. Thus, our study verifies the use of immobilized pure cellulase to successfully hydrolyze raw material, which is a significant advancement in lignocellulosic biorefineries and the reusability of enzymes.
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Affiliation(s)
- Pallavi Punia
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, 125001, Haryana, India
| | - Lakhvinder Singh
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, 125001, Haryana, India.
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Sundaray K, Baral B, Subudhi U. DNA polyhedrons cube, prism, and square pyramid protect the catalytic activity of catalase: A thermodynamics and kinetics study. Int J Biol Macromol 2024; 264:130557. [PMID: 38431020 DOI: 10.1016/j.ijbiomac.2024.130557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
DNA is widely used as building block material for the construction of polyhedral nanostructures. DNA polyhedrons (DNA prism, cube, and square pyramid) are small 3D wireframed nanostructures with tunable shapes and sizes. Despite substantial progress in synthesis, the study regarding cellular responses to DNA polyhedrons is limited. Herein, the molecular interaction between DNA polyhedrons and the antioxidant enzyme, catalase has been explored. The enzymatic activity of bovine liver catalase (BLC) remains unaltered in the presence of DNA polyhedrons after 1 h of incubation. However, the activity of BLC was protected after 24 h of incubation in the presence of DNA polyhedrons as compared to the natural unfolding. The kinetics study confirmed the protective role of DNA polyhedrons on BLC with lower KM and higher catalytic efficiency. Furthermore, no profound conformational changes of BLC occur in the presence of DNA polyhedrons as observed in spectroscopic studies. From fluorescence quenching data we confirmed the binding between DNA polyhedrons and BLC. The thermodynamic parameters indicate that non-covalent bonds played a major role during the interaction of BLC with DNA polyhedrons. Moreover, the hepatic catalase activity remains unaltered in the presence of DNA polyhedrons. The cytotoxicity assay revealed that DNA polyhedrons were biocompatible in the cellular environment. The protective role of DNA polyhedrons on enzyme activity and the unaltered conformational change of protein ensures the biocompatibility of DNA polyhedrons in the cellular environment.
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Affiliation(s)
- Kajal Sundaray
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bineeth Baral
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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Williams AE, Gittis AG, Botello K, Cruz P, Martin-Martin I, Valenzuela Leon PC, Sumner B, Bonilla B, Calvo E. Structural and functional comparisons of salivary α-glucosidases from the mosquito vectors Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus. Insect Biochem Mol Biol 2024; 167:104097. [PMID: 38428508 PMCID: PMC10955559 DOI: 10.1016/j.ibmb.2024.104097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Mosquito vectors of medical importance both blood and sugar feed, and their saliva contains bioactive molecules that aid in both processes. Although it has been shown that the salivary glands of several mosquito species exhibit α-glucosidase activities, the specific enzymes responsible for sugar digestion remain understudied. We therefore expressed and purified three recombinant salivary α-glucosidases from the mosquito vectors Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus and compared their functions and structures. We found that all three enzymes were expressed in the salivary glands of their respective vectors and were secreted into the saliva. The proteins, as well as mosquito salivary gland extracts, exhibited α-glucosidase activity, and the recombinant enzymes displayed preference for sucrose compared to p-nitrophenyl-α-D-glucopyranoside. Finally, we solved the crystal structure of the Ae. aegypti α-glucosidase bound to two calcium ions at a 2.3 Ångstrom resolution. Molecular docking suggested that the Ae. aegypti α-glucosidase preferred di- or polysaccharides compared to monosaccharides, consistent with enzymatic activity assays. Comparing structural models between the three species revealed a high degree of similarity, suggesting similar functional properties. We conclude that the α-glucosidases studied herein are important enzymes for sugar digestion in three mosquito species.
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Affiliation(s)
- Adeline E Williams
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Apostolos G Gittis
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Karina Botello
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Phillip Cruz
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Paola Carolina Valenzuela Leon
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Benjamin Sumner
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Brian Bonilla
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
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Nguyen DK, Liu TW, Hsu SJ, Huynh QDT, Thi Duong TL, Chu MH, Wang YH, Vo TH, Lee CK. Xanthine oxidase inhibition study of isolated secondary metabolites from Dolichandrone spathacea (Bignoniaceae): In vitro and in silico approach. Saudi Pharm J 2024; 32:101980. [PMID: 38439949 PMCID: PMC10909772 DOI: 10.1016/j.jsps.2024.101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
Xanthine oxidase (XO) has been widely recognized as a pivotal enzyme in developing hyperuricemia, primarily contributing to the excessive production of uric acid during purine metabolism in the liver. One of the standard treatment approaches involves reducing uric acid levels by inhibiting XO activity. In this study, the leaf extract of Dolichandrone spathacea, traditionally used in folk medicine, was found to inhibit XO activity in the ethyl acetate and butanol fractions at a concentration of 100 µg/mL, their values were 78.57 ± 3.85 % (IC50 = 55.93 ± 5.73 µg/ml) and 69.43 ± 8.68 % (IC50 = 70.17 ± 7.98 µg/ml), respectively. The potential XO inhibitory components were isolated by bioactivity assays and the HR-ESI-MS and NMR spectra system. The main constituents of leaf extracts of Dolichandrone spathacea, six compounds, namely trans-4-methoxycinnamic acid (3), trans-3,4-dimethoxycinnamic acid (4), p-coumaric acid (5), martynoside (6), 6-O-(p-methoxy-E-cinnamoyl)-ajugol (7), and scolymoside (17), were identified as potent XO inhibitors with IC50 values ranging from 19.34 ± 1.63 μM to 64.50 ± 0.94 μM. The enzyme kinetics indicated that compounds 3-5, 7, and 17 displayed competitive inhibition like allopurinol, while compound 6 displayed a mixed-type inhibition. Computational studies corroborated these experimental results, highlighting the interactions between potential metabolites and XO enzyme. The hydrogen bonds played crucial roles in the binding interaction, especially, scolymoside (17) forms a hydrogen bond with Mos3004, exhibited the lowest binding energy (-18.3286 kcal/mol) corresponding to the lowest IC50 (19.34 ± 1.63 μM). Furthermore, nine compounds were isolated for the first time from this plant. In conclusion, Dolichandrone spathacea and its constituents possess the potential to modulate the xanthine oxidase enzyme involved in metabolism.
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Affiliation(s)
- Dang-Khoa Nguyen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Viet Nam
| | - Ta-Wei Liu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Su-Jung Hsu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Quoc-Dung Tran Huynh
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Truc-Ly Thi Duong
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Man-Hsiu Chu
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Yun-Han Wang
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Thanh-Hoa Vo
- School of Medicine, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 700000, Viet Nam
| | - Ching-Kuo Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
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Schmutzer M, Dasmeh P, Wagner A. Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation. J Mol Evol 2024; 92:104-120. [PMID: 38470504 PMCID: PMC10978624 DOI: 10.1007/s00239-024-10161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
Virtually all enzymes catalyse more than one reaction, a phenomenon known as enzyme promiscuity. It is unclear whether promiscuous enzymes are more often generalists that catalyse multiple reactions at similar rates or specialists that catalyse one reaction much more efficiently than other reactions. In addition, the factors that shape whether an enzyme evolves to be a generalist or a specialist are poorly understood. To address these questions, we follow a three-pronged approach. First, we examine the distribution of promiscuity in empirical enzymes reported in the BRENDA database. We find that the promiscuity distribution of empirical enzymes is bimodal. In other words, a large fraction of promiscuous enzymes are either generalists or specialists, with few intermediates. Second, we demonstrate that enzyme biophysics is not sufficient to explain this bimodal distribution. Third, we devise a constraint-based model of promiscuous enzymes undergoing duplication and facing selection pressures favouring subfunctionalization. The model posits the existence of constraints between the catalytic efficiencies of an enzyme for different reactions and is inspired by empirical case studies. The promiscuity distribution predicted by our constraint-based model is consistent with the empirical bimodal distribution. Our results suggest that subfunctionalization is possible and beneficial only in certain enzymes. Furthermore, the model predicts that conflicting constraints and selection pressures can cause promiscuous enzymes to enter a 'frustrated' state, in which competing interactions limit the specialisation of enzymes. We find that frustration can be both a driver and an inhibitor of enzyme evolution by duplication and subfunctionalization. In addition, our model predicts that frustration becomes more likely as enzymes catalyse more reactions, implying that natural selection may prefer catalytically simple enzymes. In sum, our results suggest that frustration may play an important role in enzyme evolution.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pouria Dasmeh
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Santa Fe Institute, Santa Fe, NM, USA.
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Wang HL, Sun HP, Zheng PR, Cheng RT, Liu ZW, Yuan H, Gao WY, Li H. Re-investigation of in vitro activity of acetohydroxyacid synthase I holoenzyme from Escherichia coli. Arch Biochem Biophys 2024; 754:109962. [PMID: 38499055 DOI: 10.1016/j.abb.2024.109962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Acetohydroxyacid synthase (AHAS) is one of the key enzymes of the biosynthesis of branched-chain amino acids, it is also an effective target for the screening of herbicides and antibiotics. In this study we present a method for preparing Escherichia coli AHAS I holoenzyme (EcAHAS I) with exceptional stability, which provides a solid ground for us to re-investigate the in vitro catalytic properties of the protein. The results show EcAHAS I synthesized in this way exhibits similar function to Bacillus subtilis acetolactate synthase in its catalysis with pyruvate and 2-ketobutyrate (2-KB) as dual-substrate, producing four 2-hydroxy-3-ketoacids including (S)-2-acetolactate, (S)-2-aceto-2-hydroxybutyrate, (S)-2-propionyllactate, and (S)-2-propionyl-2-hydroxybutyrate. Quantification of the reaction indicates that the two substrates almost totally consume, and compound (S)-2-aceto-2- hydroxybutyrate forms in the highest yield among the four major products. Moreover, the protein also condenses two molecules of 2-KB to furnish (S)-2-propionyl-2-hydroxybutyrate. Further exploration manifests that EcAHAS I ligates pyruvate/2-KB and nitrosobenzene to generate two arylhydroxamic acids N-hydroxy-N-phenylacetamide and N-hydroxy-N-phenyl- propionamide. These findings enhance our comprehension of the catalytic characteristics of EcAHAS I. Furthermore, the application of this enzyme as a catalyst in construction of C-N bonds displays promising potential.
