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de Magalhães MTQ, de Araújo TS, Silva BM, Icart LP, Scapin SMN, da Silva Almeida M, Lima LMTR. Mutations in asparaginase II from E. coli and implications for inactivation and PEGylation. Biophys Chem 2023; 299:107041. [PMID: 37257341 DOI: 10.1016/j.bpc.2023.107041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
All clinically-used asparaginases convert L-asparagine (L-Asn) to l-aspartate (L-Asp) and l-glutamine (L-Gln) to L-glutamate (L-Glu), which has been useful in reducing bioavailable asparagine and glutamine in patients under treatment for acute lymphoblastic leukemia. The E. coli type 2 L-asparaginase (EcA2) can present different sequences among varying bacterial strains, which we hypothesized that might affect their biological function, stability and interchangeability. Here we report the analysis of two EcA2 provided by the public health system of a middle-income country. These enzymes were reported to have similar specific activity in vitro, whereas they differ in vivo. Protein sequencing by LC-MS-MS and peptide mapping by MALDI-ToF-MS of their tryptic digests revealed that Aginasa™ share similar sequence to EcA2 from E. coli strain BL21(DE3), while Leuginase™ has sequence equivalent to EcA2 from E. coli strain AS1.357. The two amino acid differences between Aginasa™ (64D and 252 T) and Leuginase™ (64 N and 252S) resulted in structural divergences in solution as accessed by small-angle X-ray scattering and molecular dynamics simulation trajectories. The conformational variability further results in dissimilar surface accessibility with major consequences for PEGylation, as well as different susceptibility to degradation by limited proteolysis. The present results reveal that the sequence variations between these two EcA2 variants results in conformational changes associated with differential conformational plasticity, potentially affecting physico-chemical and biological properties, including proteolytic and immunogenic silent inactivation.
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Affiliation(s)
- Mariana T Q de Magalhães
- Laboratório de Biofísica de Macromoléculas - LBM, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biomédicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Talita Stelling de Araújo
- Protein Advanced Biochemistry - PAB, Centro Nacional de Biologia Estrutural e Bioimagem - CENABIO, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Bioquímica Médica Leopoldo De Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Bruno Marques Silva
- Laboratório de Biofísica de Macromoléculas - LBM, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biomédicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Luis Peña Icart
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Sandra M N Scapin
- Laboratório de Macromoléculas e Bioquímica (LAMAC), Coordenação-Geral de Metrologia em Biologia (COBIO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ 25250-020, Brazil.
| | - Marcius da Silva Almeida
- Protein Advanced Biochemistry - PAB, Centro Nacional de Biologia Estrutural e Bioimagem - CENABIO, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Luís Maurício T R Lima
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Laboratório de Macromoléculas e Bioquímica (LAMAC), Coordenação-Geral de Metrologia em Biologia (COBIO), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ 25250-020, Brazil; Programa de Pós-Graduação em Quimica Biologica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
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2
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Nag R, Joshi S, Rathore AS, Majumder S. Profiling Enzyme Activity of l-Asparaginase II by NMR-Based Methyl Fingerprinting at Natural Abundance. J Am Chem Soc 2023; 145:10826-10838. [PMID: 37154467 DOI: 10.1021/jacs.3c02154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
l-asparaginase II (MW 135 kDa) from E. coli is an FDA-approved protein drug used for the treatment of childhood leukemia. Despite its long history as a chemotherapeutic, the structural basis of enzyme action, in solution, remains widely contested. In this work, methyl-based 2D [1H-13C]-heteronuclear single-quantum correlation (HSQC) NMR, at natural abundance, has been used to profile the enzymatic activity of the commercially available enzyme drug. The [1H-13C]-HSQC NMR spectra of the protein reveal the role of a flexible loop segment in the activity of the enzyme, in solution. Addition of asparagine to the protein results in distinct conformational changes of the loop that could be signatures of intermediates formed in the catalytic reaction. To this end, an isothermal titration calorimetry (ITC)-based assay has been developed to measure the enzymatic reaction enthalpy, as a marker for its activity. Combining both ITC and NMR, it was shown that the disruption of the protein conformation can result in the loss of function. The scope, robustness, and validity of the loop fingerprints in relation to enzyme activity have been tested under different solution conditions. Overall, our results indicate that 2D NMR can be used reliably to gauge the structure-function of this enzyme, bypassing the need to label the protein. Such natural abundant NMR methods can be potentially extended to probe the structure-function aspects of high-molecular-weight protein therapeutics (glycosylated protein drugs, enzymes, therapeutic monoclonal antibodies, antibody-drug conjugates, and Fc-fusion proteins), where (a) flexible loops are required for their function and (b) isotope labeling may not be straightforward.
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Affiliation(s)
- Rachayita Nag
- Biophysics & Structural Genomics, Saha Institute of Nuclear Physics, Kolkata 700064, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Srishti Joshi
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Anurag Singh Rathore
- Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Subhabrata Majumder
- Biophysics & Structural Genomics, Saha Institute of Nuclear Physics, Kolkata 700064, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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3
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Comparative structural and kinetic study for development of a novel candidate L-asparaginase based pharmaceutical. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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4
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Sharma A, Kaushik V, Goel M. Insights into the Distribution and Functional Properties of l-Asparaginase in the Archaeal Domain and Characterization of Picrophilus torridus Asparaginase Belonging to the Novel Family Asp2like1. ACS OMEGA 2022; 7:40750-40765. [PMID: 36406543 PMCID: PMC9670692 DOI: 10.1021/acsomega.2c01127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
l-Asparaginase catalyzes the hydrolysis of l-asparagine to aspartic acid and ammonia and is used in the medical and food industries. In this investigation, from the proteomes of 176 archaeal organisms (with completely sequenced genomes), 116 homologs of l-asparaginase were obtained from 86 archaeal organisms segregated into Asp1, Asp2, IaaA, Asp2like1, and Asp2like2 families based on the conserved domain. The similarities and differences in the structure of selected representatives from each family are discussed. From the two novel archaeal l-asparaginase families Asp2like1 and Asp2like2, a representative of Asp2like1 family Picrophilus torridus asparaginase (PtAsp2like1) was characterized in detail to find its suitability in therapeutics. PtAsp2like1 was a glutaminase-free asparaginase that showed the optimum activity at 80 °C and pH 10.0. The Km of PtAsp2like1 toward substrate l-asparagine was 11.69 mM. This study demonstrates the improved mapping of asparaginases in the archaeal domain, facilitating future focused research on archaeal asparaginases for therapeutic applications.
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5
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Electroenzymatic Model System for the Determination of Catalytic Activity of Erwinia carotovora L-Asparaginase. Processes (Basel) 2022. [DOI: 10.3390/pr10071313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An electrochemical method for the determination of the catalytic activity of L-asparaginase (ASNase) from Erwinia carotovora was proposed. Our approach is based on the electrooxidation of amino acids from L-asparaginase polypeptide backbones. The electrochemical behavior of ASNase on electrodes obtained by screen-printing modified with single-wall carbon nanotubes (SPE/SWCNTs) as sensing elements demonstrated a broad oxidation peak at 0.5–0.6 V centered at 0.531 ± 0.010 V. We have shown that in the presence of the substrate L-asparagine, the oxidation current of the enzyme was reduced in a concentration-dependent manner. The specificity of electrochemical analysis was confirmed in experiments with glycine, an amino acid with no substrate activity on ASNase and does not reduce the oxidation peak of L-asparaginase. The addition of glycine did not significantly influence the amplitude of the oxidation current. The innovative aspects of the proposed electrochemical sensor are the direct monitoring of ASNase catalytic activity and a reagentless approach, which does not require additional reagents or labels.
