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Teng FY, Feng JM, Ma FC, Wang ZX, Lu YY, Qi YX. Characterization of an agmatine N-acetyltransferase from Bactrocera dorsalis that modulates ovary development. Insect Biochem Mol Biol 2024; 170:104130. [PMID: 38734116 DOI: 10.1016/j.ibmb.2024.104130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
Agmatine N-acetyltransferase (AgmNAT), which catalyzes the formation of N-acetylagmatine from acetyl-CoA and agmatine, is a member of the GCN5-related N-acetyltransferase family. So far, knowledge of the physiological roles of AgmNAT in insects is limited. Here, we identified one gene encoding protein homologous to that of Drosophila AgmNAT using sequence information from an activity-verified Drosophila AgmNAT in a BLAST search of the Bactrocera dorsalis genome. We expressed and purified B. dorsalis AgmNAT in Escherichia coli and used the purified enzyme to define the substrate specificity for acyl-CoA and amine substrates. Our application of the screening strategy to BdorAgmNAT led to the identification of agmatine as the best amine substrate for this enzyme, with the highest kcat/Km value. We successfully obtained a BdorAgmNAT knockout strain based on a wild-type strain (WT) using the CRISPR/Cas9 technique. The ovary development of the BdorAgmNAT knockout mutants was delayed for 10 days compared with the WT specimens. Moreover, mutants had a much smaller mature ovary size and laid far fewer eggs than WT. Loss of function of BdorAgmNAT caused by RNAi with mature WT females did not affect their fecundity. These findings indicate that BdorAgmNAT is critical for oogenesis. Our data provide the first evidence for AgmNAT in regulating ovary development.
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Affiliation(s)
- Fei-Yue Teng
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Ji-Mei Feng
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Fu-Cai Ma
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Zhuo-Xin Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yong-Yue Lu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yi-Xiang Qi
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China.
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2
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Bursch KL, Olp MD, Smith BC. Analysis of continuous enzyme kinetic data using ICEKAT. Methods Enzymol 2023; 690:109-129. [PMID: 37858527 PMCID: PMC10691744 DOI: 10.1016/bs.mie.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
ICEKAT (Interactive Continuous Enzyme Analysis Tool) is an interactive web-based program for calculating initial rates and kinetic parameters (e.g., Vmax, kcat, KM, EC50, IC50) from continuous enzyme kinetic assay data that satisfy Michaelis-Menten and steady-state kinetic assumptions. ICEKAT is valuable in educational and research settings to consistently and accurately calculate initial rates and kinetic parameters, increasing assay veracity and reproducibility. Provided freely online to the scientific community, ICEKAT has been cited in at least 26 publications, and the initial journal article has been accessed nearly 9000 times since its debut in 2020 (Olp et al., 2020). Here, we provide in-depth instructions for software use, offer vital considerations for data analysis, and highlight updated software features for new and existing users. Through ICEKAT, we aim for the analysis of data from continuous enzyme kinetic studies worldwide to become more rapid, reliable, and repeatable. ICEKAT remains free of charge and available to all scientists at https://icekat.herokuapp.com/icekat; the source code for local use is found at https://github.com/SmithLabMCW/icekat.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Michael D Olp
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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3
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Paulukinas RD. Detection and quantification of UV-transparent keto-androgens by dinitrophenylhydrazine derivatization for discontinuous kinetic assays. Methods Enzymol 2023; 689:377-385. [PMID: 37802579 DOI: 10.1016/bs.mie.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Kinetic assays with recombinant enzymes are critical to determine the steady state kinetic parameters for androgen conversion to understand their role in androgen biosynthesis and metabolism. Detection and quantification of 5α-reduced androgens remain difficult to assay because they are UV-transparent compounds. Therefore, radioactive isotopic versions of these compounds are often required to conduct steady-state kinetics. Here we developed a derivatization protocol with dinitrophenylhydrazine (DNPH) to form hydrazones on the ketones of androgens enabling them to be detected by UV-reverse phase high performance liquid chromatography (RP-HPLC). We determined the kinetic parameters for the conversion of 5α-androstane-3,17-dione (5AD) to 5α-dihydrotestosterone (DHT), 11-keto-5α-androstane-3,17-dione (11K-5AD) to 11-keto-5α-dihydrotestosterone (11K-DHT), and 11β-hydroxy-5α-androstane-3,17-dione (11β-OH-5AD) to 11β-hydroxy-5α-dihydrotestosterone (11β-OH-DHT) catalyzed by recombinant aldo-keto reductase 1C3 (AKR1C3) as measured by product formation post DNPH derivatization.
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Affiliation(s)
- Ryan D Paulukinas
- Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States.