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Affiliation(s)
- Hai-Ling Wang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Hui-Peng Sun
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Pei-Rong Zheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Rui-Tong Cheng
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhi-Wen Liu
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Heng Yuan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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Puri S, Singh PP, Bora PS, Sharma U. Chemometric guided isolation of new triterpenoid saponins as acetylcholinesterase inhibitors from seeds of Achyranthes bidentata Blume. Fitoterapia 2024; 175:105925. [PMID: 38537885 DOI: 10.1016/j.fitote.2024.105925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
Achyranthes bidentata Blume (Amaranthaceae) is an annual or perennial herb widely used as ethnomedicine in Traditional Chinese Medicine for treating fever, cold, ulcers, mensural pain, dementia, and osteoporosis. In the current study, UPLC-IM-Q-TOF-MS/MS-based chemometric approach was adopted for the tentative identification of fifty-six compounds in the extract and fractions of A.bidentata seeds. Further, the chemometric-guided isolation led to the isolation of two previously undescribed oleanane-type triterpenoid saponins, named achyranosides A-B (27 and 30), along with three known compounds (31, 44, and 23) from water fraction of A. bidentata seeds. The structures of new compounds were elucidated based on the detailed analysis of NMR, HR-ESI-MS, FT-IR spectral data, and GC-FID techniques. The isolated compounds in vitro acetylcholinesterase inhibitory activity revealed the promising activity of chikusetsusaponin IVa (23) (IC50 = 63.7 μM) with mixed type of AChE inhibition in enzyme kinetic studies. Additionally, in silico binding free energy of isolated compounds disclosed the greater stability of enzyme-ligand complex owing to underlying multiple H-bond interactions. Overall, the study demonstrates the effectiveness of a chemometric-guided approach for the phytochemical exploration and isolation of new oleanane-type triterpenoid saponins from A. bidentata seeds.
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Affiliation(s)
- Shivani Puri
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prithvi Pal Singh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prateek Singh Bora
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Upendra Sharma
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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12
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Khoshnevisan G, Emamzadeh R, Nazari M, Oliayi M, Sariri R. Uncovering the role of sorbitol in Renilla luciferase kinetics: Insights from spectroscopic and molecular dynamics studies. Biochem Biophys Rep 2024; 37:101617. [PMID: 38371529 PMCID: PMC10873868 DOI: 10.1016/j.bbrep.2023.101617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 02/20/2024] Open
Abstract
Renilla luciferase catalyzes the oxidation of coelenterazine to coelenteramide, resulting in the emission of a photon of light. This study investigated the impact of sorbitol on the structural and kinetic properties of Renilla luciferase using circular dichroism, fluorescence spectroscopy, and molecular dynamics simulations. Our investigation, carried out using circular dichroism and fluorescence analyses, as well as a thermal stability assay, has revealed that sorbitol induces conformational changes in the enzyme but does not improve its thermal stability. Moreover, through kinetic studies, it has been demonstrated that at a concentration of 0.4 M, sorbitol enhances the catalytic efficiency of Renilla luciferase. However, at higher concentrations, sorbitol results in a decrease in catalytic efficiency. Additionally, molecular dynamics simulations have shown that sorbitol increases the presence of hydrophobic pockets on the enzyme's surface. These simulations have also provided evidence that at a concentration of 0.4 M, sorbitol facilitates substrate access to the active site of the enzyme. Nevertheless, at higher concentrations, sorbitol obstructs substrate trafficking, most likely due to its impact on the gateway to the active site. This study may provide insights into the kinetic changes observed in enzymes with buried active sites, such as those with α/β hydrolase fold.
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Affiliation(s)
| | - Rahman Emamzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mahboobeh Nazari
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mina Oliayi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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13
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Tanaka Y, Uchihashi T, Nakamura A. Product inhibition slow down the moving velocity of processive chitinase and sliding-intermediate state blocks re-binding of product. Arch Biochem Biophys 2024; 752:109854. [PMID: 38081338 DOI: 10.1016/j.abb.2023.109854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023]
Abstract
Processive movement is the key reaction for crystalline polymer degradation by enzyme. Product release is an important phenomenon in resetting the moving cycle, but how it affects chitinase kinetics was unknown. Therefore, we investigated the effect of diacetyl chitobiose (C2) on the biochemical activity and movement of chitinase A from Serratia marcescens (SmChiA). The apparent inhibition constant of C2 on crystalline chitin degradation of SmChiA was 159 μM. The binding position of C2 obtained by X-ray crystallography was at subsite +1, +2 and Trp275 interact with C2 at subsite +1. This binding state is consistent with the competitive inhibition obtained by biochemical analysis. The apparent inhibition constant of C2 on the moving velocity of high-speed (HS) AFM observations was 330 μM, which is close to the biochemical results, indicating that the main factor in crystalline chitin degradation is also the decrease in degradation activity due to inhibition of processive movement. The Trp275 is a key residue for making a sliding intermediate complex. SmChiA W275A showed weaker activity and affinity than WT against crystalline chitin because it is less processive than WT. In addition, biochemical apparent inhibition constant for C2 of SmChiA W275A was 45.6 μM. W275A mutant showed stronger C2 inhibition than WT even though the C2 binding affinity is weaker than WT. This result indicated that Trp275 is important for the interaction at subsite +1, but also important for making sliding intermediate complex and physically block the rebinding of C2 on the catalytic site for crystalline chitin degradation.
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Affiliation(s)
- Yoshiko Tanaka
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya,Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Aichi, 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka, 422-8529, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi, 444-8787, Japan.
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Vyas K, Prabaker S, Prabhu D, Sakthivelu M, Rajamanikandan S, Velusamy P, Su CH, Gopinath SCB, Pachaiappan R. Study of an inhibitory effect of plant polyphenolic compounds against digestive enzymes using bench-working experimental evidence predicted by molecular docking and dynamics. Int J Biol Macromol 2024; 259:129222. [PMID: 38185307 DOI: 10.1016/j.ijbiomac.2024.129222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The substantial nutritional content and diversified biological activity of plant-based nutraceuticals are due to polyphenolic chemicals. These chemicals are important and well-studied plant secondary metabolites. Their protein interactions are extensively studied. This relationship is crucial for the logical development of functional food and for enhancing the availability and usefulness of polyphenols. This study highlights the influence of protein types and polyphenols on the interaction, where the chemical bindings predominantly consist of hydrophobic interactions and hydrogen bonds. The interaction between polyphenolic compounds (PCs) and digestive enzymes concerning their inhibitory activity has not been fully studied. Therefore, we have examined the interaction of four digestive enzymes (α-amylase, pepsin, trypsin, and α-chymotrypsin) with four PCs (curcumin, diosmin, morin, and 2',3',4'-trihydroxychalcone) through in silico and in vitro approaches. In vitro plate assays, enzyme kinetics, spectroscopic assays, molecular docking, and simulations were performed. We observed all these PCs have significant docking scores and preferable interaction with the active site of the digestive enzymes, resulting in the reduction of enzyme activity. The enzyme-substrate binding mechanism was determined using the Lineweaver Burk plot, indicating that the inhibition occurred competitively. Among four PCs diosmin and morin has the highest interaction energy over digestive enzymes with IC50 value of 1.13 ± 0.0047 and 1.086 ± 0.0131 μM. Kinetic studies show that selected PCs inhibited pepsin, trypsin, and chymotrypsin competitively and inhibited amylase in a non-competitive manner, especially by 2',3',4'-trihydroxychalcone. This study offers insights into the mechanisms by which the selected PCs inhibit the enzymes and has the potential to enhance the application of curcumin, diosmin, morin, and 2',3',4'-trihydroxychalcone as natural inhibitors of digestive enzymes.
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Affiliation(s)
- Kaushal Vyas
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu District, Tamil Nadu, India
| | - Supraja Prabaker
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu District, Tamil Nadu, India
| | - Dhamodharan Prabhu
- Centre for Drug Discovery, Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
| | - Meenakumari Sakthivelu
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu District, Tamil Nadu, India
| | - Sundararaj Rajamanikandan
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
| | - Palaniyandi Velusamy
- Research & Development, Sree Balaji Medical College and Hospital (SBMCH), Bharath Institute of Higher Education and research (BIHER), Chromepet 600 044, Tamil Nadu, India.
| | - Chia-Hung Su
- Department of Chemical Engineering, Ming Chi University of Technology, Taishan, Taipei 24301, Taiwan
| | - Subash C B Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600 Arau, Perlis, Malaysia; Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia; Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600 Arau, Perlis, Malaysia; Department of Computer Science and Engineering, Faculty of Science and Information Technology, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Raman Pachaiappan
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu District, Tamil Nadu, India.
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Patial V, Kumar S, Joshi R, Singh D. Biochemical characterization of glutaminase-free L-asparaginases from Himalayan Pseudomonas and Rahnella spp. for acrylamide mitigation. Int J Biol Macromol 2024; 257:128576. [PMID: 38048933 DOI: 10.1016/j.ijbiomac.2023.128576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
L-asparaginase having low glutaminase activity is important in clinical and food applications. Herein, glutaminase-free L-asparaginase (type I) coding genes from Pseudomonas sp. PCH182 (Ps-ASNase I) and Rahnella sp. PCH162 (Rs-ASNase I) was amplified using gene-specific primers, cloned into a pET-47b(+) vector, and plasmids were transformed into Escherichia coli (E. coli). Further, affinity chromatography purified recombinant proteins to homogeneity with monomer sizes of ~37.0 kDa. Purified Ps-ASNase I and Rs-ASNase I were active at wide pHs and temperatures with optimum activity at 50 °C (492 ± 5 U/mg) and 37 °C (308 ± 4 U/mg), respectively. Kinetic constant Km and Vmax for L-asparagine (Asn) were 2.7 ± 0.06 mM and 526.31 ± 4.0 U/mg for Ps-ASNase I, and 4.43 ± 1.06 mM and 434.78 ± 4.0 U/mg for Rs-ASNase I. Circular dichroism study revealed 29.3 % and 24.12 % α-helix structures in Ps-ASNase I and Rs-ASNase I, respectively. Upon their evaluation to mitigate acrylamide formation, 43 % and 34 % acrylamide (AA) reduction were achieved after pre-treatment of raw potato slices, consistent with 65 % and 59 % Asn reduction for Ps-ASNase I and Rs-ASNase I, respectively. Current findings suggested the potential of less explored intracellular L-asparaginase in AA mitigation for food safety.