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6
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Pokrovskaya MV, Pokrovsky VS, Aleksandrova SS, Sokolov NN, Zhdanov DD. Molecular Analysis of L-Asparaginases for Clarification of the Mechanism of Action and Optimization of Pharmacological Functions. Pharmaceutics 2022; 14:pharmaceutics14030599. [PMID: 35335974 PMCID: PMC8948990 DOI: 10.3390/pharmaceutics14030599] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022] Open
Abstract
L-asparaginases (EC 3.5.1.1) are a family of enzymes that catalyze the hydrolysis of L-asparagine to L-aspartic acid and ammonia. These proteins with different biochemical, physicochemical and pharmacological properties are found in many organisms, including bacteria, fungi, algae, plants and mammals. To date, asparaginases from E. coli and Dickeya dadantii (formerly known as Erwinia chrysanthemi) are widely used in hematology for the treatment of lymphoblastic leukemias. However, their medical use is limited by side effects associated with the ability of these enzymes to hydrolyze L-glutamine, as well as the development of immune reactions. To solve these issues, gene-editing methods to introduce amino-acid substitutions of the enzyme are implemented. In this review, we focused on molecular analysis of the mechanism of enzyme action and to optimize the antitumor activity.
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Affiliation(s)
- Marina V. Pokrovskaya
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.V.P.); (S.S.A.); (N.N.S.)
| | - Vadim S. Pokrovsky
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia;
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Federal Territory Sirius, Olimpiisky Prospect 1, 354340 Sochi, Russia
| | - Svetlana S. Aleksandrova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.V.P.); (S.S.A.); (N.N.S.)
| | - Nikolay N. Sokolov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.V.P.); (S.S.A.); (N.N.S.)
| | - Dmitry D. Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.V.P.); (S.S.A.); (N.N.S.)
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia;
- Correspondence:
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7
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Wang N, Ji W, Wang L, Wu W, Zhang W, Wu Q, Du W, Bai H, Peng B, Ma B, Li L. Overview of the structure, side effects, and activity assays of l-asparaginase as a therapy drug of acute lymphoblastic leukemia. RSC Med Chem 2022; 13:117-128. [PMID: 35308022 PMCID: PMC8864486 DOI: 10.1039/d1md00344e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/09/2022] [Indexed: 01/14/2023] Open
Abstract
l-Asparaginase (l-ASNase is the abbreviation, l-asparagine aminohydrolase, E.C.3.5.1.1) is an enzyme that is clinically employed as an antitumor agent for the treatment of acute lymphoblastic leukemia (ALL). Although l-ASNase is known to deplete l-asparagine (l-Asn), causing cytotoxicity in leukemia cells, the specific molecular signaling pathways are not well defined. Because of the deficiencies in the production and administration of current formulations, the l-ASNase agent in clinical use is still associated with serious side effects, so controlling its dose and activity monitoring during therapy is crucial for improving the treatment success rate. Accordingly, it is urgent to summarize and develop effective analytical methods to detect l-ASNase activity in treatment. However, current reports on these detection methods are fragmented and also have not been systematically summarized and classified, thereby not only delaying the investigations of specific molecular mechanisms, but also hindering the development of novel detection methods. Herein, in this review, we provided a detailed summary of the l-ASNase structures, antitumor mechanism and side effects, and current detection approaches, such as fluorescence assays, colorimetric assays, spectroscopic assays and some other assays. All of them possess unique advantages and disadvantages, so it has been difficult to establish clear criteria for clinical application. We hope that this review will be of some value in promoting the development of l-ASNase activity detection methods.
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Affiliation(s)
- Nanxiang Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Wenhui Ji
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Lan Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Wanxia Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Wei Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Wei Du
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical UniversityXi'an710072China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical UniversityXi'an710072China
| | - Bo Ma
- School of Pharmaceutical Sciences, Nanjing Tech UniversityNanjing211800China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech UniversityNanjing211800China
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8
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Sharma D, Saini R, Mishra A. Natural phytocompounds physalin D, withaferin a and withanone target L-asparaginase of Mycobacterium tuberculosis: a molecular dynamics study. J Biomol Struct Dyn 2022; 41:2645-2659. [PMID: 35132949 DOI: 10.1080/07391102.2022.2036239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Tuberculosis is a major infectious disease that is responsible for high mortality in humans. The reason for the global burden is the emergence of new antibiotic resistant strains of Mycobacteria that showed resistance against the currently given therapy. It is identified that the pathogen utilizes the L-asparaginase enzyme as a virulence factor for survival benefits inside the host. Therefore, L-asparaginase of Mycobacterium tuberculosis is a promising therapeutic drug target. In view of the light, the present study explores thirty phytocompounds from medicinal plants to determine the binding affinity in the catalytic site of L-asparaginase. The studies initiated with the construction of the 3 D structure of L-asparaginase using homology modeling. Using the robustness of molecular docking with binding energy cut-off value < -9.0 kcal/mol and 100 ns molecular dynamics simulations, three phytocompounds viz., Physalin D (-9.11 kcal/mol), Withanone (-9.45 kcal/mol) and Withaferin A (-9. 67 kcal/mol) showed strong binding potential compared to the product, L-aspartate (-5.87 kcal/mol). The active site residues identified are Thr 12, Asp 51, Ser 53, Thr 84, Asp 85, and Lys 157. Upon MD simulations, the phytocompounds and the product L-aspartate remain present in the same catalytic pocket of the enzyme. The RMSD, RMSF, radius of gyration and H-bond analysis of enzyme ligand complexes efficiently showed the stability of ligands at the docked site. Further, ADME studies distinctly demonstrate the potential of selected phytoconstituents as therapeutics. Thus, serve as safe and low-cost alternatives to chemical compounds to be used in combination therapy for treatment of tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deepankar Sharma
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Ravi Saini
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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9
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Mukherjee R, Bera D. Biochemical characterization and thermodynamic principles of purified l-Asparaginase from novel Brevibacillus borstelensis ML12. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Revealing Escherichia coli type II L-asparaginase active site flexible loop in its open, ligand-free conformation. Sci Rep 2021; 11:18885. [PMID: 34556749 PMCID: PMC8460627 DOI: 10.1038/s41598-021-98455-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/30/2021] [Indexed: 11/08/2022] Open
Abstract
Since 1993, when the structure of Escherichia coli type II L-asparaginase (EcAII) in complex with L-aspartate was firstly reported, many structures of the wild type and mutated enzyme have been deposited in the Protein Data Bank. None of them report the full structure of the monomer in its ligand-free, open conformation, mainly because of the high dynamic and flexibility of the active site flexible loop. Here we report for the first time the structure of EcAII wild type in its open conformation comprising, for at least one protomer, clear electron density for the active site flexible loop (PDB ID: 6YZI). The structural element is highly mobile and it is transposed onto the rigid part of the active site upon substrate binding to allow completion of the enzyme catalytic center, thanks to key residues that serve as hinges and anchoring points. In the substrate binding pocket, several highly conserved water molecules are coordinated by residues involved in substrate binding, comprising two water molecules very likely involved in the enzyme catalytic process. We also describe, by molecular dynamics simulations, how the transposition of the loop, besides providing the proximity of residues needed for catalysis, causes a general stabilization of the protein.
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11
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Guimarães AVF, Frota NF, Lourenzoni MR. Molecular dynamics simulations of human L-asparaginase1: Insights into structural determinants of enzymatic activity. J Mol Graph Model 2021; 109:108007. [PMID: 34461521 DOI: 10.1016/j.jmgm.2021.108007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/05/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
The l-asparaginase enzyme is used in cancer therapy, mainly acute lymphoid leukemia (ALL). Commercial enzymes (EcASNase2) cause adverse reactions during treatment, such as immunogenicity. A human enzyme could be a non-immunogenic substitute. However, no candidate was found showing efficient kinetic properties. HASNase1 is an l-asparaginase that comes from the N-terminal domain of a protein called 60 kDa-lysophospholipase and its 3D structure has not been resolved. HASNase1 is homologous to EcASNase1 and gpASNase1, and this last one has shown efficient kinetic properties. Homology modeling was used to find the 3D structure of hASNase1, so one could submit it to Molecular Dynamics (MD), in order to understand structural differences that lead to different catalytic efficiency compared to EcASNase2 and gpASNase1. The interaction potential between L-Asn and active site residues showed that the substrate can rotate in the site when Region1 is open. Region1 residues sequence favors deformations and movements as shown in MD. Region2-A is linear in gpASNase1, and it features a helix portion in hASNase1, which leaves the Tyr308 position projected to the active site ratifying its role in catalytic efficiency. Analysis of Lys188 orientation and movement showed the effect of positive cooperativity in hASNase1. It was found that the presence of Asn at the allosteric site helps, not only in Region1 stabilization, but also in Lys188 stabilization for the maintenance of the triad. Despite structural similarities in hASNase1, gpASNase1, and EcASNase2, there are differences in structural determinants that, in addition to allosterism, may explain the different kinetic properties.