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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Quaye JA, Ball J, Gadda G. Kinetic solvent viscosity effects uncover an internal isomerization of the enzyme-substrate complex in Pseudomonas aeruginosa PAO1 NADH:Quinone oxidoreductase. Arch Biochem Biophys 2022; 727:109342. [PMID: 35777523 DOI: 10.1016/j.abb.2022.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/02/2022]
Abstract
NAD(P)H:quinone oxidoreductases (NQOs) play an essential protective role as antioxidants in the detoxification of quinones in both Prokaryotes and Eukaryotes. NQO from Pseudomonas aeruginosa PAO1 uses FMN to catalyze the two-electron reduction of various quinones with NADH. In this study, steady-state kinetics, kinetic solvent viscosity effects, and rapid reaction kinetics were used to determine which kinetic steps control the overall turnover of the enzyme with benzoquinone or juglone. The rate constant for flavin reduction (kred) at pH 6.0 was 12.9 ± 0.3 s-1, and the Kd for NADH was at least an order of magnitude lower than 90 μM. With benzoquinone, the kcat value was 11.7 ± 0.3 s-1, consistent with flavin reduction being almost entirely rate-limiting for overall turnover. With juglone, a kcat value of 10.0 ± 0.5 s-1 was recorded. The normalized plot of the relative solvent viscosity effects on the kcat values established that hydride transfer from NADH to the FMN and quinol product release, with a calculated rate constant (kP-rel) of 52 s-1, are partially rate-limiting for the overall turnover of NQO. Kinetic solvent viscosity effects with glucose or sucrose revealed a hyperbolic dependence on the kcat and kcat/Km values with benzoquinone or juglone, respectively, consistent with the presence of a solvent-sensitive internal isomerization of the enzyme-substrate complex (ES). The data demonstrate opposing effects of benzoquinone and juglone on the equilibrium of the NQO ES isomerization with glucose or sucrose. Thus, our study demonstrates how quinol substrate properties alter the equilibrium of NQO ES isomerization.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Jacob Ball
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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Lohithakshan A, Narayanasamy R, Deshmukh P, Usharani D, Kumar R. Insights into the role of F26 residue in the FMN: ATP adenylyltransferase activity of Staphylococcus aureus FAD synthetase. Biochim Biophys Acta Proteins Proteom 2022; 1870:140781. [PMID: 35421609 DOI: 10.1016/j.bbapap.2022.140781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
The bifunctional flavin adenine dinucleotide synthetase (FADS) synthesizes the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) co-factors essential for the function of flavoproteins. The Staphylococcus aureus FADS (SaFADS) produces FMN from riboflavin (RF) by ATP:riboflavin kinase (RFK) activity at its C-terminal domain. The N-terminal domain converts FMN to FAD under a reducing environment by FMN:ATP adenylyltransferase (FMNAT) activity which is reversible (FAD pyrophosphorylase activity). Herein, we investigated the role of F26 residue of the 24-GFFD-28 motif of SaFADS FMNAT domain, mostly conserved in the reducing agent-dependent FADSs. The steady-state kinetics studies showed changes in the KmATP values for mutants, indicating that the F26 residue is crucial for the FMNAT activity. Further, the FMNAT activity of the F26S mutant was observed to be higher than that of the wild-type SaFADS and its other variants at lower reducing agent concentration. In addition, the FADpp activity was inhibited by an excess of FAD substrate, which was more potent in the mutants. The altered orientation of the F26 side-chain observed in the molecular dynamics analysis suggested its plausible involvement in stabilizing FMN and ATP substrates in their respective binding pockets. Also, the SaFADS ternary complex formed with reduced FMN exhibited significant structural changes in the β4n-β5n and L3n regions compared to the oxidised FMN bound and apo forms of SaFADS. Overall, our data suggests the functional role of F26 residue in the FMNAT domain of SaFADS.
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Affiliation(s)
- Anusree Lohithakshan
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Raja Narayanasamy
- Department of Food Safety and Analytical Quality Control Laboratory, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prashant Deshmukh
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Dandamudi Usharani
- Department of Food Safety and Analytical Quality Control Laboratory, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ravi Kumar
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Patel SM, Seravalli J, Stiers KM, Tanner JJ, Becker DF. Kinetics of human pyrroline-5-carboxylate reductase in L-thioproline metabolism. Amino Acids 2021; 53:1863-1874. [PMID: 34792644 PMCID: PMC8876999 DOI: 10.1007/s00726-021-03095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022]
Abstract
L-Thioproline (L-thiazolidine-4-carboxylate, L-T4C) is a cyclic sulfur-containing analog of L-proline found in multiple kingdoms of life. The oxidation of L-T4C leads to L-cysteine formation in bacteria, plants, mammals, and protozoa. The conversion of L-T4C to L-Cys in bacterial cell lysates has been attributed to proline dehydrogenase and L-Δ1-pyrroline-5-carboxylate (P5C) reductase (PYCR) enzymes but detailed kinetic studies have not been conducted. Here, we characterize the dehydrogenase activity of human PYCR isozymes 1 and 2 with L-T4C using NAD(P)+ as the hydride acceptor. Both PYCRs exhibit significant L-T4C dehydrogenase activity; however, PYCR2 displays nearly tenfold higher catalytic efficiency (136 M-1 s-1) than PYCR1 (13.7 M-1 s-1). Interestingly, no activity was observed with either L-Pro or the analog DL-thiazolidine-2-carboxylate, indicating that the sulfur at the 4-position is critical for PYCRs to utilize L-T4C as a substrate. Inhibition kinetics show that L-Pro is a competitive inhibitor of PYCR1 [Formula: see text] with respect to L-T4C, consistent with these ligands occupying the same binding site. We also confirm by mass spectrometry that L-T4C oxidation by PYCRs leads to cysteine product formation. Our results suggest a new enzyme function for human PYCRs in the metabolism of L-T4C.
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Affiliation(s)
- Sagar M Patel
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Javier Seravalli
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Kyle M Stiers
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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Sha Z, Montano MM, Rochon K, Mears JA, Deredge D, Wintrode P, Szweda L, Mikita N, Lee I. A structure and function relationship study to identify the impact of the R721G mutation in the human mitochondrial lon protease. Arch Biochem Biophys 2021; 710:108983. [PMID: 34228963 DOI: 10.1016/j.abb.2021.108983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Lon is an ATP-dependent protease belonging to the "ATPase associated with diverse cellular activities" (AAA+) protein family. In humans, Lon is translated as a precursor and imported into the mitochondria matrix through deletion of the first 114 amino acid residues. In mice, embryonic knockout of lon is lethal. In humans, some dysfunctional lon mutations are tolerated but they cause a developmental disorder known as the CODAS syndrome. To gain a better understanding on the enzymology of human mitochondrial Lon, this study compares the structure-function relationship of the WT versus one of the CODAS mutants R721G to identify the mechanistic features in Lon catalysis that are affected. To this end, steady-state kinetics were used to quantify the difference in ATPase and ATP-dependent peptidase activities between WT and R721G. The Km values for the intrinsic as well as protein-stimulated ATPase were increased whereas the kcat value for ATP-dependent peptidase activity was decreased in the R721G mutant. The mutant protease also displayed substrate inhibition kinetics. In vitro studies revealed that R721G did not degrade the endogenous mitochondrial Lon substrate pyruvate dehydrogenase kinase isoform 4 (PDK4) effectively like WT hLon. Furthermore, the pyruvate dehydrogenase complex (PDH) protected PDK4 from hLon degradation. Using hydrogen deuterium exchange/mass spectrometry and negative stain electron microscopy, structural perturbations associated with the R721G mutation were identified. To validate the in vitro findings under a physiologically relevant condition, the intrinsic stability as well as proteolytic activity of WT versus R721G mutant towards PDK 4 were compared in cell lysates prepared from immortalized B lymphocytes expressing the respective protease. The lifetime of PDK4 is longer in the mutant cells, but the lifetime of Lon protein is longer in the WT cells, which corroborate the in vitro structure-functional relationship findings.