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Affiliation(s)
- Vijeta Patial
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061, Himachal Pradesh, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Subhash Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061, Himachal Pradesh, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061, Himachal Pradesh, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176 061, Himachal Pradesh, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201 002, India.
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16
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Fanaei-Kahrani Z, Emamzadeh R, Nazari M. Uncovering the role of leucine 59 in Renilla luciferase stability and activity with error-prone PCR: Implications for protein engineering. Protein Expr Purif 2024; 214:106378. [PMID: 37816476 DOI: 10.1016/j.pep.2023.106378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023]
Abstract
A new variant of Renilla luciferase, named Met C-SRLuc 8, was obtained from a random mutagenesis library and expressed in Escherichia coli BL21 (DE3) plys and purified. The results of the enzyme's binding affinity, kinetic stability, and bioinformatic studies demonstrated that leucine 59, located within the hot-spot foldon in the N-terminal domain of the protein, plays a significant role in the stability and activity of Renilla luciferase. These findings may facilitate the engineering of different variants of this enzyme to achieve thermally stable versions for various biotechnological applications.
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Affiliation(s)
- Zahra Fanaei-Kahrani
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rahman Emamzadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mahboobeh Nazari
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran; Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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17
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Plapp BV. Solvent isotope and mutagenesis studies on the proton relay system in yeast alcohol dehydrogenase 1. Chem Biol Interact 2024; 388:110853. [PMID: 38151107 PMCID: PMC10843573 DOI: 10.1016/j.cbi.2023.110853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Alcohol dehydrogenase catalyzes the reversible transfer of a hydride directly from an alcohol to the nicotinamide ring of NAD+ to form an aldehyde and NADH, and the proton from the alcohol probably is transferred through a hydrogen-bonded system to the imidazole of His-48. Studies of the pH dependencies, and solvent and substrate isotope effects on the wild-type and the enzyme with His-48 substituted with Gln-48 were used to demonstrate a role for the proton relay system. The H48Q substitution increases affinities for NAD+ and NADH by ∼2-fold, suggesting that the overall protein structure is maintained. In contrast, catalytic efficiencies (V/Km) on ethanol and acetaldehyde and affinity for 2,2,2-trifluoroethanol are decreased by about 10-fold. The pH dependencies for catalytic efficiencies on ethanol and acetaldehyde (log V/Km versus pH), show pK values of about 7.5 for wild-type enzyme, but ethanol oxidation by H48Q ADH is essentially linear over the pH range from 5.5 to 9.2 with a slope of 0.47. Steady-state kinetics and substrate isotope effects suggest that the kinetic mechanism of H48Q ADH has become partly random for oxidation of ethanol. Both wild-type and H48Q ADHs have pH-independent isotope effects for oxidation (V1/Kb) of 1-butanol/1-butanol-d9 of 4, suggesting that hydride transfer is a major rate-limiting step. The pH dependence for butanol oxidation by wild type ADH shows a wavy profile over the pH range from pH 6 to 10, with a ∼2.3-fold larger V1/Kb in D2O than in H2O, an "inverse" isotope effect. The substrate isotope effect of 4 is not altered by the solvent isotope effect, suggesting concerted proton/hydride transfer. The solvent isotope effect can be explained by a ground state with a water bound to the catalytic zinc in the enzyme-NAD+ complex, and a transition state that resembles a complex with NADH and aldehyde. In contrast, the H48Q enzyme has a diminished inverse solvent isotope effect of ∼1.3 and an essentially linear pH dependence with a slope of log V1/Kb against pH of 0.49 for oxidation of 1-butanol, which together are consistent with a transition state where hydroxide ion directly accepts a proton from the 2'-hydroxyl group of the nicotinamide ribose in the proton relay system in the enzyme-NAD+-alcohol complex. The results support a catalytic role for His-48 in the proton relay system.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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18
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Poudel PB, Dhakal D, Lee JC, Sohng JK. Functional characterization of a naphthalene-O-methyltransferase from Nocardia sp. CS682. Enzyme Microb Technol 2024; 172:110351. [PMID: 37939423 DOI: 10.1016/j.enzmictec.2023.110351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Abstract
Methylation plays important roles in biosynthesis, metabolism, signal transduction, detoxification, protein sorting and repair, and nucleic acid processing. Generally the methyltransferases transfer methyl groups in various natural products using S-adenosyl methionine (SAM) as a cofactor. In this study, we examined and functionally characterized ThnM3 (enzyme), by testing various substrates with different chemical structures. Among the tested substrates, 1,8-dihydroxynaphthalene was the best substrate for methylation. Whole-cell biotransformation was performed using the enzyme in engineered Escherichia coli to produce 8-methoxynaphthalene-1-ol, and 1,8-dimethoxynaphthalene derivatives of 1,8-dihydroxynaphthalene. The products were confirmed using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopic analyses. Therefore, this study is the first to amplify, express the thnM3 (gene), and functionally characterize theThnM3, which exhibits the regioselective modifications of 1,8-dihydroxynaphthalene.
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Affiliation(s)
- Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Jong Cheol Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea; Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea.
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19
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Wang S, Wang M, Cui J, Lian D, Li L. Inhibition Effect of Okanin Toward Human Cytochrome P450 3A4 and 2D6 with Multi-spectroscopic Studies and Molecular Docking. J Fluoresc 2024; 34:203-212. [PMID: 37191827 DOI: 10.1007/s10895-023-03258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Okanin, a major flavonoid of a popular herb tea, Coreopsis tinctoria Nutt., showed strong inhibition on CYP3A4 and CYP2D6. The strong interaction between okanin and CYPs were determined by enzyme kinetics, multispectral technique and molecular docking. The inhibition type of two enzymes, CYP3A4 and CYP2D6, by okanin are mixed and non-competitive inhibition type, respectively. The IC50 values and the binding constant of okanin to CYP3A4 can be deduced that the interaction was stronger than that of CYP2D6. The Conformations of CYP3A4 and CYP2D6 were changed by okanin. The evidence from fluorescence measurement along with molecular docking verified that these two CYPs were bound with okanin by hydrogen bonds and hydrophobic forces. Our investigation suggested that okanin may lead to interactions between herb and drug by inhibiting CYP3A4 and CYP2D6 activities, thus its consumption should be taken with caution.
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Affiliation(s)
- Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, 130032, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, 130032, China
| | - Jingjing Cui
- The College of Chemistry, Changchun Normal University, Changchun, 130032, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, 130032, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, 130032, China.
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20
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Irwin R, Harkness RW, Forman-Kay JD. A FRET-Based Assay and Computational Tools to Quantify Enzymatic Rates and Explore the Mechanisms of RNA Deadenylases in Heterogeneous Environments. Methods Mol Biol 2024; 2723:69-91. [PMID: 37824065 DOI: 10.1007/978-1-0716-3481-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
We developed a medium-throughput assay that can measure the time-dependent distribution of RNA products generated as a deadenylase degrades a polyadenosine (poly(A)) RNA tract, thereby providing insight into the mechanism of deadenylation. Importantly, this assay can be performed in both homogeneous and heterogeneous environments without relying on gel electrophoresis of RNA products or coupled enzymatic reactions that indirectly report on the RNA distribution through the detection of freed adenosine monophosphate. In parallel, we have established an open-source, Python-based command-line software package, deadenylationkinetics, that can be used to numerically simulate and/or fit the datasets afforded by our assay with different deadenylation mechanisms to determine the most likely case and estimate the associated rate constants. In this chapter, we detail the implementation of our method and the quantification of poly(A) RNA binding and degradation kinetics in application to a truncated version of CNOT7 from the CCR4-NOT deadenylation complex, which serves as a model deadenylase with enhanced activity.
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Affiliation(s)
- Rose Irwin
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Robert W Harkness
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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21
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Fischer K, Wacht M. Fluorimetric microplate assay for the determination of extracellular alkaline phosphatase kinetics and inhibition kinetics in activated sludge. MethodsX 2023; 11:102255. [PMID: 37448954 PMCID: PMC10336153 DOI: 10.1016/j.mex.2023.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
The microbial enzyme alkaline phosphatase contributes to the removal of organic phosphorus compounds from wastewaters. To cope with regulatory threshold values for permitted maximum phosphor concentrations in treated wastewaters, a high activity of this enzyme in the biological treatment stage, e.g., the activated sludge process, is required. To investigate the reaction dynamics of this enzyme, to analyze substrate selectivities, and to identify potential inhibitors, the determination of enzyme kinetics is necessary. A method based on the application of the synthetic fluorogenic substrate 4-methylumbelliferyl phosphate is proven for soils, but not for activated sludges. Here, we adapt this procedure to the latter. The adapted method offers the additional benefit to determine inhibition kinetics. In contrast to conventional photometric assays, no particle removal, e.g., of sludge pellets, is required enabling the analysis of the whole sludge suspension as well as of specific sludge fractions. The high sensitivity of fluorescence detection allows the selection of a wide substrate concentration range for sound modeling of kinetic functions.•Fluorescence array technique for fast and sensitive analysis of high sample numbers•No need for particle separation - analysis of the whole (diluted) sludge suspension•Simultaneous determination of standard and inhibition kinetics.
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Rehman S, Yang YS, Patria RD, Zulfiqar T, Khanzada NK, Khan RJ, Lin CSK, Lee DJ, Leu SY. Substrate-related factors and kinetic studies of Carbohydrate-Rich food wastes on enzymatic saccharification. Bioresour Technol 2023; 390:129858. [PMID: 37863332 DOI: 10.1016/j.biortech.2023.129858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/08/2023] [Accepted: 10/08/2023] [Indexed: 10/22/2023]
Abstract
Food waste biorefinery is a sustainable approach to producing green chemicals, however the essential substrate-related factors hindering the efficacy of enzymatic hydrolysis have never been clarified. This study explored the key rate-limiting parameters and mechanisms of carbohydrate-rich food after different cooking and storing methods, i.e., impacts of compositions, structural diversities, and hornification. Shake-flask enzymatic kinetics determined the optimal dosages (0.5 wt% glucoamylase, 3 wt% cellulase) for food waste hydrolysis. First order kinetics and simulation results determined that reaction coefficient (K) of cooked starchy food was ∼ 3.63 h-1 (92 % amylum digestibility) within 2 h, while those for cooked cellulosic vegetables were 0.25-0.5 h-1 after 12 h of hydrolysis. Drying and frying reduced ∼ 71-89 % hydrolysis rates for rice, while hydrothermal pretreatment increased the hydrolysis rate by 82 % on vegetable wastes. This study provided insights into advanced control strategy and reduced the operational costs by optimized enzyme doses for food waste valorization.