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Affiliation(s)
- Ana Virginia Frota Guimarães
- Programa de Pós Graduação em Biotecnologia de Recursos Naturais, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici, 825, zip-code: 60356-000, Fortaleza, CE, Brazil; Fundação Oswaldo Cruz - Ceará, Fiocruz - CE, Protein Engineering and Health Solutions Group - GEPeSS, zip-code: 60175-047, Fortaleza, CE, Brazil
| | - Natália Fernandes Frota
- Fundação Oswaldo Cruz - Ceará, Fiocruz - CE, Protein Engineering and Health Solutions Group - GEPeSS, zip-code: 60175-047, Fortaleza, CE, Brazil
| | - Marcos Roberto Lourenzoni
- Fundação Oswaldo Cruz - Ceará, Fiocruz - CE, Protein Engineering and Health Solutions Group - GEPeSS, zip-code: 60175-047, Fortaleza, CE, Brazil.
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12
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Shrestha R, Das C. Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis. Acta Crystallogr F Struct Biol Commun 2021; 77:163-170. [PMID: 34100774 PMCID: PMC8186415 DOI: 10.1107/s2053230x21005124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal-lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalanine residue of the flap interacts with a conserved aspartate residue of the Ins-1 β-turn to form a closed `lid' over the active site in the substrate-bound state. Analyses of these two residues (Phe403 and Asp315) in Sst2 showed that their interaction plays an important role in controlling the flexibility of Ins-2. The Lys63-linked diubiquitin substrate-bound form of Sst2 showed that the conserved phenylalanine also interacts with Thr316 of Ins-1, which is substituted by tyrosine in other AMSH orthologs. Although Thr316 makes no direct interaction with the substrate, its mutation to alanine resulted in a significant loss of activity. In order to understand the contribution of Thr316 to catalysis, the crystal structure of this mutant was determined. In spite of the effect of the mutation on catalytic activity, the structure of the Sst2 Thr316Ala mutant did not reveal significant changes in either the overall structure or the active-site arrangement relative to the wild type. The Phe403-Thr316 van der Waals interaction is impaired by the Thr316Ala mutation, abrogating the adoption of the closed active-site conformation required for catalysis. Since van der Waals interactions with phenylalanine are conserved across substrate-bound forms of AMSH-LP and Sst2, these interactions may be critical for loop immobilization and the positioning of the isopeptide bond of Lys63-linked polyubiquitin-chain substrates.
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Affiliation(s)
- Rashmi Shrestha
- Chemistry Department, Berea College, CPO 2191, Berea, KY 40404, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Nagaratnam N, Delker SL, Jernigan R, Edwards TE, Snider J, Thifault D, Williams D, Nannenga BL, Stofega M, Sambucetti L, Hsieh JJ, Flint AJ, Fromme P, Martin-Garcia JM. Structural insights into the function of the catalytically active human Taspase1. Structure 2021; 29:873-885.e5. [PMID: 33784495 DOI: 10.1016/j.str.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/07/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse models of glioblastoma. Taspase1 is synthesized as an inactive proenzyme, becoming active upon intramolecular cleavage. The activation process changes the conformation of a long fragment at the C-terminus of the α subunit, for which no full-length structural information exists and whose function is poorly understood. We present a cloning strategy to generate a circularly permuted form of Taspase1 to determine the crystallographic structure of active Taspase1. We discovered that this region forms a long helix and is indispensable for the catalytic activity of Taspase1. Our study highlights the importance of this element for the enzymatic activity of Ntn-hydrolases, suggesting that it could be a potential target for the design of inhibitors with potential to be developed into anticancer therapeutics.
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Affiliation(s)
- Nirupa Nagaratnam
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Silvia L Delker
- Beryllium Discovery Corp., with present address of UCB Biosciences, Bedford, MA 01730, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., with present address of UCB Biosciences, Bedford, MA 01730, USA
| | - Janey Snider
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Darren Thifault
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Dewight Williams
- Eyring Materials Center, Arizona State University, Tempe, AZ 85257, USA
| | - Brent L Nannenga
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Mary Stofega
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - Lidia Sambucetti
- Division of Biosciences, SRI International Menlo Park, Menlo Park, CA 94025, USA
| | - James J Hsieh
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Andrew J Flint
- Frederick National Lab for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", Spanish National Research Council (CSIC), Madrid 28006, Spain.
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14
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Costa-Silva T, Costa I, Biasoto H, Lima G, Silva C, Pessoa A, Monteiro G. Critical overview of the main features and techniques used for the evaluation of the clinical applicability of L-asparaginase as a biopharmaceutical to treat blood cancer. Blood Rev 2020; 43:100651. [DOI: 10.1016/j.blre.2020.100651] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/14/2019] [Accepted: 12/23/2019] [Indexed: 12/16/2022]
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15
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Dumina MV, Eldarov MA, Zdanov DD, Sokolov NN. [L-asparaginases of extremophilic microorganisms in biomedicine]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:105-123. [PMID: 32420891 DOI: 10.18097/pbmc20206602105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
L-asparaginase is extensively used in the treatment of acute lymphoblastic leukemia and several other lymphoproliferative diseases. In addition to its biomedical application, L-asparaginase is also of prospective use in food industry to reduce the formation of acrylamide, which is classified as probably neurotoxic and carcinogenic to human, and in biosensors for determination of L-asparagine level in medicine and food chemistry. The importance of L-asparaginases in different fields, disadvantages of commercial ferments, and the fact that they are widespread in nature stimuli the search for biobetter L-asparaginases from new producing microorganisms. In this regard, extremofile microorganisms exhibit unique physiological properties such as thermal stability, adaptability to extreme cold conditions, salt and pH tolerance and so provide one of the most valuable sources for novel L-asparaginases. The present review summarizes the recent results on studying the structural, functional, physicochemical and kinetic properties, stability of extremophilic L-asparaginases in comparison with their mesophilic homologues.
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Affiliation(s)
- M V Dumina
- Research Center of Biotechnology RAS, Moscow, Russia
| | - M A Eldarov
- Research Center of Biotechnology RAS, Moscow, Russia
| | - D D Zdanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - N N Sokolov
- Institute of Biomedical Chemistry, Moscow, Russia
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16
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Microbial enzymes for deprivation of amino acid metabolism in malignant cells: biological strategy for cancer treatment. Appl Microbiol Biotechnol 2020; 104:2857-2869. [PMID: 32037468 DOI: 10.1007/s00253-020-10432-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Amino acid deprivation therapy (AADT) is emerging as a promising strategy for the development of novel therapeutics against cancer. This biological therapy relies upon the differences in the metabolism of cancer and normal cells. The rapid growth of tumors results in decreased expression of certain enzymes leading to auxotrophy for some specific amino acids. These auxotrophic tumors are targeted by amino acid-depleting enzymes. The depletion of amino acid selectively inhibits tumor growth as the normal cells can synthesize amino acids by their usual machinery. The enzymes used in AADT are mostly obtained from microbes for their easy availability. Microbial L-asparaginase is already approved by FDA for the treatment of acute lymphoblastic leukemia. Arginine deiminase and methionase are under clinical trials and the therapeutic potential of lysine oxidase, glutaminase and phenylalanine ammonia lyase is also being explored. The present review provides an overview of microbial amino acid depriving enzymes. Various attributes of these enzymes like structure, mode of action, production, formulations, and targeted cancers are discussed. The challenges faced and the combat strategies to establish AADT in standard cancer armamentarium are also reviewed.Key Points • Amino acid deprivation therapy is a potential therapy for auxotrophic tumors. • Microbial enzymes are used due to their ease of manipulation and high productivity. • Enzyme properties are improved by PEGylation, encapsulation, and genetic engineering. • AADT can be employed as combinational therapy for better containment of cancer.