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Affiliation(s)
- Zhou Sha
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Monica M Montano
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kristy Rochon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Patrick Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Luke Szweda
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Natalie Mikita
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA; Department of Chemistry, Missouri Western State University, St. Joseph, MO, 64507, USA.
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
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De Silva AJ, Sehgal R, Kim J, Bellizzi JJ. Steady-state kinetic analysis of halogenase-supporting flavin reductases BorF and AbeF reveals different kinetic mechanisms. Arch Biochem Biophys 2021; 704:108874. [PMID: 33862020 DOI: 10.1016/j.abb.2021.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 11/28/2022]
Abstract
The short-chain flavin reductases BorF and AbeF reduce FAD to FADH2, which is then used by flavin-dependent halogenases (BorH and AbeH respectively) to regioselectively chlorinate tryptophan in the biosynthesis of indolotryptoline natural products. Recombinant AbeF and BorF were overexpressed and purified as homodimers from E. coli, and copurified with substoichiometric amounts of FAD, which could be easily removed. AbeF and BorF can reduce FAD, FMN, and riboflavin in vitro and are selective for NADH over NADPH. Initial velocity studies in the presence and absence of inhibitors showed that BorF proceeds by a sequential ordered kinetic mechanism in which FAD binds first, while AbeF follows a random-ordered sequence of substrate binding. Fluorescence quenching experiments verified that NADH does not bind BorF in the absence of FAD, and that both AbeF and BorF bind FAD with higher affinity than FADH2. pH-rate profiles of BorF and AbeF were bell-shaped with maximum kcat at pH 7.5, and site-directed mutagenesis of BorF implicated His160 and Arg38 as contributing to the catalytic activity and the pH dependence.
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Affiliation(s)
- Aravinda J De Silva
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Rippa Sehgal
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Jennifer Kim
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA.
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Patel SM, Seravalli J, Liang X, Tanner JJ, Becker DF. Disease variants of human Δ 1-pyrroline-5-carboxylate reductase 2 (PYCR2). Arch Biochem Biophys 2021; 703:108852. [PMID: 33771508 DOI: 10.1016/j.abb.2021.108852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Pyrroline-5-carboxylate reductase (PYCR in humans) catalyzes the final step of l-proline biosynthesis by catalyzing the reduction of L-Δ1-pyrroline-5-carboxylate (L-P5C) to l-proline using NAD(P)H as the hydride donor. In humans, three isoforms PYCR1, PYCR2, and PYCR3 are known. Recent genome-wide association and clinical studies have revealed that homozygous mutations in human PYCR2 lead to postnatal microcephaly and hypomyelination, including hypomyelinating leukodystrophy type 10. To uncover biochemical and structural insights into human PYCR2, we characterized the steady-state kinetics of the wild-type enzyme along with two protein variants, Arg119Cys and Arg251Cys, that were previously identified in patients with microcephaly and hypomyelination. Kinetic measurements with PYCR2 suggest a sequential binding mechanism with L-P5C binding before NAD(P)H and NAD(P)+ releasing before L-Pro. Both disease-related variants are catalytically impaired. Depending on whether NADPH or NADH was used, the catalytic efficiency of the R119C protein variant was 40 or 366 times lower than that of the wild-type enzyme, while the catalytic efficiency of the R251C protein variant was 7 or 26 times lower than that of the wild-type enzyme. In addition, thermostability and circular dichroism measurements suggest that the R251C protein variant has a pronounced folding defect. These results are consistent with the involvement of Arg119Cys and Arg251Cys in disease pathology.
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Roberts KM, Connor GC, Cave CH, Rowe GT, Page CA. The metal- and substrate-dependences of 2,4'-dihydroxyacetophenone dioxygenase. Arch Biochem Biophys 2020; 691:108441. [PMID: 32531315 DOI: 10.1016/j.abb.2020.108441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
While the enzyme, 2,4'-dihydroxyacetophenone dioxygenase (DAD), has been known for decades, very little has been characterized of the mechanism of the DAD-catalyzed oxidative cleavage of its reported substrate, 2,4'-dihydroxyacetophenone (DHA). The purpose of this study was to identify the active metal center and to characterize the substrate-dependence of the kinetics of the reaction to lay the foundation for deeper mechanistic investigation. To this, the DAD V1M mutant (bDAD) was overexpressed, purified, and reconstituted with various metal ions. Kinetic assays evaluating the activity of the reconstituted enzyme as well as the substrate- and product-dependences of the reaction kinetics were performed. The results from reconstitution of the apoprotein with a variety of metal ions support the requirement for an Fe3+ center for enzyme activity. Reaction rates showed simple saturation kinetics for DHA with values for kcat and KDHA of 2.4 s-1 and 0.7 μM, respectively, but no significant dependence on the concentration of O2. A low-level inhibition (KI = 1100 μM) by the 4HB product was observed. The results support a minimal kinetic model wherein DHA binds to resting ferric enzyme followed by rapid addition of O2 to yield an intermediate complex that irreversibly collapses to products.
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Affiliation(s)
- Kenneth M Roberts
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Gabrielle C Connor
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - C Haley Cave
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Gerard T Rowe
- Department of Chemistry and Physics, University of South Carolina Aiken, Aiken, SC, 29801, USA.
| | - Clinton A Page
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, 29801, USA.
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Yang F, Liu L, Liu Y, Li S. Effect of K225 residue to the catalytic efficiency of Kex2 protease. Protein Expr Purif 2020; 176:105725. [PMID: 32800900 DOI: 10.1016/j.pep.2020.105725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/14/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
The gene encoding S. cerevisiae Kex2 protease derivative Kex2-667 (encoding the N-terminal 20th to 667th amino acid residues of Kex2 protease, containing the propeptide, catalytic domain, P domain and Ser/Thr enrichment region) and its 225th amino acid residue mutant K225L were overexpressed in Pichia pastoris. Proteases were purified by dialysis and anion exchange chromatography (Q-FF). Their properties were further investigated. For catalysis efficiency, the value of Kcat/Km of Kex2-667-K225L was 3 folds higher than that of Kex2-667. Both were quite stable at 25 °C and 37 °C after 8 h of incubation at pH5.6, while Kex2-667 remained nearly 90% of the total activity while Kex2-667-K225L remained only 80%. The stability of Kex2-667-K225L was lower than that of Kex2-667 from pH4.0 to pH9.0. Due to the mutation site K225 was located at one of the calcium ion binding sites, it resulted in a tighter calcium ion binding region, which may be the reason why the catalytic efficiency of Kex2-667-K225L was improved while the stability was a little decreased.