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Affiliation(s)
- Shazia Rehman
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Yvette Shihui Yang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Raffel Dharma Patria
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Talha Zulfiqar
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Noman Khalid Khanzada
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Rabia Jalil Khan
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong; Research Institute for Smart Energy (RISE), The Hong Kong Polytechnic University, Hong Kong; Research Centre for Resources Engineering towards Carbon Neutrality (RCRE), The Hong Kong Polytechnic University, Hong Kong.
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23
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Alserae H, Deng S. Assay of cellulose 1,4-β-cellobiosidase activity in soil. J Microbiol Methods 2023; 215:106861. [PMID: 38030086 DOI: 10.1016/j.mimet.2023.106861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
As the most abundant biopolymer on earth, cellulose undergoes degradation by a diverse set of enzymes with varying specificities that act in synergism. An assay protocol was developed to detect and quantify activity of cellulose 1,4-β-cellobiosidase (EC 3.2.1.91) in soil. The optimum pH and temperature for β-cellobiosidase activity were approximately pH 5.5 and 60 °C, respectively. In the tested six soils, the Michaelis constants (Km) ranged from 0.08 to 0.51 mM, and maximum velocity (Vmax) ranged from 71.5 to 318.1 μmol kg soil-1 h-1. The temperature coefficient (Q10) ranged from 1.72 to 1.99 at non-denaturing temperatures from 10 to 50 °C, and the activation energy (Ea) ranged from 42.5 to 53.7 kJ mol-1. The assay procedure provided reproducible results with a coefficient of variance ≤4.7% and demonstrated a limit of quantification (LOQ) of 50.9 μmol p-nitrophenol release kg-1 soil h-1 for β-cellobiosidase activity in soil. Notably, the developed assay protocol offers reproducibility and precision comparable to bench-scale assays while reducing costs associated with reagents, supplies, and labor.
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Affiliation(s)
- Hussein Alserae
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA; Department of Soil Sciences and Water Recourses, University of Baghdad, Baghdad, Iraq
| | - Shiping Deng
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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24
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Deen MC, Gilormini PA, Vocadlo DJ. Strategies for quantifying the enzymatic activities of glycoside hydrolases within cells and in vivo. Curr Opin Chem Biol 2023; 77:102403. [PMID: 37856901 DOI: 10.1016/j.cbpa.2023.102403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023]
Abstract
Within their native milieu of the cell, the activities of enzymes are controlled by a range of factors including protein interactions and post-translational modifications. The involvement of these factors in fundamental cell biology and the etiology of diseases is stimulating interest in monitoring enzyme activities within tissues. The creation of synthetic substrates, and their use with different imaging modalities, to detect and quantify enzyme activities has great potential to propel these areas of research. Here we describe the latest developments relating to the creation of substrates for imaging and quantifying the activities of glycoside hydrolases, focusing on mammalian systems. The limitations of current tools and the difficulties within the field are summarised, as are prospects for overcoming these challenges.
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Affiliation(s)
- Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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25
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Syngkli S, Das B. Purification and characterization of human glycerol 3-phosphate dehydrogenases (mitochondrial and cytosolic) by NAD +/NADH redox method. Biochimie 2023; 214:199-215. [PMID: 37481063 DOI: 10.1016/j.biochi.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
Abstract
Glycerol 3-phosphate (G3P) shuttle is composed of mGPDH and cGPDH and serves as the interface between carbohydrate- and lipid-metabolism. Recently, these metabolic enzymes have been implicated in type II diabetes mellitus but the detailed kinetic parameters and crystal structure of human mGPDH is unknown, though fewer studies on cGPDH are available. To characterize these enzymes, the human mGPDH and cGPDH genes were optimized and cloned into the pET-SUMO vector and pET-24a(+) vector, respectively, and over-expressed in Escherichia coli BL21 (DE3). However, SUMO-mGPDH was expressed as inclusion bodies. Hence, various culture parameters, solubilizing agents and expression vectors were used to solubilize the protein but they did not produce functional SUMO-mGPDH. Over-expression of SUMO-mGPDH along with molecular chaperone (pG-KJE8) produced a functional SUMO-mGPDH. The functional SUMO-mGPDH was purified and characterized using NAD+/NADH redox method. cGPDH was also over-expressed and purified for its characterization. DLS analysis and CD spectra of the purified proteins were performed. The mGPDH was a monomeric enzyme with MW of ∼74 kDa and displayed optimal activity in the Tris-HCl buffer (pH 7.4); while, cGPDH was a homodimer with a monomeric MW of ∼37 kDa and showed optimal activity in imidazole buffer (pH 8.0). The Kmapp was 0.475 mM for G3P, and 0.734 mM for DHAP. These methods may be used to characterize these enzymes to understand their role in metabolic disorders.
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Affiliation(s)
- Superior Syngkli
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India
| | - Bidyadhar Das
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India.
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26
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Karakhim SO. Kinetics of the enzyme titration process by reversible modifiers. Biochimie 2023; 214:11-26. [PMID: 37279802 DOI: 10.1016/j.biochi.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/08/2023]
Abstract
The effect of reversible modifiers on the initial rate of enzyme catalysed reactions has been investigated in a quasi-equilibrium approximation using the general modifier mechanism of Botts and Morales. It has been shown that, when investigating the dependence of the initial rate on the modifier concentration at a fixed substrate concentration, the kinetics of enzyme titration by reversible modifiers can generally be described using two kinetic constants. Just as the dependence of the initial rate on the substrate concentration (at a fixed modifier concentration) is described using two kinetic constants: the Michaelis constant Km and the limiting rate Vm. Only one constant M50 is needed to describe the kinetics of linear inhibition, and in the case of nonlinear inhibition and activation, along with M50 the constant QM is also needed. Knowing the values of the constants M50 and QM, it is possible to unambiguously determine the modification efficiency, that is, to calculate how many times the initial rate of the enzyme catalysed reaction will change when a certain modifier concentration is added to the incubation medium. The properties of these fundamental constants have been analysed in detail and the dependence of these constants on other parameters of the Botts-Morales model have been shown. Equations describing the dependence of relative reaction rates on the modifier concentration using these kinetic constants are presented. Various ways of linearising these equations for calculating the kinetic constants M50 and QM from experimental data are also presented.
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Affiliation(s)
- S O Karakhim
- Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, 9 Leontovicha Street, Kyiv, 01054, Ukraine.
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27
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Fernandes SA, Dasgupta S, Tupe RS, Pathan EK. Structure-guided approach to modify the substrate specificity of the protein human deglycase-1 (hDJ-1). Biochem Biophys Res Commun 2023; 679:122-128. [PMID: 37688845 DOI: 10.1016/j.bbrc.2023.08.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/26/2023] [Indexed: 09/11/2023]
Abstract
Glycation is a non-enzymatic reaction wherein sugars or dicarbonyls such as methylglyoxal (MGO) and glyoxal (GO) react with proteins, leading to protein inactivation. The hydrolysing enzyme human deglycase-1 (hDJ-1) is reported to decrease glycative stress by deglycating the modified proteins, specifically at cysteine, lysine, and arginine sites. This specificity of hDJ-1 is thought to be regulated by its active site cysteine residue (Cys106). Structural analysis of hDJ-1 by molecular docking and simulation studies, however, indicates a possible role of glutamate (Glu18) in determining its substrate specificity. To elucidate this, Glu18 present at the catalytic site of hDJ-1 was modified to aspartate (Asp18) by SDM, and the resultant mutant was termed mutant DJ-1 (mDJ-1). Both hDJ-1 and mDJ-1 were heterologously expressed in Escherichia coli BL21 (DE3) strain and purified to homogeneity. The hDJ-1 showed kcat values of 1.45 × 103 s-1, 3.6 × 102 s-1, and 3.1 × 102 s-1, and Km values 0.181 mM, 18.18 mM, and 12.5 mM for N-acetylcysteine (NacCys), N-acetyllysine (NacLys), and N-acetylarginine (NacArg), respectively. The mDJ-1 showed altered kcat values (8 × 102 s-1, 3.8 × 102 s-1, 4.9 × 102 s-1) and Km values of 0.14 mM, 6.25 mM, 5.88 mM for NacCys, NacLys and NacArg, respectively. A single amino acid change (Glu18 to Asp18) improved the substrate specificity of mDJ-1 toward NacLys and NacArg. Understanding hDJ-1's structure and enhanced functionality will facilitate further exploration of its therapeutic potential for the treatment of glycation-induced diabetic complications.
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Affiliation(s)
- Sera A Fernandes
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, 412115, Maharashtra, India
| | - Subrata Dasgupta
- Department of Bioscience and Bioengineering, Indian Institute of Technology (IIT), Bombay, Powai, Mumbai, 400076, Maharashtra, India
| | - Rashmi S Tupe
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, 412115, Maharashtra, India.
| | - Ejaj K Pathan
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, 412115, Maharashtra, India.