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17
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Lu X, Chen J, Jiao L, Zhong L, Lu Z, Zhang C, Lu F. Improvement of the activity of l-asparaginase I improvement of the catalytic activity of l-asparaginase I from Bacillus megaterium H-1 by in vitro directed evolution. J Biosci Bioeng 2019; 128:683-689. [DOI: 10.1016/j.jbiosc.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/17/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
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18
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Feng Y, Liu S, Pang C, Gao H, Wang M, Du G. Improvement of catalytic efficiency and thermal stability of l-asparaginase from Bacillus subtilis 168 through reducing the flexibility of the highly flexible loop at N-terminus. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Rice Husk as an Inexpensive Renewable Immobilization Carrier for Biocatalysts Employed in the Food, Cosmetic and Polymer Sectors. Catalysts 2018. [DOI: 10.3390/catal8100471] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The high cost and environmental impact of fossil-based organic carriers represent a critical bottleneck to their use in large-scale industrial processes. The present study demonstrates the applicability of rice husk as inexpensive renewable carrier for the immobilization of enzymes applicable sectors where the covalent anchorage of the protein is a pre-requisite for preventing protein contamination while assuring the recyclability. Rice husk was oxidized and then functionalized with a di-amino spacer. The morphological characterization shed light on the properties that affect the functionalization processes. Lipase B from Candida antarctica (CaLB) and two commercial asparaginases were immobilized covalently achieving higher immobilization yield than previously reported. All enzymes were immobilized also on commercial epoxy methacrylic resins and the CaLB immobilized on rice husk demonstrated a higher efficiency in the solvent-free polycondensation of dimethylitaconate. CaLB on rice husk appears particularly suitable for applications in highly viscous processes because of the unusual combination of its low density and remarkable mechanical robustness. In the case of the two asparaginases, the biocatalyst immobilized on rice husk performed in aqueous solution at least as efficiently as the enzyme immobilized on methacrylic resins, although the rice husk loaded a lower amount of protein.
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20
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Kataria A, Singh J, Kundu B. Identification and validation of
l
‐asparaginase as a potential metabolic target against
Mycobacterium tuberculosis. J Cell Biochem 2018; 120:143-154. [DOI: 10.1002/jcb.27169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Arti Kataria
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
| | - Jasdeep Singh
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences Indian Institute of Technology Delhi New Delhi India
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21
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Li X, Zhang X, Xu S, Zhang H, Xu M, Yang T, Wang L, Qian H, Zhang H, Fang H, Osire T, Rao Z, Yang S. Simultaneous cell disruption and semi-quantitative activity assays for high-throughput screening of thermostable L-asparaginases. Sci Rep 2018; 8:7915. [PMID: 29784948 PMCID: PMC5962637 DOI: 10.1038/s41598-018-26241-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/04/2018] [Indexed: 12/20/2022] Open
Abstract
L-asparaginase, which catalyses the hydrolysis of L-asparagine to L-aspartate, has attracted the attention of researchers due to its expanded applications in medicine and the food industry. In this study, a novel thermostable L-asparaginase from Pyrococcus yayanosii CH1 was cloned and over-expressed in Bacillus subtilis 168. To obtain thermostable L-asparaginase mutants with higher activity, a robust high-throughput screening process was developed specifically for thermophilic enzymes. In this process, cell disruption and enzyme activity assays are simultaneously performed in 96-deep well plates. By combining error-prone PCR and screening, six brilliant positive variants and four key amino acid residue mutations were identified. Combined mutation of the four residues showed relatively high specific activity (3108 U/mg) that was 2.1 times greater than that of the wild-type enzyme. Fermentation with the mutant strain in a 5-L fermenter yielded L-asparaginase activity of 2168 U/mL.
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Affiliation(s)
- Xu Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Shuqin Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hengwei Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Li Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Haifeng Qian
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huiling Zhang
- School of Agriculture Ningxia University, Yinchuan, 750021, China
| | - Haitian Fang
- School of Agriculture Ningxia University, Yinchuan, 750021, China
| | - Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Shangtian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA
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22
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The role of zinc and its compounds in leukemia. J Biol Inorg Chem 2018; 23:347-362. [DOI: 10.1007/s00775-018-1545-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/09/2018] [Indexed: 12/23/2022]
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23
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Chao WC, Shen JY, Yang CH, Lan YK, Yuan JH, Lin LJ, Yang HC, Lu JF, Wang JS, Wee K, Chen YH, Chou PT. The In Situ Tryptophan Analogue Probes the Conformational Dynamics in Asparaginase Isozymes. Biophys J 2017; 110:1732-1743. [PMID: 27119634 DOI: 10.1016/j.bpj.2016.03.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 03/10/2016] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
Dynamic water solvation is crucial to protein conformational reorganization and hence to protein structure and functionality. We report here the characterization of water dynamics on the L-asparaginase structural homology isozymes L-asparaginases I (AnsA) and II (AnsB), which are shown via fluorescence spectroscopy and dynamics in combination with molecular dynamics simulation to have distinct catalytic activity. By use of the tryptophan (Trp) analog probe 2,7-diaza-tryptophan ((2,7-aza)Trp), which exhibits unique water-catalyzed proton-transfer properties, AnsA and AnsB are shown to have drastically different local water environments surrounding the single Trp. In AnsA, (2,7-aza)Trp exhibits prominent green N(7)-H emission resulting from water-catalyzed excited-state proton transfer. In stark contrast, the N(7)-H emission is virtually absent in AnsB, which supports a water-accessible and a water-scant environment in the proximity of Trp for AnsA and AnsB, respectively. In addition, careful analysis of the emission spectra and corresponding relaxation dynamics, together with the results of molecular dynamics simulations, led us to propose two structural states associated with the rearrangement of the hydrogen-bond network in the vicinity of Trp for the two Ans. The water molecules revealed in the proximity of the Trp residue have semiquantitative correlation with the observed emission spectral variations of (2,7-aza)Trp between AnsA and AnsB. Titration of aspartate, a competitive inhibitor of Ans, revealed an increase in N(7)-H emission intensity in AnsA but no obvious spectral changes in AnsB. The changes in the emission profiles reflect the modulation of structural states by locally confined environment and trapped-water collective motions.
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Affiliation(s)
- Wei-Chih Chao
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Jiun-Yi Shen
- Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, Taiwan
| | - Cheng-Han Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Yi-Kang Lan
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Jui-Hung Yuan
- Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, Taiwan
| | - Li-Ju Lin
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Jyh-Feng Lu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Jinn-Shyan Wang
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Kevin Wee
- Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, Taiwan
| | - You-Hua Chen
- Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, Taiwan
| | - Pi-Tai Chou
- Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, Taiwan.
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24
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The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity. Sci Rep 2017; 7:41643. [PMID: 28139703 PMCID: PMC5282591 DOI: 10.1038/srep41643] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/22/2016] [Indexed: 01/17/2023] Open
Abstract
Many side effects of current FDA-approved L-asparaginases have been related to their secondary L-glutaminase activity. The Wolinella succinogenes L-asparaginase (WoA) has been reported to be L-glutaminase free, suggesting it would have fewer side effects. Unexpectedly, the WoA variant with a proline at position 121 (WoA-P121) was found to have L-glutaminase activity in contrast to Uniprot entry P50286 (WoA-S121) that has a serine residue at this position. Towards understanding how this residue impacts the L-glutaminase property, kinetic analysis was coupled with crystal structure determination of these WoA variants. WoA-S121 was confirmed to have much lower L-glutaminase activity than WoA-P121, yet both showed comparable L-asparaginase activity. Structures of the WoA variants in complex with L-aspartic acid versus L-glutamic acid provide insights into their differential substrate selectivity. Structural analysis suggests a mechanism by which residue 121 impacts the conformation of the conserved tyrosine 27, a component of the catalytically-important flexible N-terminal loop. Surprisingly, we could fully model this loop in either its open or closed conformations, revealing the roles of specific residues of an evolutionary conserved motif among this L-asparaginase family. Together, this work showcases critical residues that influence the ability of the flexible N-terminal loop for adopting its active conformation, thereby effecting substrate specificity.