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Affiliation(s)
- Fan Yang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology, 200237, Shanghai, China
| | - Li Liu
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology, 200237, Shanghai, China
| | - Yingying Liu
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology, 200237, Shanghai, China
| | - Suxia Li
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology, 200237, Shanghai, China.
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13
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Rejali NA, Zuiter AM, Quackenbush JF, Wittwer CT. Reverse transcriptase kinetics for one-step RT-PCR. Anal Biochem 2020; 601:113768. [PMID: 32416095 DOI: 10.1016/j.ab.2020.113768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
Understanding reverse transcriptase (RT) activity is critical for designing fast one-step RT-PCRs. We report a stopped-flow assay that monitors SYBR Green I fluorescence to investigate RT activity in PCR conditions. We studied the influence of PCR conditions on RT activity and assessed the accuracy of cDNA synthesis predictions for one-step RT-PCR. Nucleotide incorporation increased from 26 to 89 s-1 between 1.5 and 6 mM MgCl2 but was largely unaffected by changes in KCl. Conversely, increasing KCl from 15 to 75 mM increased apparent rate constants for RT-oligonucleotide binding (0.010-0.026 nM-1 s-1) and unbinding (0.2-1.5 s-1). All rate constants increased between 22 and 42 °C. When evaluated by PCR quantification cycle, cDNA predictions differed from experiments using RNase H+ RT (average 1.7 cycles) and RNase H- (average 4.5 cycles). Decreasing H+ RT concentrations 10 to 104-fold from manufacturer recommendations improved cDNA predictions (average 0.8 cycles) and increased RT-PCR assay efficiency. RT activity assays and models can be used to aid assay design and improve the speed of RT-PCRs. RT type and concentration must be selected to promote rapid cDNA synthesis but minimize nonspecific amplification. We demonstrate 2-min one-step RT-PCR of a Zika virus target using reduced RT concentrations and extreme PCR.
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Affiliation(s)
- Nick A Rejali
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Aisha M Zuiter
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - John F Quackenbush
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA.
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14
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Abstract
This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.
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15
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Du K, Zhang X, Zou Z, Li B, Gu S, Zhang S, Qu X, Ling Y, Zhang H. Epigenetically modified N 6-methyladenine inhibits DNA replication by human DNA polymerase η. DNA Repair (Amst) 2019; 78:81-90. [PMID: 30991231 DOI: 10.1016/j.dnarep.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 01/06/2023]
Abstract
N6-methyladenine (6mA), as a newly reported epigenetic marker, plays significant roles in regulation of various biological processes in eukaryotes. However, the effect of 6mA on human DNA replication remain elusive. In this work, we used Y-family human DNA polymerase η as a model to investigate the kinetics of bypass of 6mA by hPol η. We found 6mA and its intermediate hypoxanthine (I) on template partially inhibited DNA replication by hPol η. dTMP incorporation opposite 6mA and dCMP incorporation opposite I can be considered as correct incorporation. However, both 6mA and I reduced correct incorporation efficiency, next-base extension efficiency, and the priority in extension beyond correct base pair. Both dTMP incorporation opposite 6mA and dCTP opposite I showed fast burst phases. However, 6mA and I reduced the burst incorporation rates (kpol) and increased the dissociation constant (Kd,dNTP), compared with that of dTMP incorporation opposite unmodified A. Biophysical binding assays revealed that both 6mA and I on template reduced the binding affinity of hPol η to DNA in binary or ternary complex compared with unmodified A. All the results explain the inhibition effects of 6mA and I on DNA replication by hPol η, providing new insight in the effects of epigenetically modified 6mA on human DNA replication.
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Affiliation(s)
- Ke Du
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China; Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiangqian Zhang
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Bianbian Li
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shiling Gu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoyi Qu
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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16
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Hwang CC, Chang PR, Hsieh CL, Chou YH, Wang TP. Thermodynamic analysis of remote substrate binding energy in 3α-hydroxysteroid dehydrogenase/carbonyl reductase catalysis. Chem Biol Interact 2019; 302:183-189. [PMID: 30794798 DOI: 10.1016/j.cbi.2019.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/30/2019] [Accepted: 02/14/2019] [Indexed: 11/16/2022]
Abstract
The binding energy of enzyme and substrate is used to lower the activation energy for the catalytic reaction. 3α-HSD/CR uses remote binding interactions to accelerate the reaction of androsterone with NAD+. Here, we examine the enthalpic and entropic components of the remote binding energy in the 3α-HSD/CR-catalyzed reaction of NAD+ with androsterone versus the substrate analogs, 2-decalol and cyclohexanol, by analyzing the temperature-dependent kinetic parameters through steady-state kinetics. The effects of temperature on kcat/Km for 3α-HSD/CR acting on androsterone, 2-decalol, and cyclohexanol show the reactions are entropically favorable but enthalpically unfavorable. Thermodynamic analysis from the temperature-dependent values of Km and kcat shows the binding of the E-NAD+ complex with either 2-decalol or cyclohexanol to form the ternary complex is endothermic and entropy-driven, and the subsequent conversion to the transition state is both enthalpically and entropically unfavorable. Hence, solvation entropy may play an important role in the binding process through both the desolvation of the solute molecules and the release of bound water molecules from the active site into bulk solvent. As compared to the thermodynamic parameters of 3α-HSD/CR acting on cyclohexanol, the hydrophobic interaction of the B-ring of steroids with the active site of 3α-HSD/CR contributes to catalysis by increasing exclusively the entropy of activation (ΔTΔS‡ = 1.8 kcal/mol), while the BCD-ring of androsterone significantly lowers ΔΔH‡ by 10.4 kcal/mol with a slight entropic penalty of -1.9 kcal/mol. Therefore, the remote non-reacting sites of androsterone may induce a conformational change of the substrate binding loop with an entropic cost for better interaction with the transition state to decrease the enthalpy of activation, significantly increasing catalytic efficiency.