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28
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Jangra A, Chaturvedi S, Sihag S, Sharma G, Tiwari S, Chhokar V. Identification and functional characterization of a novel aldo-keto reductase from Aloe vera. Planta 2023; 258:107. [PMID: 37897513 DOI: 10.1007/s00425-023-04256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
MAIN CONCLUSION The present investigation profoundly asserted the catalytic potential of plant-based aldo-ketoreductase, postulating its role in polyketide biosynthesis and providing new insights for tailored biosynthesis of vital plant polyketides for therapeutics. Plants hold great potential as a future source of innovative biocatalysts, expanding the possibilities within chemical reactions and generating a variety of benefits. The aldo-keto reductase (AKR) superfamily includes a huge collection of NAD(P)H-dependent oxidoreductases that carry out a variety of redox reactions essential for biosynthesis, detoxification, and intermediary metabolism. The present study involved the isolation, cloning, and purification of a novel aldo-ketoreductase (AvAKR) from the leaves of Aloe vera (Aloe barbadensis Miller) by heterologous gene expression in Escherichia coli based on the unigene sequences of putative ketoreductase and cDNA library screening by oligonucleotide hybridization. The in-silico structural analysis, phylogenetic relationship, and molecular modeling were outranged to approach the novelty of the sequence. Additionally, agroinfiltration of the candidate gene tagged with a green fluorescent protein (GFP) was employed for transient expression in the Nicotiana benthamiana to evaluate the sub-cellular localization of the candidate gene. The AvAKR preferred cytoplasmic localization and shared similarities with the known plant AKRs, keeping the majority of the conserved active-site residues in the AKR superfamily enzymes. The enzyme facilitated the NADPH-dependent reduction of various carbonyl substrates, including benzaldehyde and sugars, proclaiming a broad spectrum range. Our study successfully isolated and characterized a novel aldo-ketoreductase (AvAKR) from Aloe vera, highlighting its versatile NADPH-dependent carbonyl reduction proficiency therewith showcasing its potential as a versatile biocatalyst in diverse redox reactions.
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Affiliation(s)
- Alka Jangra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Siddhant Chaturvedi
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Goswami Tulsidas Government Post Graduate College (Bundelkhand University, Jhansi), Karwi, Chitrakoot, Uttar Pradesh, 210205, India
| | - Sonia Sihag
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Garima Sharma
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
| | - Vinod Chhokar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India.
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29
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Abhishek S, Deeksha W, Nethravathi KR, Davari MD, Rajakumara E. Allosteric crosstalk in modular proteins: Function fine-tuning and drug design. Comput Struct Biotechnol J 2023; 21:5003-5015. [PMID: 37867971 PMCID: PMC10589753 DOI: 10.1016/j.csbj.2023.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
Modular proteins are regulatory proteins that carry out more than one function. These proteins upregulate or downregulate a biochemical cascade to establish homeostasis in cells. To switch the function or alter the efficiency (based on cellular needs), these proteins require different facilitators that bind to a site different from the catalytic (active/orthosteric) site, aka 'allosteric site', and fine-tune their function. These facilitators (or effectors) are allosteric modulators. In this Review, we have discussed the allostery, characterized them based on their mechanisms, and discussed how allostery plays an important role in the activity modulation and function fine-tuning of proteins. Recently there is an emergence in the discovery of allosteric drugs. We have also emphasized the role, significance, and future of allostery in therapeutic applications.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | - Waghela Deeksha
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | | | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Eerappa Rajakumara
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
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30
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. Eur Biophys J 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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31
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Aktar MS, de Serrano V, Ghiladi R, Franzen S. Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B. J Inorg Biochem 2023; 247:112332. [PMID: 37480762 DOI: 10.1016/j.jinorgbio.2023.112332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
The dehaloperoxidase-hemoglobin (DHP), first isolated from the coelom of a marine terebellid polychaete, Amphitrite ornata, is an example of a multi-functional heme enzyme. Long known for its reversible oxygen (O2) binding, further studies have established DHP activity as a peroxidase, oxidase, oxygenase, and peroxygenase. The specific reactivity depends on substrate binding at various internal and external binding sites. This study focuses on comparison of the binding and reactivity of the substrate 2,4-dichlorophenol (DCP) in the isoforms DHPA and B. There is strong interest in the degradation of DCP because of its wide use in the chemical industry, presence in waste streams, and particular reactivity to form dioxins, some of the most toxic compounds known. The catalytic efficiency is 3.5 times higher for DCP oxidation in DHPB than DHPA by a peroxidase mechanism. However, DHPA and B both show self-inhibition even at modest concentrations of DCP. This phenomenon is analogous to the self-inhibition of 2,4,6-trichlorophenol (TCP) at higher concentration. The activation energies of the electron transfer steps in DCP in DHPA and DHPB are 19.3 ± 2.5 and 24.3 ± 3.2 kJ/mol, respectively, compared to 37.2 ± 6.5 kJ/mol in horseradish peroxidase (HRP), which may be a result of the more facile electron transfer of an internally bound substrate in DHPA. The x-ray crystal structure of DHPA bound with DCP determined at 1.48 Å resolution, shows tight substrate binding inside the heme pocket of DHPA (PDB 8EJN). This research contributes to the studies of DHP as a naturally occurring bioremediation enzyme capable of oxidizing a wide range of environmental pollutants.
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Affiliation(s)
- Mst Sharmin Aktar
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Reza Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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Paweł R, Aleksandra U, Elżbieta R. Enzymatic kinetics of photosystem II with DCBQ as a substrate in extended Michaelis-Menten model. J Photochem Photobiol B 2023; 247:112780. [PMID: 37678075 DOI: 10.1016/j.jphotobiol.2023.112780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
This study aimed to examine enzymatic kinetics of photosystem II (PSII) of maize mesophyll chloroplasts using the artificial electron acceptor 2,6-dichloro-1,4-benzoquinone (DCBQ) as a substrate. We extended Michealis-Menten kinetics model assuming that DCBQ can accept electrons from PSII in two ways: from a QB directly or from QA by docking in the QB site. We used a Clark oxygen electrode for measuring the PSII activity, depending on the concentration of DCBQ. We found that: [1] DCBQ acts as an electron acceptor or [2] as an inhibitor for PSII. At a concentration < 0.2 mM, DCBQ accepted electrons from the QB at a rate of 889 electrons/s, while at >> 0.2 mM it replaced QB following which the activity decreased to zero. DCBQ located in the QB also increased the affinity of the substrate to PSII. We determined the kinetic parameters for the chloroplasts of plants growing under high and low light intensity, to change thylakoid stacking and thus the rate of electron transport. The parameter KmB, which is a measure of the affinity of DCBQ to PSII, showed quantitative changes based on light intensity, while K was proportional to the size of the plastoquinone pool. We believe that our model can be applied as a tool to study "State transitions" and induced changes in grana stacking in plants exposed to various stresses, which will facilitate the regulation of electron transfer pathways through an appropriate balance between linear and cyclic electron transport.
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Affiliation(s)
- Rogowski Paweł
- Department of Molecular Plant Physiology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Urban Aleksandra
- Department of Molecular Plant Physiology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Romanowska Elżbieta
- Department of Molecular Plant Physiology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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33
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Dementiev A, Lillington SP, Jin S, Kim Y, Jedrzejczak R, Michalska K, Joachimiak A, O'Malley MA. Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis. Appl Microbiol Biotechnol 2023; 107:5999-6011. [PMID: 37548665 PMCID: PMC10485095 DOI: 10.1007/s00253-023-12684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelD's kinetics do not change with domain fusion, exhibiting high modularity.
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Affiliation(s)
- Alexey Dementiev
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Shiyan Jin
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Youngchang Kim
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Robert Jedrzejczak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Karolina Michalska
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA.
- Biological Engineering Program, University of California, Santa Barbara, CA, USA.
- Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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Guevara L, Gouge M, Ohler A, Hill SG, Patel S, Offenbacher AR. Effect of solvent viscosity on the activation barrier of hydrogen tunneling in the lipoxygenase reaction. Arch Biochem Biophys 2023; 747:109740. [PMID: 37678425 DOI: 10.1016/j.abb.2023.109740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Hydrogen tunneling in enzyme reactions has played an important role in linking protein thermal motions to the chemical steps of catalysis. Lipoxygenases (LOXs) have served as model systems for such reactions, showcasing deep hydrogen tunneling mechanisms associated with enzymatic C-H bond cleavage from polyunsaturated fatty acids. Here, we examined the effect of solvent viscosity on the protein thermal motions associated with LOX catalysis using trehalose and glucose as viscogens. Kinetic analysis of the reaction of the paradigm plant orthologue, soybean lipoxygenase (SLO), with linoleic acid revealed no effect on the first-order rate constants, kcat, or activation energy, Ea. Further studies of SLO active site mutants displaying varying Eas, which have been used to probe catalytically relevant motions, likewise provided no evidence for viscogen-dependent motions. Kinetic analyses were extended to a representative fungal LOX from M. oryzae, MoLOX, and a human LOX, 15-LOX-2. While MoLOX behaved similarly to SLO, we show that viscogens inhibit 15-LOX-2 activity. The latter implicates viscogen sensitive, conformational motions in animal LOX reactions. The data provide insight into the role of water hydration layers in facilitating hydrogen (quantum) tunneling in LOX.
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Affiliation(s)
- Luis Guevara
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Melissa Gouge
- Department of Chemistry and Biochemistry, Ohio Northern University, Ada, OH, 45810, USA
| | - Amanda Ohler
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - S Gage Hill
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Soham Patel
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA.
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Liang C, Zang J, Ndi C, Semple SJ, Buirchell B, Coriani S, Møller BL, Staerk D. Identification of new PTP1B-inhibiting decipiene diterpenoid esters from Eremophila clarkei by high-resolution PTP1B inhibition profiling, enzyme kinetics analysis, and molecular docking. Bioorg Chem 2023; 139:106744. [PMID: 37517158 DOI: 10.1016/j.bioorg.2023.106744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
In this study, an extract of the leaves of Eremophila clarkei Oldfield & F.Muell. showed protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with an IC50 value of 33.0 μg/mL. The extract was therefore investigated by high-resolution PTP1B inhibition profiling to pinpoint the constituents responsible for the activity. Subsequent isolation and purification using analytical-scale HPLC led to identification of eight previously undescribed decipiene diterpenoids, eremoclarkanes A-H, as well as eremoclarkic acid, a biogenetically related new phenolic acid. In addition, one known decipiene diterpenoid and ten known O-methylated flavonoids were isolated. The structures of the isolated compounds were elucidated by extensive analysis of their HRMS and 1D and 2D NMR spectra. The absolute configuration of decipiene diterpenoids was determined by comparison of experimental and calculated ECD spectra. The flavonoid hispidulin (2b) and the four decipiene diterpenoids 13a, 13b, 13f, and 14b exhibited PTP1B inhibitory activity with IC50 values ranging from 22.8 to 33.6 μM. This is the first report of PTP1B inhibitory activity of decipienes, and enzyme kinetics revealed that 13a and 13b are competitive inhibitors of PTP1B, whereas 13f and 14b displayed mixed-type-mode inhibition of PTP1B. Finally, molecular docking indicated that 13a, 13b, 13f, and 14b showed comparable binding affinity towards the active and/or allosteric site of PTP1B enzyme. Structure-activity relationship (SAR) of the identified O-methylated flavonoids and decipiene diterpenoids towards PTP1B is discussed. Plausible enzymatic and photochemically driven routes for the formation of the decipienes and conversion products thereof are presented and discussed.