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25
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Costa IM, Schultz L, de Araujo Bianchi Pedra B, Leite MSM, Farsky SHP, de Oliveira MA, Pessoa A, Monteiro G. Recombinant L-asparaginase 1 from Saccharomyces cerevisiae: an allosteric enzyme with antineoplastic activity. Sci Rep 2016; 6:36239. [PMID: 27824095 PMCID: PMC5099943 DOI: 10.1038/srep36239] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 10/12/2016] [Indexed: 01/16/2023] Open
Abstract
L-asparaginase (L-ASNase) (EC 3.5.1.1) is an important enzyme for the treatment of acute lymphoblastic leukaemia. Currently, the enzyme is obtained from bacteria, Escherichia coli and Erwinia chrysanthemi. The bacterial enzymes family is subdivided in type I and type II; nevertheless, only type II have been employed in therapeutic proceedings. However, bacterial enzymes are susceptible to induce immune responses, leading to a high incidence of adverse effects compromising the effectiveness of the treatment. Therefore, alternative sources of L-ASNase may be useful to reduce toxicity and enhance efficacy. The yeast Saccharomyces cerevisiae has the ASP1 gene responsible for encoding L-asparaginase 1 (ScASNase1), an enzyme predicted as type II, like bacterial therapeutic isoforms, but it has been poorly studied. Here we characterised ScASNase1 using a recombinant enzyme purified by affinity chromatography. ScASNase1 has specific activity of 196.2 U/mg and allosteric behaviour, like type I enzymes, but with a low K0.5 = 75 μM like therapeutic type II. We showed through site-directed mutagenesis that the T64-Y78-T141-K215 residues are involved in catalysis. Furthermore, ScASNase1 showed cytotoxicity for the MOLT-4 leukemic cell lineage. Our data show that ScASNase1 has characteristics described for the two subfamilies of l-asparaginase, types I and II, and may have promising antineoplastic properties.
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Affiliation(s)
- Iris Munhoz Costa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Leonardo Schultz
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, São Vicente/SP 11330-900, Brazil
| | - Beatriz de Araujo Bianchi Pedra
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Mariana Silva Moreira Leite
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Sandra H P Farsky
- Department of Clinical and Toxicological Analysis School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Marcos Antonio de Oliveira
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, São Vicente/SP 11330-900, Brazil
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Gisele Monteiro
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
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26
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Sun Z, Qin R, Li D, Ji K, Wang T, Cui Z, Huang Y. A novel bacterial type II l -asparaginase and evaluation of its enzymatic acrylamide reduction in French fries. Int J Biol Macromol 2016; 92:232-239. [DOI: 10.1016/j.ijbiomac.2016.07.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
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27
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Prihanto AA, Wakayama M. Marine Microorganism: An Underexplored Source of l-Asparaginase. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:1-25. [PMID: 27770857 DOI: 10.1016/bs.afnr.2016.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
l-Asparaginase (EC 3.5.1.1) is an enzyme that catalyzes the hydrolysis of l-asparagine to l-aspartic acid. This enzyme has an important role in medicine and food. l-Asparaginase is a potential drug in cancer therapy. Furthermore, it is also applied for reducing acrylamide, a carcinogenic compound in baked and fried foods. Until now, approved l-asparaginases for both applications are few due to their lack of appropriate properties. As a result, researchers have been enthusiastically seeking new sources of enzyme with better performance. A great number of terrestrial l-asparaginase-producing microorganisms have been reported but unfortunately, almost all failed to meet criteria for cancer therapy and acrylamide reducing agent. As a largest area than Earth, marine environment, by contrast, has not been optimally explored yet. So far, a great challenge facing an exploration of marine microorganisms is mainly due to their harsh, mysterious, and dangerous environment. It is clear that marine environment, a gigantic potential source for marine natural products is scantily revealed, although several approaches and technologies have been developed. This chapter presents the historical of l-asparaginase discovery and applications. It is also discussed, how the marine environment, even though offering a great potency but is still one of the less explored area for l-asparaginase-producing microorganisms.
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Affiliation(s)
- A A Prihanto
- Faculty of Fisheries and Marine Science, Brawijaya University, Malang, Indonesia.
| | - M Wakayama
- College of Life Sciences, Ritsumeikan University, Shiga, Japan
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28
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Nguyen HA, Su Y, Lavie A. Structural Insight into Substrate Selectivity of Erwinia chrysanthemi L-asparaginase. Biochemistry 2016; 55:1246-53. [PMID: 26855287 PMCID: PMC4776285 DOI: 10.1021/acs.biochem.5b01351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
l-Asparaginases of bacterial
origin are a mainstay of
acute lymphoblastic leukemia treatment. The mechanism of action of
these enzyme drugs is associated with their capacity to deplete the
amino acid l-asparagine from the blood. However, clinical
use of bacterial l-asparaginases is complicated by their
dual l-asparaginase and l-glutaminase activities.
The latter, even though representing only ∼10% of the overall
activity, is partially responsible for the observed toxic side effects.
Hence, l-asparaginases devoid of l-glutaminase activity
hold potential as safer drugs. Understanding the key determinants
of l-asparaginase substrate specificity is a prerequisite
step toward the development of enzyme variants with reduced toxicity.
Here we present crystal structures of the Erwinia chrysanthemil-asparaginase in complex with l-aspartic acid
and with l-glutamic acid. These structures reveal two enzyme
conformations—open and closed—corresponding to the inactive
and active states, respectively. The binding of ligands induces the
positioning of the catalytic Thr15 into its active conformation, which
in turn allows for the ordering and closure of the flexible N-terminal
loop. Notably, l-aspartic acid is more efficient than l-glutamic acid in inducing the active positioning of Thr15.
Structural elements explaining the preference of the enzyme for l-asparagine over l-glutamine are discussed with guidance
to the future development of more specific l-asparaginases.
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Affiliation(s)
- Hien Anh Nguyen
- The Jesse Brown VA Medical Center , Chicago, Illinois 60607, United States.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Ying Su
- The Jesse Brown VA Medical Center , Chicago, Illinois 60607, United States.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Arnon Lavie
- The Jesse Brown VA Medical Center , Chicago, Illinois 60607, United States.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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29
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Bueno AN, Shrestha RK, Ronau JA, Babar A, Sheedlo MJ, Fuchs JE, Paul LN, Das C. Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase. Biochemistry 2016; 54:6038-51. [PMID: 26368668 DOI: 10.1021/acs.biochem.5b00631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The endosome-associated deubiquitinase (DUB) AMSH is a member of the JAMM family of zinc-dependent metallo isopeptidases with high selectivity for Lys63-linked polyubiquitin chains, which play a key role in endosomal-lysosomal sorting of activated cell surface receptors. The catalytic domain of the enzyme features a flexible flap near the active site that opens and closes during its catalytic cycle. Structural analysis of its homologues, AMSH-LP (AMSH-like protein) and the fission yeast counterpart, Sst2, suggests that a conserved Phe residue in the flap may be critical for substrate binding and/or catalysis. To gain insight into the contribution of this flap in substrate recognition and catalysis, we generated mutants of Sst2 and characterized them using a combination of enzyme kinetics, X-ray crystallography, molecular dynamics simulations, and isothermal titration calorimetry (ITC). Our analysis shows that the Phe residue in the flap contributes key interactions during the rate-limiting step but not to substrate binding, since mutants of Phe403 exhibit a defect only in kcat but not in KM. Moreover, ITC studies show Phe403 mutants have similar KD for ubiquitin compared to the wild-type enzyme. The X-ray structures of both Phe403Ala and the Phe403Trp, in both the free and ubiquitin bound form, reveal no appreciable structural change that might impair substrate or alter product binding. We observed that the side chain of the Trp residue is oriented identically with respect to the isopeptide moiety of the substrate as the Phe residue in the wild-type enzyme, so the loss of activity seen in this mutant cannot be explained by the absence of a group with the ability to provide van der Waals interactions that facilitate the hyrdolysis of the Lys63-linked diubiquitin. Molecular dynamics simulations indicate that the flap in the Trp mutant is quite flexible, allowing almost free rotation of the indole side chain. Therefore, it is possible that these different dynamic properties of the flap in the Trp mutant, compared to the wild-type enzyme, manifest as a defect in interactions that facilitate the rate-limiting step. Consistent with this notion, the Trp mutant was able to cleave Lys48-linked and Lys11-linked diubiquitin better than the wild-type enzyme, indicating altered mobility and hence reduced selectivity.