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Affiliation(s)
- Chi-Ching Hwang
- Department of Biochemistry, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
| | - Pei-Ru Chang
- Department of Biochemistry, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Chia-Lin Hsieh
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Yun-Hao Chou
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
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17
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Abstract
The chapter focuses on the methods involved in producing and characterizing two key nickel-iron-sulfur enzymes in the Wood-Ljungdahl pathway (WLP) of anaerobic conversion of carbon dioxide fixation into acetyl-CoA: carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS). The WLP is used for biosynthesis of cell material and energy conservation by anaerobic bacteria and archaea, and it is central to several industrial biotechnology processes aimed at using syngas and waste gases for the production of fuels and chemicals. The pathway can run in reverse to allow organisms, e. g., methanogens and sulfate reducers, to grow on acetate. The CODH and ACS intertwine to form a tenacious CODH/ACS complex that converts CO2, a methyl group, and coenzyme A into acetyl-CoA. CODH also behaves as a modular unit that can function as an independent homodimer. Besides coupling to ACS, CODH can interact with hydrogenases to couple CO oxidation to H2 formation. These enzymes have been purified and characterized from several microbes.
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Affiliation(s)
- Rodney Burton
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Daniel Esckilsen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Seth Wiley
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States.
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18
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Gurevic I, Islam Z, Świderek K, Trepka K, Ghosh AK, Moliner V, Kohen A. Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase. ACS Catal 2018; 8:10241-10253. [PMID: 31275729 DOI: 10.1021/acscatal.8b02554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TSase), an enzyme responsible for the de novo biosynthesis of 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) necessary for DNA synthesis, has been a drug target for decades. TSase is a highly conserved enzyme across species ranging from very primitive organisms to mammals. Among the many conserved active site residues, an asparagine (N177, using Escherichia coli residues numbering) appears to make direct hydrogen bonds with both the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate and its pyrimidine ring's N3. Recent studies have reassessed the TSase catalytic mechanism, focusing on the degree of negative charge accumulation at the O4 carbonyl of the substrate during two critical H-transfers - a proton abstraction and a hydride transfer. To obtain insights into the role of this conserved N177 on the hydride transfer, we examined its aspartic acid (D) and serine (S) mutants - each of which is expected to alter hydrogen bonding and charge stabilization around the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate. Steady-state kinetics, substrate binding order studies and temperature-dependency analysis of intrinsic KIEs for the hydride transfer step of the TSase catalytic cycle suggest the active site of N177D is not precisely organized for that step. A smaller disruption was observed for N177S, which could be rationalized by partial compensation by water molecules and rearrangement of other residues toward preparation of the system for the hydride transfer under study. These experimental findings are qualitatively mirrored by QM/MM computational simulations, thereby shedding light on the sequence and synchronicity of steps in the TSase-catalyzed reaction. This information could potentially inform the design of mechanism-based drugs targeting this enzyme.
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Affiliation(s)
- Ilya Gurevic
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Zahidul Islam
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Kai Trepka
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Ananda K. Ghosh
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
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19
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Wells EA, Anderson MA, Zeczycki TN. 15(V/K) kinetic isotope effect and steady-state kinetic analysis for the transglutaminase 2 catalyzed deamidation and transamidation reactions. Arch Biochem Biophys 2018; 643:57-61. [PMID: 29477769 DOI: 10.1016/j.abb.2018.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/18/2018] [Accepted: 02/19/2018] [Indexed: 10/18/2022]
Abstract
The Ca2+-dependent deamidation and transamidation activities of transglutaminase 2 (TG2) are important to numerous physiological and pathological processes. Herein, we have examined the steady-state kinetics and 15(V/K) kinetic isotope effects (KIEs) for the TG2-catalyzed deamidation and transamidation of N-Benzyloxycarbonyl-l-Glutaminylglycine (Z-Gln-Gly) using putrescine as the acyl acceptor substrate. Kinetic parameters determined from initial velocity plots are consistent with previously proposed mechanisms. Significant differences in the 15(V/K) KIEs on NH3 release determined for the deamidation (0.2%) and the transamidation (2.3%) of Z-Gln-Gly suggest the rate-limiting steps of TG2 active site acylation are dependent on the presence of the acyl acceptor. We propose a plausible mechanistic explanation where substrate-induced conformational changes may play a role in promoting catalysis.
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Affiliation(s)
- Evan A Wells
- Department of Biochemistry and Molecular Biology and the East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University, Greenville, NC, United States
| | - Mark A Anderson
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology and the East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University, Greenville, NC, United States.
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20
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Hon J, Hwang MS, Charnetzki MA, Rashed IJ, Brady PB, Quillin S, Makinen MW. Kinetic characterization of the inhibition of protein tyrosine phosphatase-1B by Vanadyl (VO 2+) chelates. J Biol Inorg Chem 2017; 22:1267-1279. [PMID: 29071441 DOI: 10.1007/s00775-017-1500-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Protein tyrosine phosphatases (PTPases) are a prominent focus of drug design studies because of their roles in homeostasis and disorders of metabolism. These studies have met with little success because (1) virtually all inhibitors hitherto exhibit only competitive behavior and (2) a consensus sequence H/V-C-X5-R-S/T characterizes the active sites of PTPases, leading to low specificity of active site directed inhibitors. With protein tyrosine phosphatase-1B (PTP1B) identifed as the target enzyme of the vanadyl (VO2+) chelate bis(acetylacetonato)oxidovanadium(IV) [VO(acac)2] in 3T3-L1 adipocytes [Ou et al. J Biol Inorg Chem 10: 874-886, 2005], we compared the inhibition of PTP1B by VO(acac)2 with other VO2+-chelates, namely, bis(2-ethyl-maltolato)oxidovanadium(IV) [VO(Et-malto)2] and bis(3-hydroxy-2-methyl-4(1H)pyridinonato)oxidovanadium(IV) [VO(mpp)2] under steady-state conditions, using the soluble portion of the recombinant human enzyme (residues 1-321). Our results differed from those of previous investigations because we compared inhibition in the presence of the nonspecific substrate p-nitrophenylphosphate and the phosphotyrosine-containing undecapeptide DADEpYLIPQQG mimicking residues 988-998 of the epidermal growth factor receptor, a relevant, natural substrate. While VO(Et-malto)2 acts only as a noncompetitive inhibitor in the presence of either subtrate, VO(acac)2 exhibits classical uncompetitive inhibition in the presence of DADEpYLIPQQG but only apparent competitive inhibition with p-nitrophenylphosphate as substrate. Because uncompetitive inhibitors are more potent pharmacologically than competitive inhibitors, structural characterization of the site of uncompetitive binding of VO(acac)2 may provide a new direction for design of inhibitors for therapeutic purposes. Our results suggest also that the true behavior of other inhibitors may have been masked when assayed with only p-nitrophenylphosphate as substrate.