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Affiliation(s)
- Chao Liang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jie Zang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Chi Ndi
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Frome Road, Adelaide 5000, Australia
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Frome Road, Adelaide 5000, Australia
| | - Bevan Buirchell
- Wise Owl Consulting, Como, Western Australia 6152, Australia
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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Kovermann M, Stefan A, Palazzetti C, Immler F, Dal Piaz F, Bernardi L, Cimone V, Bellone ML, Hochkoeppler A. The Mycobacterium tuberculosis protein tyrosine phosphatase MptpA features a pH dependent activity overlapping the bacterium sensitivity to acidic conditions. Biochimie 2023; 213:66-81. [PMID: 37201648 DOI: 10.1016/j.biochi.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023]
Abstract
The Mycobacterium tuberculosis low-molecular weight protein tyrosine phosphatase (MptpA) is responsible for the inhibition of phagosome-lysosome fusion and is essential for the bacterium pathogenicity. This inhibition implies that M. tuberculosis is not exposed to a strongly acidic environment in vivo, enabling successful propagation in host cells. Remarkably, MptpA has been previously structurally and functionally investigated, with special emphasis devoted to the enzyme properties at pH 8.0. Considering that the virulence of M. tuberculosis is strictly dependent on the avoidance of acidic conditions in vivo, we analysed the pH-dependence of the structural and catalytic properties of MptpA. Here we show that this enzyme undergoes pronounced conformational rearrangements when exposed to acidic pH conditions, inducing a severe decrease of the enzymatic catalytic efficiency at the expense of phosphotyrosine (pTyr). In particular, a mild decrease of pH from 6.5 to 6.0 triggers a significant increase of K0.5 of MptpA for phosphotyrosine, the phosphate group of which we determined to feature a pKa2 equal to 5.7. Surface plasmon resonance experiments confirmed that MptpA binds poorly to pTyr at pH values < 6.5. Notably, the effectiveness of the MptpA competitive inhibitor L335-M34 at pH 6 does largely outperform the inhibition exerted at neutral or alkaline pH values. Overall, our observations indicate a pronounced sensitivity of MptpA to acidic pH conditions, and suggest the search for competitive inhibitors bearing a negatively charged group featuring pKa values lower than that of the substrate phosphate group.
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Affiliation(s)
- Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätstraße 10, 78464, Konstanz, Germany
| | - Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy
| | - Chiara Palazzetti
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Fabian Immler
- Department of Chemistry, University of Konstanz, Universitätstraße 10, 78464, Konstanz, Germany
| | - Fabrizio Dal Piaz
- Department of Medicine, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Luca Bernardi
- Department of Industrial Chemistry "Toson Montanaro", University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Valentina Cimone
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Maria Laura Bellone
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy.
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Poonkuzhali K, Seenivasagan R, Prabhakaran J, Karthika A. Synthesis and characterization of chemical engineered PLGA nanosphere: Triggering mechanism of Catechol-O-methyltransferase inhibition on in vivo neurodegeneration. Bioorg Chem 2023; 139:106673. [PMID: 37354660 DOI: 10.1016/j.bioorg.2023.106673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
Chemically engineered PLGA nanospheres are one of the emerging technologies for treating neurodegenerative disorders by inhibiting Catechol-O-methyltransferase (COMT). PLGA-MATPM nanospheres were chemically synthesized using PLGA and MATPM (N-allyl-N-(3-(m-tolyloxy)propyl) methioninate). The tailored PLGA nanospheres induce dose-dependent COMT inhibition in competitive kinetic mode. The interactions between COMT and PLGA nanosphere are explained by spectroscopic and molecular dynamics analysis. PLGA-MATPM NPs suppressed the growth of neuroblastoma cells due to the neurodegenerative toxicity of MPTP induction, demonstrating its potency as a cure for neurological disorders. PLGA-MATPM NPs cross the blood-brain barrier more effectively than those in the blood. Furthermore, PLGA nanospheres showed the most neurodegenerative recovery against MPTP-induced C57BL/6 mice. Using magnetic resonance imaging (MRI), it was validated for quality images of cerebral blood flow (CBF).
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Affiliation(s)
- K Poonkuzhali
- Bioprocess and Microbial Laboratory, Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry - 605 014, India.
| | - R Seenivasagan
- Department of Biotechnology, Arulmigu Kalasalingam College of Arts and Science, Krishnankoil - 626126, Tamil Nadu, India
| | - J Prabhakaran
- Organic Synthesis Laboratory, Department of Chemistry, School of Physical, Chemical and Applied Sciences, Pondicherry University, Pondicherry - 605 014, India
| | - A Karthika
- Department of Microbiology, The Standard Fireworks Rajaratnam College for Women, Sivakasi - 626123, Tamil Nadu, India
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38
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Sands D, Davis A, Banfield S, Pottie IR, Darvesh S. Solvents and detergents compatible with enzyme kinetic studies of cholinesterases. Chem Biol Interact 2023; 383:110667. [PMID: 37579937 DOI: 10.1016/j.cbi.2023.110667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are enzymes that serve a wide range of physiological functions including the hydrolysis of the neurotransmitter acetylcholine and several other xenobiotics. The development of inhibitors for these enzymes has been the focus for the treatment of several conditions, such as Alzheimer's disease. Novel chemical entities are evaluated as potential inhibitors of AChE and BChE using enzyme kinetics. A common issue encountered in these studies is low aqueous solubility of the possible inhibitor. Additives such as cosolvents or detergents can be included in these studies improve the aqueous solubility. Typical cosolvents include acetonitrile or dimethyl sulfoxide while typical detergents include Polysorbate 20 (Tween 20) or 3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate (CHAPS). When solubility is not improved, these molecules are often not evaluated further. To address this issue eleven cosolvents and six detergents that could facilitate aqueous solubility were evaluated to understand how they would affect cholinesterase enzymes using Ellman's assay. These studies show that propylene glycol, acetonitrile, methanol, Tween 20, Polysorbate 80 (Tween 80), polyoxyethylene 23 lauryl ether (Brij 35) and polyoxyethylene 10 oleoyl ether (Brij 96v) have the least inhibitory effects towards cholinesterase activity. It is concluded that these cosolvents and detergents should be considered as solubilizing agents for evaluation of potential cholinesterase inhibitors with low aqueous solubility.
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Affiliation(s)
- Dane Sands
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew Davis
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Scott Banfield
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian R Pottie
- Department of Chemistry and Physics, Mount St. Vincent University, Halifax, Nova Scotia, Canada; Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Sultan Darvesh
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Chemistry and Physics, Mount St. Vincent University, Halifax, Nova Scotia, Canada; Department of Medicine (Geriatric Medicine & Neurology), Halifax, Nova Scotia, Canada.
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39
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Joompang A, Anwised P, Klaynongsruang S, Taemaitree L, Wanthong A, Choowongkomon K, Daduang S, Katekaew S, Jangpromma N. Rational design of an N-terminal cysteine-containing tetrapeptide that inhibits tyrosinase and evaluation of its mechanism of action. Curr Res Food Sci 2023; 7:100598. [PMID: 37790858 PMCID: PMC10543783 DOI: 10.1016/j.crfs.2023.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/05/2023] Open
Abstract
There has been a resurgence of interest in bioactive peptides as therapeutic agents. This is particularly interesting for tyrosinase, which can be inhibited by thiol-containing peptides. This work demonstrates that an N-terminal cysteine-containing tetrapeptide can be rationally designed to inhibit tyrosinase activity in vitro and in cells. The tetrapeptide cysteine (C), arginine (R), asparagine (N) and leucine (L) or CRNL is a potent inhibitor of tyrosinase activity with an IC50 value of 39.62 ± 6.21 μM, which is comparable to currently used tyrosinase inhibitors. Through structure-activity studies and computational modeling, we demonstrate the peptide interacts with the enzyme via electrostatic (R with E322), hydrogen bonding (N with N260) and hydrophobic (L with V248) intermolecular interactions and that a combination of these is required for potent activity. Moreover, copper chelating activity might be one of the mechanisms of tyrosinase inhibition by CRNL. Kinetic studies show that tetrapeptide is a competitive inhibitor with two-step irreversible inhibition. In addition, CRNL had no toxicity and could reduce melanin levels in the murine melanoma cell line (B16F1). Overall, CRNL is a very promising candidate for hyperpigmentation treatment.
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Affiliation(s)
- Anupong Joompang
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Preeyanan Anwised
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sompong Klaynongsruang
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lapatrada Taemaitree
- Department of Integrated Science, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Anuwat Wanthong
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sakda Daduang
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Somporn Katekaew
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nisachon Jangpromma
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
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40
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Plapp BV, Kratzer DA, Souhrada SK, Warth E, Jacobi T. Specific base catalysis by yeast alcohol dehydrogenase I with substitutions of histidine-48 by glutamate or serine residues in the proton relay system. Chem Biol Interact 2023; 382:110558. [PMID: 37247811 PMCID: PMC10527620 DOI: 10.1016/j.cbi.2023.110558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
His-48 in yeast alcohol dehydrogenase I (His 51 in horse liver alcohol dehydrogenase) is a highly conserved residue in the active sites of many alcohol dehydrogenases. The imidazole group of His-48 may participate in base catalysis of proton transfer as it is linked by hydrogen bonds through the 2'-hydroxyl group of the nicotinamide ribose and the hydroxyl group of Thr-45 to the hydroxyl group of the alcohol bound to the catalytic zinc. In this study, His-48 was substituted with a glutamic acid residue to determine if a carboxylate could replace imidazole or to a serine residue to determine if the exposure of the 2'-hydroxyl group of the ribose to solvent would allow proton transfer to water without base catalysis. At pH 7.3, the H48E substitution increases affinity for NAD+ and NADH 17- or 2.6-fold, but decreases catalytic efficiency (V/Km) on ethanol by 70-fold and on acetaldehyde by 6-fold relative to wild-type enzyme. The H48S substitution increases affinity for coenzymes by 2-fold and decreases (V/Km) on ethanol and acetaldehyde only by ∼3-fold. The substituted enzymes show substrate deuterium isotope (H/D) effects of 3-4 for turnover number (V1) and catalytic efficiency (V1/Kb) for ethanol oxidation, indicating that hydrogen transfer is partially rate-limiting and suggesting a somewhat more random mechanism for binding of ethanol and NAD+. For reduction of acetaldehyde, the deuterium isotope effects are small, and the kinetic mechanism appears to be ordered for binding of NADH first and acetaldehyde next. The pH dependencies for H48E and H48S ADHs can be described by a mechanism with pK values of about 6-7 and 9. However, the pH dependencies for oxidation of ethanol and butanol by the H48S enzyme are also simply described by a straight line, with slopes of log V1/Kb against pH of 0.37 or 0.43, respectively. The linear dependence apparently represents catalysis by hydroxide that has a low activity coefficient due to the protein environment, or to a kinetically complex proton transfer. The effects of the substitutions of His-48 show that this residue contributes to catalysis, although many dehydrogenases also have other residues.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Darla Ann Kratzer
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Susan K Souhrada
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Edda Warth
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Tobias Jacobi
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA, 52242, USA.