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Affiliation(s)
- Amy N Bueno
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Rashmi K Shrestha
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Judith A Ronau
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Aditya Babar
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Michael J Sheedlo
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Julian E Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Lake N Paul
- Bindley Biosciences Center, Purdue University , West Lafayette, Indiana 47907, United States
| | - Chittaranjan Das
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States
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30
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Schalk AM, Antansijevic A, Caffrey M, Lavie A. Experimental Data in Support of a Direct Displacement Mechanism for Type I/II L-Asparaginases. J Biol Chem 2016; 291:5088-100. [PMID: 26733195 DOI: 10.1074/jbc.m115.699884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/02/2023] Open
Abstract
Bacterial L-asparaginases play an important role in the treatment of certain types of blood cancers. We are exploring the guinea pig L-asparaginase (gpASNase1) as a potential replacement of the immunogenic bacterial enzymes. The exact mechanism used by L-asparaginases to catalyze the hydrolysis of asparagine into aspartic acid and ammonia has been recently put into question. Earlier experimental data suggested that the reaction proceeds via a covalent intermediate using a ping-pong mechanism, whereas recent computational work advocates the direct displacement of the amine by an activated water. To shed light on this controversy, we generated gpASNase1 mutants of conserved active site residues (T19A, T116A, T19A/T116A, K188M, and Y308F) suspected to play a role in hydrolysis. Using x-ray crystallography, we determined the crystal structures of the T19A, T116A, and K188M mutants soaked in asparagine. We also characterized their steady-state kinetic properties and analyzed the conversion of asparagine to aspartate using NMR. Our structures reveal bound asparagine in the active site that has unambiguously not formed a covalent intermediate. Kinetic and NMR assays detect significant residual activity for all of the mutants. Furthermore, no burst of ammonia production was observed that would indicate covalent intermediate formation and the presence of a ping-pong mechanism. Hence, despite using a variety of techniques, we were unable to obtain experimental evidence that would support the formation of a covalent intermediate. Consequently, our observations support a direct displacement rather than a ping-pong mechanism for l-asparaginases.
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Affiliation(s)
- Amanda M Schalk
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Aleksandar Antansijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and the Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
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31
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Long S, Zhang X, Rao Z, Chen K, Xu M, Yang T, Yang S. Amino acid residues adjacent to the catalytic cavity of tetramer l -asparaginase II contribute significantly to its catalytic efficiency and thermostability. Enzyme Microb Technol 2016; 82:15-22. [DOI: 10.1016/j.enzmictec.2015.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/19/2015] [Accepted: 08/13/2015] [Indexed: 11/17/2022]
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32
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Lopes AM, Oliveira-Nascimento LD, Ribeiro A, Tairum CA, Breyer CA, Oliveira MAD, Monteiro G, Souza-Motta CMD, Magalhães PDO, Avendaño JGF, Cavaco-Paulo AM, Mazzola PG, Rangel-Yagui CDO, Sette LD, Converti A, Pessoa A. Therapeuticl-asparaginase: upstream, downstream and beyond. Crit Rev Biotechnol 2015; 37:82-99. [DOI: 10.3109/07388551.2015.1120705] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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33
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Purification and Characterization of Asparaginase from Phaseolus vulgaris Seeds. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:309214. [PMID: 26413120 PMCID: PMC4564614 DOI: 10.1155/2015/309214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/19/2015] [Indexed: 11/18/2022]
Abstract
L-asparaginase from bacteria has been used in treatment of acute lymphoblastic leukemia. The aim of this study was to purify and characterize L-asparaginase from Phaseolus vulgaris seeds instead of microbial sources. L-asparaginase was purified to apparent homogeneity. The enzyme has molecular mass of 79 kDa. The purified asparaginase had very low activity toward a number of asparagine and glutamine analogues. L-asparaginase was free from glutaminase activity. Kinetic parameters, Km and Vmax of purified enzyme, were found to be 6.72 mM and 0.16 μM, respectively. The enzyme had optimum pH at 8.0. The enzyme showed high stability at alkaline pH (pH 7.5–9.0) when incubated for up to 24 h. L-asparaginase had the same temperature optimum and thermal stability at 37°C. K+ was able to greatly enhance the activity of asparaginase by 150% compared with other metals tested. In conclusion, L-asparaginase showed no glutaminase activity and good stability over a wide range of physiological conditions, and thus it could be used as a potential candidate for treatment of acute lymphoblastic leukemia.
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34
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Anishkin A, Vanegas JM, Rogers DM, Lorenzi PL, Chan WK, Purwaha P, Weinstein JN, Sukharev S, Rempe SB. Catalytic Role of the Substrate Defines Specificity of Therapeutic l-Asparaginase. J Mol Biol 2015; 427:2867-85. [DOI: 10.1016/j.jmb.2015.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/20/2015] [Accepted: 06/26/2015] [Indexed: 12/23/2022]
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35
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Tackling Critical Catalytic Residues in Helicobacter pylori L-Asparaginase. Biomolecules 2015; 5:306-17. [PMID: 25826146 PMCID: PMC4496674 DOI: 10.3390/biom5020306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/19/2015] [Accepted: 03/19/2015] [Indexed: 11/17/2022] Open
Abstract
Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of l-ASN and, to a variable extent, of l-GLN, on which leukemia cells are dependent for survival. In contrast to other known l-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards l-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in l-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features.
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36
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Maggi M, Chiarelli LR, Valentini G, Scotti C. Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 2015; 10:e0117025. [PMID: 25664771 PMCID: PMC4321988 DOI: 10.1371/journal.pone.0117025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/18/2014] [Indexed: 01/19/2023] Open
Abstract
Bacterial L-asparaginases have been used as anti-cancer drugs for over 4 decades though presenting, along with their therapeutic efficacy, several side effects due to their bacterial origin and, seemingly, to their secondary glutaminase activity. Helicobacter pylori type II L-asparaginase possesses interesting features, among which a reduced catalytic efficiency for L-GLN, compared to the drugs presently used in therapy. In the present study, we describe some enzyme variants with catalytic and in vitro cytotoxic activities different from the wild type enzyme. Particularly, replacements on catalytic threonines (T16D and T95E) deplete the enzyme of both its catalytic activities, once more underlining the essential role of such residues. One serendipitous mutant, M121C/T169M, had a preserved efficiency vs L-asparagine but was completely unable to carry out L-glutamine hydrolysis. Interestingly, this variant did not exert any cytotoxic effect on HL-60 cells. The M121C and T169M single mutants had reduced catalytic activities (nearly 2.5- to 4-fold vs wild type enzyme, respectively). Mutant Q63E, endowed with a similar catalytic efficiency versus asparagine and halved glutaminase efficiency with respect to the wild type enzyme, was able to exert a cytotoxic effect comparable to, or higher than, the one of the wild type enzyme when similar asparaginase units were used. These findings may be relevant to determine the role of glutaminase activity of L-asparaginase in the anti-proliferative effect of the drug and to shed light on how to engineer the best asparaginase/glutaminase combination for an ever improved, patients-tailored therapy.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Protein Biochemistry, University of Pavia, Pavia, Italy
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Molecular Microbiology, University of Pavia, Pavia, Italy
| | - Giovanna Valentini
- Department of Biology and Biotechnologies “Lazzaro Spallanzani”, Laboratory of Protein Biochemistry, University of Pavia, Pavia, Italy
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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Singh J, Srivastava A, Jha P, Sinha KK, Kundu B. l-Asparaginase as a new molecular target against leishmaniasis: insights into the mechanism of action and structure-based inhibitor design. MOLECULAR BIOSYSTEMS 2015; 11:1887-96. [DOI: 10.1039/c5mb00251f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
l-Asparaginases belong to a family of amidohydrolases that catalyze the conversion of l-asparagine into l-aspartic acid and ammonia.