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Affiliation(s)
- Jason Hon
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Michelle S Hwang
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Meara A Charnetzki
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Issra J Rashed
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Patrick B Brady
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Sarah Quillin
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Marvin W Makinen
- Department of Biochemistry and Molecular Biology Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
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21
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Gu S, Xiong J, Shi Y, You J, Zou Z, Liu X, Zhang H. Error-prone bypass of O 6-methylguanine by DNA polymerase of Pseudomonas aeruginosa phage PaP1. DNA Repair (Amst) 2017. [PMID: 28651167 DOI: 10.1016/j.dnarep.2017.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O6-Methylguanine (O6-MeG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, generally leads to G:C to A:T mutagenesis. To study DNA replication encountering O6-MeG by the DNA polymerase (gp90) of P. aeruginosa phage PaP1, we analyzed steady-state and pre-steady-state kinetics of nucleotide incorporation opposite O6-MeG by gp90 exo-. O6-MeG partially inhibited full-length extension by gp90 exo-. O6-MeG greatly reduces dNTP incorporation efficiency, resulting in 67-fold preferential error-prone incorporation of dTTP than dCTP. Gp90 exo- extends beyond T:O6-MeG 2-fold more efficiently than C:O6-MeG. Incorporation of dCTP opposite G and incorporation of dCTP or dTTP opposite O6-MeG show fast burst phases. The pre-steady-state incorporation efficiency (kpol/Kd,dNTP) is decreased in the order of dCTP:G>dTTP:O6-MeG>dCTP:O6-MeG. The presence of O6-MeG at template does not affect the binding affinity of polymerase to DNA but it weakened their binding in the presence of dCTP and Mg2+. Misincorporation of dTTP opposite O6-MeG further weakens the binding affinity of polymerase to DNA. The priority of dTTP incorporation opposite O6-MeG is originated from the fact that dTTP can induce a faster conformational change step and a faster chemical step than dCTP. This study reveals that gp90 bypasses O6-MeG in an error-prone manner and provides further understanding in DNA replication encountering mutagenic alkylation DNA damage for P. aeruginosa phage PaP1.
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Affiliation(s)
- Shiling Gu
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Jingyuan Xiong
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Ying Shi
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Jia You
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Zhenyu Zou
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Xiaoying Liu
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Huidong Zhang
- Public Health Laboratory Sciences and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China.
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22
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Hwang CC, Chang PR, Wang TP. Contribution of remote substrate binding energy to the enzymatic rate acceleration for 3α-hydroxysteroid dehydrogenase/carbonyl reductase. Chem Biol Interact 2017; 276:133-140. [PMID: 28137513 DOI: 10.1016/j.cbi.2017.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/20/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
3α-Hydroxysteroid dehydrogenase/carbonyl reductase (3α-HSD/CR) catalyzes the oxidation of androsterone with NAD+ to form androstanedione and NADH with the rate limiting step being the release of NADH. In this study, we elucidate the role of remote substrate binding interactions contributing to the rate enhancement by 3α-HSD/CR through steady-state kinetic studies with the truncated substrate analogs. No enzyme activity was detected for methanol, ethanol, and 2-propanol, which lack the steroid scaffold of androsterone, implying that the steroid scaffold plays an important role in enzyme catalytic specificity. As compared to cyclohexanol, the activity for 2-decalol, androstenol, and androsterone increases by 0.9-, 90-, and 200-fold in kcat, and 37-, 1.9 × 106-, and 1.8 × 106-fold in kcat/KB, respectively. The rate limiting step is hydride transfer for 3α-HSD/CR catalyzing the reaction of cyclohexanol with NAD+ based on the observed rapid equilibrium ordered mechanism and equal deuterium isotope effects of 3.9 on V and V/K for cyclohexanol. The kcat/KB value results in ΔG‡ of 14.7, 12.6, 6.2, and 6.2 kcal/mol for the 3α-HSD/CR catalyzed reaction of cyclohexanol, 2-decalol, androstenol, and androsterone, respectively. Thus, the uniform binding energy from the B-ring of steroids with the active site of 3α-HSD/CR equally contributes 2.1 kcal/mol to stabilize both the transition state and ground state of the ternary complex, leading to the similarity in kcat for 2-decalol and cyclohexanol. Differential binding interactions of the remote BCD-ring and CD-ring of androsterone with the active site of 3α-HSD/CR contribute 8.5 and 6.4 kcal/mol to the stabilization of the transition state, respectively. The removal of the carbonyl group at C17 of androsterone has small effects on catalysis. Both uniform and differential binding energies from the remote sites of androsterone compared to cyclohexanol contribute to the 3α-HSD/CR catalysis, resulting in the increases in kcat and kcat/KB.
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Affiliation(s)
- Chi-Ching Hwang
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
| | - Pei-Ru Chang
- Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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23
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Sehanobish E, Dow BA, Davidson VL. Analytical Methods for Assessing the Effects of Site-Directed Mutagenesis on Protein-Cofactor and Protein-Protein Functional Relationships. Methods Mol Biol 2017; 1498:421-438. [PMID: 27709593 DOI: 10.1007/978-1-4939-6472-7_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To completely understand the role of an amino acid residue that is targeted for site-directed mutagenesis a thorough analysis of the impact that the mutation has on the function of the protein is required. General methods for performing site-directed mutagenesis and expressing the recombinant protein variant are described. Protein-cofactor interactions are important because cofactors are often directly involved in facilitating catalysis by enzymes and in electron transfer by redox proteins. Many cofactors also have characteristic spectroscopic properties. As such, general methods are described to analyze the spectroscopic, redox and catalytic properties of protein-bound cofactors. Methods for assessing the effects of a mutation on protein-protein interactions are also described. Lastly, methods for assessing the overall structural integrity of the protein are described, as this is important to ensure that the mutation has not caused a global disruption of protein structure, rather than a specific effect on function.