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Bursch KL, Olp MD, Smith BC. Analysis of continuous enzyme kinetic data using ICEKAT. Methods Enzymol 2023; 690:109-129. [PMID: 37858527 PMCID: PMC10691744 DOI: 10.1016/bs.mie.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
ICEKAT (Interactive Continuous Enzyme Analysis Tool) is an interactive web-based program for calculating initial rates and kinetic parameters (e.g., Vmax, kcat, KM, EC50, IC50) from continuous enzyme kinetic assay data that satisfy Michaelis-Menten and steady-state kinetic assumptions. ICEKAT is valuable in educational and research settings to consistently and accurately calculate initial rates and kinetic parameters, increasing assay veracity and reproducibility. Provided freely online to the scientific community, ICEKAT has been cited in at least 26 publications, and the initial journal article has been accessed nearly 9000 times since its debut in 2020 (Olp et al., 2020). Here, we provide in-depth instructions for software use, offer vital considerations for data analysis, and highlight updated software features for new and existing users. Through ICEKAT, we aim for the analysis of data from continuous enzyme kinetic studies worldwide to become more rapid, reliable, and repeatable. ICEKAT remains free of charge and available to all scientists at https://icekat.herokuapp.com/icekat; the source code for local use is found at https://github.com/SmithLabMCW/icekat.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Michael D Olp
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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Li N, Wang Z, Tian H, Megharaj M, He W. Ecotoxicity of soil Pb pollution reflected by soil β-glucosidase: Comparison of extracellular and intracellular enzyme pool. Sci Total Environ 2023; 882:163364. [PMID: 37031929 DOI: 10.1016/j.scitotenv.2023.163364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/01/2023]
Abstract
Lead (Pb) is a major environmental pollutant that threatens the soil environment and human health. Monitoring and assessing Pb toxicity on soil health are of paramount importance to the public. To use soil enzymes as biological indicators of Pb contamination, herein, the responses of soil β-glucosidase (BG) in different pools of soil (total, intracellular and extracellular enzyme) to Pb contamination were investigated. The results indicated that the intra-BG (intracellular BG) and extra-BG (extracellular BG) responded differently to Pb contamination. While the addition of Pb caused a significant inhibition of the intra-BG activities, the extra-BG activities were only slightly inhibited. Pb showed a non-competitive inhibition to extra-BG, while both non-competitive and uncompetitive inhibition were observed for intra-BG in the tested soils. The dose-response modeling was used to calculate ecological dose ED10, which represents the concentration of Pb pollutant that causes a 10 % reduction in Vmax, to express the ecological consequences of Pb contamination. A positive correlation was found between ecological dose ED10 values of intra-BG and soil total nitrogen (p < 0.05), which suggests soil properties may influence Pb toxicity to soil BG. Based on the differences in ED10 and inhibition rate among different enzyme pools, this study suggests that the intra-BG is more sensitive for Pb contamination assessment. From this, we propose that intra-BG should be considered when evaluating Pb contamination using soil enzymes as indicators.
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Affiliation(s)
- Ni Li
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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Adak S, Agarwal T, Das P, Ray S, Lahiri Majumder A. Characterization of myo-inositol oxygenase from rice ( OsMIOX): influence of salinity stress in different indica rice cultivars. Physiol Mol Biol Plants 2023; 29:927-945. [PMID: 37649879 PMCID: PMC10462604 DOI: 10.1007/s12298-023-01340-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Myo-inositol oxygenase (MIOX), the only catabolic enzyme of the inositol pathway, catalyzes conversion of myo-inositol to D-GlcA (glucuronic acid). The present study encompasses bioinformatic analysis of MIOX gene across phylogenetically related plant lineages and representative animal groups. Comparative motif analysis of the MIOX gene(s) across various plant groups suggested existence of abiotic- stress related cis-acting elements such as, DRE, MYB, MYC, STRE, MeJa among others. A detailed analysis revealed a single isoform of MIOX gene, located in chromosome 6 of indica rice (Oryza sativa) with an open reading frame of 938 bp coding for 308 amino acids producing a protein of ~ 35 kD. Secondary structure prediction of the protein gave the predicted number of 144 alpha helices and 154 random coils. The three-dimensional structure suggested it to be a monomeric protein with a single domain. Bacterial overexpression of the protein, purification and enzyme assay showed optimal catalytic activity at pH 7.5-8 at an optimal temperature of 37 °C with Michaelis constant of 40.92 mM. The range of Km was determined as 22.74-28.7 mM and the range of Vmax was calculated as 3.51-3.6 µM/min, respectively. Four salt-tolerant and salt-sensitive rice cultivars displayed differential gene expression of OsMIOX at different time points in different tissues under salinity and drought stress as observed from qRT-PCR data, microarray results and protein expression profile in immunoblot analysis. Gel volumetric analysis confirmed a very high expression of MIOX in roots and leaves on 7th day following germination. Microarray data showed high expression of MIOX at all developmental stages including seedling growth and reproduction. These data suggest that OsMIOX might have a role to play in rice abiotic stress responses mediated through the myo-inositol oxidation pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01340-6.
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Affiliation(s)
- Sanghamitra Adak
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
| | - Tanushree Agarwal
- Centre of Advanced Study, Department of Botany, Ballygunge Science College, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Priyanka Das
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
| | - Sudipta Ray
- Centre of Advanced Study, Department of Botany, Ballygunge Science College, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, Kolkata, 700054 India
- Present Address: Department of Microbiology and Biotechnology, Sister Nivedita University, DG 1/2, Action Area I, New Town, Kolkata, 700156 India
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Bayrakçeken Güven Z, Saracoglu I, Nagatsu A, Yilmaz MA, Basaran AA. Anti-tyrosinase and antimelanogenic effect of cinnamic acid derivatives from Prunus mahaleb L.: Phenolic composition, isolation, identification and inhibitory activity. J Ethnopharmacol 2023; 310:116378. [PMID: 36924865 DOI: 10.1016/j.jep.2023.116378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The traditional use of Prunus species against skin diseases and especially for skin lightning cosmeceutical purposes is widespread in many cultures. Prunus mahaleb L. is a well known food plant and used in the baking industry for flavoring. The fruit kernels (endocarp) are used in India for hyperpigmentation. AIM OF THE STUDY To investigate the chemical composition with the antimelanogenesis effect of P. mahaleb seed and kernel extracts and isolated compounds. MATERIALS AND METHODS Isolation studies performed from the methanol extracts obtained from kernels and structures were determined using NMR and MS analysis. Antimelanogenesis effect was determined by mushroom tyrosinase assay, cellular tyrosinase assay and melanin content assay using B16F10 murine melanoma cells. RESULTS Five cinnamic acid derivatives were isolated and their structures (2-O-β-glucopyranosyloxy-4-methoxy-hydrocinnamic acid (1), cis-melilotoside (2), dihydromelilotoside (3), trans-melilotoside (4), 2-O-β-glucosyloxy-4-methoxy trans-cinnamic acid (5)) were elucidated using advanced spectroscopic methods. Mushroom tyrosinase enzyme inhibition of extracts, fractions and pure compounds obtained from P. mahaleb kernels were investigated and structure-activity relationship revealed. According to a detailed, comprehensive and validated LC-MS/MS technique analysis, vanilic acid (41.407 mg/g), protocatechuic acid (8.992 mg/g) and ferulic acid (4.962 mg/g) in the kernel ethylacetate fraction; quinic acid (14.183 mg/g), fumaric acid (8.349 mg/g) and aconitic acid (5.574 mg/g) were found as major phenolic compounds in the water fraction. The correlation of trace element copper content in extracts and fractions with mushroom enzyme activity was determined. By examining the enzyme kinetics of the compounds with effective cinnamic acid derivatives, inhibition types and enzyme binding constants Ki were calculated. Compounds 1,3 and 5 exhibited high noncompetitive tyrosinase inhibitory activity against L-tyrosine substrates, with IC50 values of 0.22, 0.31 and 0.37 mM respectively. In addition compounds 1, 3 and 5 showed dose-dependent inhibitory effects on intracellular tyrosinase and melanin levels in α-melanocyte-stimulating hormone (α-MSH)-induced B16F10 melanoma cells. CONCLUSIONS Potent tyrosinase inhibitory compounds and extracts of P. mahaleb kernels suggest that it could be a new, non-toxic and inexpensive resource for the cosmeceutical industry and in skin diseases associated with hyperpigmentation.