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Affiliation(s)
- Jasdeep Singh
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi-110016
- India
| | - Ankit Srivastava
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi-110016
- India
| | - Pravin Jha
- National Institute of Pharmaceutical Education & Research
- Vaishali-844102
- India
| | - Kislay K. Sinha
- National Institute of Pharmaceutical Education & Research
- Vaishali-844102
- India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi-110016
- India
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38
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Tomar R, Sharma P, Srivastava A, Bansal S, Ashish, Kundu B. Structural and functional insights into an archaealL-asparaginase obtained through the linker-less assembly of constituent domains. ACTA ACUST UNITED AC 2014; 70:3187-97. [DOI: 10.1107/s1399004714023414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022]
Abstract
Covalent linkers bridging the domains of multidomain proteins are considered to be crucial for assembly and function. In this report, an exception in which the linker of a two-domain dimeric L-asparaginase fromPyrococcus furiosus(PfA) was found to be dispensable is presented. Domains of this enzyme assembled without the linker into a conjoined tetrameric form that exhibited higher activity than the parent enzyme. The global shape and quaternary structure of the conjoined PfA were also similar to the wild-type PfA, as observed by their solution scattering profiles and X-ray crystallographic data. Comparison of the crystal structures of substrate-bound and unbound enzymes revealed an altogether new active-site composition and mechanism of action. Thus, conjoined PfA is presented as a unique enzyme obtained through noncovalent, linker-less assembly of constituent domains that is stable enough to function efficiently at elevated temperatures.
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39
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Identification of Functional Regions in the Rhodospirillum rubrum l-Asparaginase by Site-Directed Mutagenesis. Mol Biotechnol 2014; 57:251-64. [DOI: 10.1007/s12033-014-9819-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Upadhyay AK, Singh A, Mukherjee KJ, Panda AK. Refolding and purification of recombinant L-asparaginase from inclusion bodies of E. coli into active tetrameric protein. Front Microbiol 2014; 5:486. [PMID: 25309524 PMCID: PMC4164012 DOI: 10.3389/fmicb.2014.00486] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/28/2014] [Indexed: 11/25/2022] Open
Abstract
A tetrameric protein of therapeutic importance, Escherichia coli L-asparaginase-II was expressed in Escherichia coli as inclusion bodies (IBs). Asparaginase IBs were solubilized using low concentration of urea and refolded into active tetrameric protein using pulsatile dilution method. Refolded asparaginase was purified in two steps by ion-exchange and gel filtration chromatographic techniques. The recovery of bioactive asparaginase from IBs was around 50%. The melting temperature (Tm) of the purified asparaginase was found to be 64°C. The specific activity of refolded, purified asparaginase was found to be comparable to the commercial asparaginase (190 IU/mg). Enzymatic activity of the refolded asparaginase was high even at four molar urea solutions, where the IB aggregates are completely solubilized. From the comparison of chemical denaturation data and activity at different concentrations of guanidine hydrochloride, it was observed that dissociation of monomeric units precedes the complete loss of helical secondary structures. Protection of the existing native-like protein structure during solubilization of IB aggregates with 4 M urea improved the propensity of monomer units to form oligomeric structure. Our mild solubilization technique retaining native-like structures, improved recovery of asparaginase in bioactive tetrameric form.
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Affiliation(s)
- Arun K Upadhyay
- Product Development Cell, National Institute of Immunology New Delhi, India
| | - Anupam Singh
- Product Development Cell, National Institute of Immunology New Delhi, India
| | - K J Mukherjee
- School for Biotechnology, Jawaharlal Nehru University New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology New Delhi, India
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41
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Borek D, Kozak M, Pei J, Jaskolski M. Crystal structure of active site mutant of antileukemicl-asparaginase reveals conserved zinc-binding site. FEBS J 2014; 281:4097-111. [DOI: 10.1111/febs.12906] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/16/2014] [Accepted: 07/01/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Dominika Borek
- Department of Crystallography; Faculty of Chemistry; A. Mickiewicz University; Poznan Poland
| | - Maciej Kozak
- Department of Crystallography; Faculty of Chemistry; A. Mickiewicz University; Poznan Poland
- Department of Macromolecular Physics; Faculty of Physics; A. Mickiewicz University; Poznan Poland
| | - Jimin Pei
- Howard Hughes Medical Institute; University of Texas Southwestern Medical Center; Dallas TX USA
| | - Mariusz Jaskolski
- Department of Crystallography; Faculty of Chemistry; A. Mickiewicz University; Poznan Poland
- Center for Biocrystallographic Research; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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42
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Mahajan RV, Kumar V, Rajendran V, Saran S, Ghosh PC, Saxena RK. Purification and characterization of a novel and robust L-asparaginase having low-glutaminase activity from Bacillus licheniformis: in vitro evaluation of anti-cancerous properties. PLoS One 2014; 9:e99037. [PMID: 24905227 PMCID: PMC4048267 DOI: 10.1371/journal.pone.0099037] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/09/2014] [Indexed: 11/18/2022] Open
Abstract
L-asparaginase having low glutaminase has been a key therapeutic agent in the treatment of acute lymphpoblastic leukemia (A.L.L). In the present study, an extracellular L-asparaginase with low glutaminase activity, produced by Bacillus licheniformis was purified to homogeneity. Protein was found to be a homotetramer of 134.8 KDa with monomeric size of 33.7 KDa and very specific for its natural substrate i.e. L-asparagine. The activity of purified L-asparaginase enhanced in presence of cations including Na+ and K+, whereas it was moderately inhibited in the presence of divalent cations and thiol group blocking reagents. The purified enzyme was maximally active over the range of pH 6.0 to 10.0 and temperature of 40°C and enzyme was stable maximum at pH 9.0 and -20°C. CD spectra of L-asparaginase predicted the enzyme to consist of 63.05% α-helix and 3.29% β-sheets in its native form with T222 of 58°C. Fluorescent spectroscopy showed the protein to be stable even in the presence of more than 3 M GdHCl. Kinetic parameters Km, Vmax and kcat of purified enzyme were found as 1.4×10(-5) M, 4.03 IU and 2.68×10(3) s(-1), respectively. The purified L-asparaginase had cytotoxic activity against various cancerous cell lines viz. Jurkat clone E6-1, MCF-7 and K-562 with IC50 of 0.22 IU, 0.78 IU and 0.153 IU respectively. However the enzyme had no toxic effect on human erythrocytes and CHO cell lines hence should be considered potential candidate for further pharmaceutical use as an anticancer drug.