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Affiliation(s)
- Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA.
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Le CQ, Oyugi M, Joseph E, Nguyen T, Ullah MH, Aubert J, Phan T, Tran J, Johnson-Winters K. Effects of isoleucine 135 side chain length on the cofactor donor-acceptor distance within F 420H 2:NADP + oxidoreductase: A kinetic analysis. Biochem Biophys Rep 2017; 9:114-20. [PMID: 28955995 DOI: 10.1016/j.bbrep.2016.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/22/2016] [Indexed: 10/29/2022] Open
Abstract
F420H2:NADP+ Oxidoreductase (Fno) catalyzes the reversible reduction of NADP+ to NADPH by transferring a hydride from the reduced F420 cofactor. Here, we have employed binding studies, steady-state and pre steady-state kinetic methods upon wtFno and isoleucine 135 (I135) Fno variants in order to study the effects of side chain length on the donor-acceptor distance between NADP+ and the F420 precursor, FO. The conserved I135 residue of Fno was converted to a valine, alanine and glycine, thereby shortening the side chain length. The steady-state kinetic analysis of wtFno and the variants showed classic Michaelis-Menten kinetics with varying FO concentrations. The data revealed a decreased kcat as side chain length decreased, with varying FO concentrations. The steady-state plots revealed non-Michaelis-Menten kinetic behavior when NADPH was varied. The double reciprocal plot of the varying NADPH concentrations displays a downward concave shape, while the NADPH binding curves gave Hill coefficients of less than 1. These data suggest that negative cooperativity occurs between the two identical monomers. The pre steady-state Abs420 versus time trace revealed biphasic kinetics, with a fast phase (hydride transfer) and a slow phase. The fast phase displayed an increased rate constant as side chain length decreased. The rate constant for the second phase, remained ~2 s-1 for each variant. Our data suggest that I135 plays a key role in sustaining the donor-acceptor distance between the two cofactors, thereby regulating the rate at which the hydride is transferred from FOH2 to NADP+. Therefore, Fno is a dynamic enzyme that regulates NADPH production.
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Key Words
- Dissociation constants
- E. coli,, Escherichia coli
- F420 cofactor
- F420 cofactor, 7,8-didemethyl-8-hydroxy-5-deazariboflavin-5′-phosphoryllactyl(glutamyl)nglutamate, A. fulgidus, Archaeoglobus fulgidus
- F420H2: NADP+ oxidoreductase
- FO, precursor of F420 cofactor
- Fno, F420H2:NADP+, oxidoreductase
- Half-site reactivity
- I135, Isoleucine 135
- IPTG, isopropyl β-D-1-thiogalactopyranoside
- Kd,, dissociation constant
- Km, Michaelis-Menten constant
- LB, Luria Bertani broth
- NADP
- NADP+, nicotinamide adenine dinucleotide phosphate
- Negative cooperativity
- PEI, Polyethyleneimine
- Pre steady-state kinetics
- Steady-state kinetics
- k, rate constant
- kcat, catalytic rate constant (turnover number), kcat /Km, catalytic efficiency
- wtFno, wild-type Fno
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25
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Perez-Abraham R, Sanchez KG, Alfonso M, Gubler U, Siekierka JJ, Goodey NM. Expression, purification and enzymatic characterization of Brugia malayi dihydrofolate reductase. Protein Expr Purif 2016; 128:81-5. [PMID: 27544923 DOI: 10.1016/j.pep.2016.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 11/16/2022]
Abstract
Brugia malayi (B. malayi) is one of the three causative agents of lymphatic filariasis, a neglected parasitic disease. Current literature suggests that dihydrofolate reductase is a potential drug target for the elimination of B. malayi. Here we report the recombinant expression and purification of a ∼20 kDa B. malayi dihydrofolate reductase (BmDHFR). A His6-tagged construct was expressed in E. coli and purified by affinity chromatography to yield active and homogeneous enzyme for steady-state kinetic characterization and inhibition studies. The catalytic activity kcat was found to be 1.4 ± 0.1 s(-1), the Michaelis Menten constant KM for dihydrofolate 14.7 ± 3.6 μM, and the equilibrium dissociation constant KD for NADPH 25 ± 24 nM. For BmDHFR, IC50 values for a six DHFR inhibitors were determined to be 3.1 ± 0.2 nM for methotrexate, 32 ± 22 μM for trimethoprim, 109 ± 34 μM for pyrimethamine, 154 ± 46 μM for 2,4-diaminoquinazoline, 771 ± 44 μM for cycloguanil, and >20,000 μM for 2,4-diaminopyrimidine. Our findings suggest that antifolate compounds can serve as inhibitors of BmDHFR.
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Affiliation(s)
- Romy Perez-Abraham
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA
| | - Karla Garabiles Sanchez
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA
| | - Melany Alfonso
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA
| | - Ueli Gubler
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA
| | - John J Siekierka
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA
| | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, NJ, 07043, USA.
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Yu W, Neckles C, Chang A, Bommineni GR, Spagnuolo L, Zhang Z, Liu N, Lai C, Truglio J, Tonge PJ. A [(32)P]NAD(+)-based method to identify and quantitate long residence time enoyl-acyl carrier protein reductase inhibitors. Anal Biochem 2015; 474:40-9. [PMID: 25684450 PMCID: PMC4454744 DOI: 10.1016/j.ab.2014.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 01/26/2023]
Abstract
The classical methods for quantifying drug-target residence time (tR) use loss or regain of enzyme activity in progress curve kinetic assays. However, such methods become imprecise at very long residence times, mitigating the use of alternative strategies. Using the NAD(P)H-dependent FabI enoyl-acyl carrier protein (enoyl-ACP) reductase as a model system, we developed a Penefsky column-based method for direct measurement of tR, where the off-rate of the drug was determined with radiolabeled [adenylate-(32)P]NAD(P(+)) cofactor. In total, 23 FabI inhibitors were analyzed, and a mathematical model was used to estimate limits to the tR values of each inhibitor based on percentage drug-target complex recovery following gel filtration. In general, this method showed good agreement with the classical steady-state kinetic methods for compounds with tR values of 10 to 100 min. In addition, we were able to identify seven long tR inhibitors (100-1500 min) and to accurately determine their tR values. The method was then used to measure tR as a function of temperature, an analysis not previously possible using the standard kinetic approach due to decreased NAD(P)H stability at elevated temperatures. In general, a 4-fold difference in tR was observed when the temperature was increased from 25 to 37 °C.