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Affiliation(s)
- Zühal Bayrakçeken Güven
- Hacettepe University, Faculty of Pharmacy, Department of Pharmacognosy, Ankara, Turkey; Erzincan Binali Yıldırım University, Faculty of Pharmacy, Department of Pharmacognosy, Erzincan, Turkey.
| | - Iclal Saracoglu
- Hacettepe University, Faculty of Pharmacy, Department of Pharmacognosy, Ankara, Turkey
| | - Akito Nagatsu
- Kinjo Gakuin University, College of Pharmacy, Department of Pharmacognosy, Nagoya, Japan
| | - Mustafa Abdullah Yilmaz
- Dicle University, Faculty of Pharmacy, Department of Analytical Chemistry, Diyarbakir, Turkey
| | - A Ahmet Basaran
- Baskent University, Faculty of Pharmacy, Department of Pharmacognosy, Ankara, Turkey
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Lukaszewicz M, Mrozek AF, Bojarska E, Stelmach J, Stepinski J, Darzynkiewicz E. Contribution of Nudt12 enzyme to differentially methylated dinucleotides of 5'RNA cap structure. Biochim Biophys Acta Gen Subj 2023:130400. [PMID: 37301333 DOI: 10.1016/j.bbagen.2023.130400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Recent findings have substantially broadened our knowledge about the diversity of modifications of the 5'end of RNAs, an issue generally attributed to mRNA cap structure (m7GpppN). Nudt12 is one of the recently described new enzymatic activities involved in cap metabolism. However, in contrast to its roles in metabolite-cap turnover (e.g., NAD-cap) and NADH/NAD metabolite hydrolysis, little is known regarding its hydrolytic activity towards dinucleotide cap structures. In order to gain further insight into this Nudt12 activity, comprehensive analysis with a spectrum of cap-like dinucleotides was performed with respect to different nucleotide types adjacent to the (m7)G moiety and its methylation status. Among the tested compounds, GpppA, GpppAm, and Gpppm6Am were identified as novel potent Nudt12 substrates, with KM values in the same range as that of NADH. Interestingly, substrate inhibition of Nudt12 catalytic activity was detected in the case of the GpppG dinucleotide, a phenomenon not reported to date. Finally, comparison of Nudt12 with DcpS and Nud16, two other enzymes with known activity on dinucleotide cap structures, revealed their overlapping and more specific substrates. Altogether, these findings provide a basis for clarifying the role of Nudt12 in cap-like dinucleotide turnover.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Aleksandra-Ferenc Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Stelmach
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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Kloska SM, Pałczyński K, Marciniak T, Talaśka T, Miller M, Wysocki BJ, Davis P, Wysocki TA. Conversion of fat to cellular fuel-Fatty acids β-oxidation model. Comput Biol Chem 2023; 104:107860. [PMID: 37028176 DOI: 10.1016/j.compbiolchem.2023.107860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
β-oxidation of fatty acids plays a significant role in the energy metabolism of the cell. This paper presents a β-oxidation model of fatty acids based on queueing theory. It uses Michaelis-Menten enzyme kinetics, and literature data on metabolites' concentration and enzymatic constants. A genetic algorithm was used to optimize the parameters for the pathway reactions. The model enables real-time tracking of changes in the concentrations of metabolites with different carbon chain lengths. Another application of the presented model is to predict the changes caused by system disturbance, such as altered enzyme activity or abnormal fatty acid concentration. The model has been validated against experimental data. There are diseases that change the metabolism of fatty acids and the presented model can be used to understand the cause of these changes, analyze metabolites abnormalities, and determine the initial target of treatment.
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Affiliation(s)
- Sylwester M Kloska
- Department of Forensic Medicine, Nicolaus Copernicus University Ludwik Rydygier Collegium Medicum, Bydgoszcz, Poland.
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Tomasz Talaśka
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Marissa Miller
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, USA
| | - Beata J Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, USA
| | - Paul Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, USA
| | - Tadeusz A Wysocki
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland; Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, USA
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Smith ET, Kruppa M, Johnson DA, Van Haeften J, Chen X, Leahy D, Peake J, Harris JM. High yield expression in Pichia pastoris of human neutrophil elastase fused to cytochrome B5. Protein Expr Purif 2023; 206:106255. [PMID: 36822453 PMCID: PMC10118287 DOI: 10.1016/j.pep.2023.106255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Recombinant human neutrophil elastase (rHNE), a serine protease, was expressed in Pichia pastoris. Glycosylation sites were removed via bioengineering to prevent hyper-glycosylation (a common problem with this system) and the cDNA was codon optimized for translation in Pichia pastoris. The zymogen form of rHNE was secreted as a fusion protein with an N-terminal six histidine tag followed by the heme binding domain of Cytochrome B5 (CytB5) linked to the N-terminus of the rHNE sequence via an enteropeptidase cleavage site. The CytB5 fusion balanced the very basic rHNE (pI = 9.89) to give a colored fusion protein (pI = 6.87), purified via IMAC. Active rHNE was obtained via enteropeptidase cleavage, and purified via cation exchange chromatography, resulting in a single protein band on SDS PAGE (Mr = 25 KDa). Peptide mass fingerprinting analysis confirmed the rHNE amino acid sequence, the absence of glycosylation and the absence of an 8 amino acid C-terminal peptide as opposed to the 20 amino acids usually missing from the C-terminus of native enzyme. The yield of active rHNE was 0.41 mg/L of baffled shaker flask culture medium. Active site titration with alpha-1 antitrypsin, a potent irreversible elastase inhibitor, quantified the concentration of purified active enzyme. The Km of rHNE with methoxy-succinyl-AAPVpNA was identical with that of the native enzyme within the assay's limit of accuracy. This is the first report of full-length rHNE expression at high yields and low cost facilitating further studies on this major human neutrophil enzyme.
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Affiliation(s)
- Eliot T Smith
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA
| | - Michael Kruppa
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA
| | - David A Johnson
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA.
| | - Jessica Van Haeften
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Xingchen Chen
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Darren Leahy
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Jonathan Peake
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Jonathan M Harris
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
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Li Y, Wang Z, Tian H, Megharaj M, Jia H, He W. Using soil enzyme V max as an indicator to evaluate the ecotoxicity of lower-ring polycyclic aromatic hydrocarbons in soil: Evidence from fluorescein diacetate hydrolase kinetics. Sci Total Environ 2023; 874:162521. [PMID: 36868272 DOI: 10.1016/j.scitotenv.2023.162521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Fluorescein diacetate hydrolase (FDA hydrolase) is a reliable biochemical biomarker of changes in soil microbial activity and quality. However, the effect and mechanism of lower-ring polycyclic aromatic hydrocarbons (PAHs) on soil FDA hydrolase are still unclear. In this work, we investigated the effects of two typical lower-ring PAHs, naphthalene (Nap) and anthracene (Ant), on the activity and kinetic characteristics of FDA hydrolases in six soils differing in their properties. Results demonstrated that the two PAHs severely inhibited the activities of the FDA hydrolase. The values of Vmax and Km dropped by 28.72-81.24 % and 35.84-74.47 % at the highest dose of Nap, respectively, indicating an uncompetitive inhibitory mechanism. Under Ant stress, the values of Vmax decreased by 38.25-84.99 %, and the Km exhibited two forms, unchanged and decreased (74.00-91.61 %), indicating uncompetitive and noncompetitive inhibition. The inhibition constant (Ki) of the Nap and Ant ranged from 0.192 to 1.051 and 0.018 to 0.087 mM, respectively. The lower Ki of Ant compared to Nap indicated a higher affinity for enzyme-substrate complex, resulting in higher toxicity of Ant than Nap to soil FDA hydrolase. The inhibitory effect of Nap and Ant on soil FDA hydrolase was mainly affected by soil organic matter (SOM). SOM influenced the affinity of PAHs with enzyme-substrate complex, which resulted in a difference in PAHs toxicity to soil FDA hydrolase. The enzyme kinetic Vmax was a more sensitive indicator than enzyme activity to evaluate the ecological risk of PAHs. This research offers a strong theoretical foundation for quality control and risk evaluation of PAH-contaminated soils through a soil enzyme-based approach.
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Affiliation(s)
- Yan Li
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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49
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McGuinness AN, Tahir A, Sutton NR, Marquis AD. Identifiability of enzyme kinetic parameters in substrate competition: a case study of CD39/NTPDase1. Purinergic Signal 2023:10.1007/s11302-023-09942-1. [PMID: 37165287 DOI: 10.1007/s11302-023-09942-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/07/2023] [Indexed: 05/12/2023] Open
Abstract
CD39 (NTPDase1-nucleoside triphosphate diphosphohydrolase 1) is a membrane-tethered ectonucleotidase that hydrolyzes extracellular ATP to ADP and ADP to AMP. This enzyme is expressed in a variety of cell types and tissues and has broadly been recognized within vascular tissue to have a protective role in converting "danger" ligands (ATP) into neutral ligands (AMP). In this study, we investigate the enzyme kinetics of CD39 using a Michaelis-Menten modeling framework. We show how the unique situation of having a reaction product also serving as a substrate (ADP) complicates the determination of the governing kinetic parameters. Model simulations using values for the kinetic parameters reported in the literature do not align with corresponding time-series data. This dissonance is explained by CD39 kinetic parameters previously being determined by graphical/linearization methods, which have been shown to distort the underlying error structure and lead to inaccurate parameter estimates. Modern methods of estimating these kinetic parameters using nonlinear least squares are still challenging due to unidentifiable parameter interactions. We propose a workflow to accurately determine these parameters by isolating the ADPase and ATPase reactions and estimating the respective ADPase parameters and ATPase parameters with independent data sets. Theoretically, this ensures all kinetic parameters are identifiable and reliable for future prospective model simulations involving CD39. These kinds of mathematical models can be used to understand how circulating purinergic nucleotides affect disease etiology and potentially inform the development of corresponding therapies.
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Affiliation(s)
- Anna N McGuinness
- Division of Cardiovascular Medicine, Department of Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Aman Tahir
- Division of Cardiovascular Medicine, Department of Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Nadia R Sutton
- Division of Cardiovascular Medicine, Department of Medicine, Michigan Medicine, Ann Arbor, MI, USA
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Andrew D Marquis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
- Applied BioMath®, MA, Concord, USA.
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50
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Teixeira O, Martins IBS, Froes TQ, de Araújo AS, Nonato MC. Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition. Biochim Biophys Acta Gen Subj 2023; 1867:130378. [PMID: 37150227 DOI: 10.1016/j.bbagen.2023.130378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Tuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.
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Affiliation(s)
- Olívia Teixeira
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Ingrid Bernardes Santana Martins
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Thamires Quadros Froes
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Alexandre Suman de Araújo
- Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil.
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