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Affiliation(s)
- Richi V. Mahajan
- Department of Microbiology, University of Delhi South Campus, New Delhi, Delhi, India
| | - Vinod Kumar
- Department of Microbiology, University of Delhi South Campus, New Delhi, Delhi, India
| | - Vinoth Rajendran
- Department of Biochemistry, University of Delhi South Campus, New Delhi, Delhi, India
| | - Saurabh Saran
- Technology Based Incubator, University of Delhi South Campus, New Delhi, Delhi, India
| | - Prahlad C. Ghosh
- Department of Biochemistry, University of Delhi South Campus, New Delhi, Delhi, India
| | - Rajendra Kumar Saxena
- Department of Microbiology, University of Delhi South Campus, New Delhi, Delhi, India
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43
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El-Nagga NEA, El-Ewasy SM, El-Shweihy NM. Microbial L-asparaginase as a Potential Therapeutic Agent for the Treatment of Acute Lymphoblastic Leukemia: The Pros and Cons. INT J PHARMACOL 2014. [DOI: 10.3923/ijp.2014.182.199] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Improvement of stability and enzymatic activity by site-directed mutagenesis of E. coli asparaginase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1219-30. [PMID: 24721562 DOI: 10.1016/j.bbapap.2014.03.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/14/2014] [Accepted: 03/31/2014] [Indexed: 11/22/2022]
Abstract
Bacterial asparaginases (EC 3.5.1.1) have attracted considerable attention because enzymes of this group are used in the therapy of certain forms of leukemia. Class II asparaginase from Escherichia coli (EcA), a homotetramer with a mass of 138 kDa, is especially effective in cancer therapy. However, the therapeutic potential of EcA is impaired by the limited stability of the enzyme in vivo and by the induction of antibodies in the patients. In an attempt to modify the properties of EcA, several variants with amino acid replacements at subunit interfaces were constructed and characterized. Chemical and thermal denaturation analysis monitored by activity, fluorescence, circular dichroism, and differential scanning calorimetry showed that certain variants with exchanges that weaken dimer-dimer interactions exhibited complex denaturation profiles with active dimeric and/or inactive monomeric intermediates appearing at low denaturant concentrations. By contrast, other EcA variants showed considerably enhanced activity and stability as compared to the wild-type enzyme. Thus, even small changes at a subunit interface may markedly affect EcA stability without impairing its catalytic properties. Variants of this type may have a potential for use in the asparaginase therapy of leukemia.
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45
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Pourhossein M, Korbekandi H. Cloning, expression, purification and characterisation of Erwinia carotovora L-asparaginase in Escherichia coli. Adv Biomed Res 2014; 3:82. [PMID: 24761390 PMCID: PMC3988593 DOI: 10.4103/2277-9175.127995] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 11/12/2013] [Indexed: 12/04/2022] Open
Abstract
Background: For the past 30 years, bacterial L-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. It is found in a variety of organisms such as microbes, plants and mammals. Their intrinsic low-rate glutaminase activity, however, causes serious side-effects, including neurotoxicity, hepatitis, coagulopathy and other dysfunctions. Erwinia carotovora asparaginase shows decreased glutaminase activity, so it is believed to have fewer side-effects in leukemia therapy. Our aim was to clone, express, purify and characterize E. carotovora asparaginase. Materials and Methods: L-asparaginase from E. carotovora NCYC 1526 (ErA) was cloned and expressed in Escherichia coli strain BL21 (DE3). The enzyme was purified to homogeneity by affinity chromatography. Various conditions were tested to maximize the production of recombinant asparaginase in E. coli. Results: A new L. asparaginase from E. carotovora NCYC 1526 (ErA) was successfully cloned, expressed and purified in E. coli BL21 (DE3). The specific activity of the enzyme was 430 IU/mg. Conclusion: The results of the present work form the basis for a new engineered form of ErA for future therapeutic use, which could be extended with crystallographic studies.
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Affiliation(s)
- Meraj Pourhossein
- Department of Anatomical Sciences and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Korbekandi
- Department of Anatomical Sciences and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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46
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Gesto DS, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Unraveling the Enigmatic Mechanism of l-Asparaginase II with QM/QM Calculations. J Am Chem Soc 2013; 135:7146-58. [DOI: 10.1021/ja310165u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diana S. Gesto
- Department of Chemistry, Sciences Faculty
of Porto University, Porto, Portugal
| | | | - Pedro A. Fernandes
- Department of Chemistry, Sciences Faculty
of Porto University, Porto, Portugal
| | - Maria J. Ramos
- Department of Chemistry, Sciences Faculty
of Porto University, Porto, Portugal
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47
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l-Asparaginase as Potent Anti-leukemic Agent and Its Significance of Having Reduced Glutaminase Side Activity for Better treatment of Acute Lymphoblastic Leukaemia. Appl Biochem Biotechnol 2012; 167:2144-59. [DOI: 10.1007/s12010-012-9755-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 05/29/2012] [Indexed: 01/19/2023]
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48
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Offman MN, Krol M, Patel N, Krishnan S, Liu J, Saha V, Bates PA. Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity. Blood 2011; 117:1614-21. [PMID: 21106986 DOI: 10.1182/blood-2010-07-298422] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using proteins in a therapeutic context often requires engineering to modify functionality and enhance efficacy. We have previously reported that the therapeutic antileukemic protein macromolecule Escherichia coli L-asparaginase is degraded by leukemic lysosomal cysteine proteases. In the present study, we successfully engineered L-asparaginase to resist proteolytic cleavage and at the same time improve activity. We employed a novel combination of mutant sampling using a genetic algorithm in tandem with flexibility studies using molecular dynamics to investigate the impact of lid-loop and mutations on drug activity. Applying these methods, we successfully predicted the more active L-asparaginase mutants N24T and N24A. For the latter, a unique hydrogen bond network contributes to higher activity. Furthermore, interface mutations controlling secondary glutaminase activity demonstrated the importance of this enzymatic activity for drug cytotoxicity. All selected mutants were expressed, purified, and tested for activity and for their ability to form the active tetrameric form. By introducing the N24A and N24A R195S mutations to the drug L-asparaginase, we are a step closer to individualized drug design.
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Affiliation(s)
- Marc N Offman
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, London, UK
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49
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Kumar S, Venkata Dasu V, Pakshirajan K. Purification and characterization of glutaminase-free L-asparaginase from Pectobacterium carotovorum MTCC 1428. BIORESOURCE TECHNOLOGY 2011; 102:2077-2082. [PMID: 20832300 DOI: 10.1016/j.biortech.2010.07.114] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 05/29/2023]
Abstract
An intracellular glutaminase-free L-asparaginase from Pectobacterium carotovorum MTCC 1428 was isolated to apparent homogeneity. The homotetramer enzyme has a molecular mass of 144.4 kDa (MALDI-TOF MS) and an isoelectric point of approximately 8.4. The enzyme is very specific for its natural substrate, L-asparagine. The activity of L-asparaginase is activated by mono cations and various effectors including Na+, K+, L-cystine, L-histidine, glutathione and 2-mercaptoethanol whereas it is moderately inhibited by various divalent cations and thiol group blocking reagents. Kinetic parameters, Km, Vmax and kcat of purified L-asparaginase from P. carotovorum MTCC 1428 were found to be 0.657 mM, 4.45 U μg(-1) and 2.751×10(3) s(-1), respectively. Optimum pH of purified L-asparaginase for the hydrolysis of L-asparagine was in the range of 8.0-10.0, and its optimum temperature was found to be 40 °C. The purified L-asparaginase has no partial glutaminase activity, which can reduce the possibility of side effects during the course of anti-cancer therapy.
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Affiliation(s)
- Sanjay Kumar
- Biochemical Engineering Laboratory, Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Bansal S, Gnaneswari D, Mishra P, Kundu B. Structural stability and functional analysis of L-asparaginase from Pyrococcus furiosus. BIOCHEMISTRY (MOSCOW) 2010; 75:375-81. [PMID: 20370616 DOI: 10.1134/s0006297910030144] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report studies on an L-asparaginase from Pyrococcus furiosus, cloned and expressed in Escherichia coli and purified to homogeneity. Protein stability and enzyme kinetic parameters were determined. The enzyme was found to be thermostable, natively dimeric, and glutaminase-free, with optimum activity at pH 9.0. It showed a K(m) of 12 mM and a substrate inhibition profile above 20 mM L-asparagine. Urea could not induce unfolding and enzyme inactivation; however, with guanidine hydrochloride (GdnCl) a two-state unfolding pattern was observed. Reduced activity and an altered near-UV-CD signal for protein at low GdnCl concentration (1 M) suggested tertiary structural changes at the enzyme active site. A homology three-dimensional model was developed and the structural information was combined with activity and stability data to give functional clues about the asparaginase.
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Affiliation(s)
- S Bansal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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