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Affiliation(s)
- Weixuan Yu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Carla Neckles
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Andrew Chang
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Gopal Reddy Bommineni
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Lauren Spagnuolo
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Zhuo Zhang
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Nina Liu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Christina Lai
- Great Neck South High School, Great Neck, NY 11020, USA
| | - James Truglio
- Great Neck South High School, Great Neck, NY 11020, USA
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
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Phillips RS. Chemistry and diversity of pyridoxal-5'-phosphate dependent enzymes. Biochim Biophys Acta 2015; 1854:1167-74. [PMID: 25615531 DOI: 10.1016/j.bbapap.2014.12.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 12/01/2022]
Abstract
Pyridoxal-5'-phosphate (PLP) is a versatile cofactor that enzymes use to catalyze a wide variety of reactions of amino acids, including transamination, decarboxylation, racemization, β- and γ-eliminations and substitutions, retro-aldol and Claisen reactions. These reactions depend on the ability of PLP to stabilize, to a varying degree, α-carbanionic intermediates. Furthermore, oxidative decarboxylations and rearrangements suggest that PLP can stabilize radical intermediates as well. The reaction mechanisms of two PLP-dependent enzymes are discussed, kynureninase and tyrosine phenol-lyase (TPL). Kynureninase catalyzes a retro-Claisen reaction of kynurenine to give anthranilate and alanine. The key step, hydration of the γ-carbonyl, is assisted by acid-base catalysis with the phosphate of the PLP, mediated by a conserved tyrosine, and an oxyanion hole. TPL catalyzes the reversible elimination of phenol, a poor leaving group, from l-tyrosine. In TPL, the Cβ-Cγ bond cleavage is accelerated by ground state strain from the bending of the substrate ring out of the plane with the Cβ-Cγ bond. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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28
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Paukner R, Staudigl P, Choosri W, Haltrich D, Leitner C. Expression, purification, and characterization of galactose oxidase of Fusarium sambucinum in E. coli. Protein Expr Purif 2015; 108:73-9. [PMID: 25543085 DOI: 10.1016/j.pep.2014.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 11/01/2022]
Abstract
A gene encoding a galactose oxidase (GalOx) was isolated from Fusarium sambucinum cultures and overexpressed in Escherichia coli yielding 4.4mg enzyme per L of growth culture with a specific activity of 159Umg(-1). By adding a C-terminal His-tag the enzyme could be easily purified with a single affinity chromatography step with high recovery rate (90%). The enzyme showed a single band on SDS-PAGE with an apparent molecular mass of 68.5kDa. The pH optimum for the oxidation of galactose was in the range of pH 6-7.5. Optimum temperature for the enzyme activity was 35°C, with a half-life of 11.2min, 5.3min, and 2.7min for incubation at 40°C, 50°C, and 60°C, respectively. From all tested substrates, the highest relative activity was found for 1-methyl-β-galactopyranoside (226Umg(-1)) and the highest catalytic efficiency (kcat/Km) for melibiose (2700mM(-1)s(-1)). The enzyme was highly specific for molecular oxygen as an electron acceptor, and showed no appreciable activity with a range of alternative acceptors investigated. Different chemicals were tested for their effect on GalOx activity. The activity was significantly reduced by EDTA, NaN3, and KCN.
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29
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Vardakou M, Salmon M, Faraldos JA, O'Maille PE. Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases. MethodsX 2014; 1:187-96. [PMID: 26150952 DOI: 10.1016/j.mex.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/15/2014] [Indexed: 11/21/2022] Open
Abstract
Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.
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30
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Khatri Y, Luthra A, Duggal R, Sligar SG. Kinetic solvent isotope effect in steady-state turnover by CYP19A1 suggests involvement of Compound 1 for both hydroxylation and aromatization steps. FEBS Lett 2014; 588:3117-22. [PMID: 24997347 DOI: 10.1016/j.febslet.2014.06.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/03/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
Abstract
CYP19A1, or human aromatase catalyzes the conversion of androgens to estrogens in a three-step reaction through the formation of 19-hydroxy and 19-aldehyde intermediates. While the first two steps of hydroxylation are thought to proceed through a high-valent iron-oxo species, controversy exists surrounding the identity of the reaction intermediate that catalyzes the lyase and aromatization reaction. We investigated the kinetic isotope effect on the steady-state turnover of Nanodisc-incorporated human CYP19A1 to explore the mechanisms of this reaction. Our experiments reveal a significant (∼ 2.5) kinetic solvent isotope effect for the C10-C19 lyase reaction, similar to that of the first two hydroxylation steps (2.7 and 1.2). These data implicate the involvement of Compound 1 as a reactive intermediate in the final aromatization step of CYP19A1.
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Affiliation(s)
- Yogan Khatri
- Department of Biochemistry, University of Illinois Urbana-Champaign, 505 S. Goodwin Avenue, Urbana, IL 61801, United States
| | - Abhinav Luthra
- Department of Biochemistry, University of Illinois Urbana-Champaign, 505 S. Goodwin Avenue, Urbana, IL 61801, United States
| | - Ruchia Duggal
- Department of Biochemistry, University of Illinois Urbana-Champaign, 505 S. Goodwin Avenue, Urbana, IL 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois Urbana-Champaign, 505 S. Goodwin Avenue, Urbana, IL 61801, United States.
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31
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Sugii T, Akanuma S, Yagi S, Yagyu K, Shimoda Y, Yamagishi A. Characterization of the low-temperature activity of Sulfolobus tokodaii glucose-1-dehydrogenase mutants. J Biosci Bioeng 2014; 118:367-71. [PMID: 24742629 DOI: 10.1016/j.jbiosc.2014.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/22/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Thermophilic enzymes are potentially useful for industrial processes because they are generally more stable than are mesophilic or psychrophilic enzymes. However, a crucial drawback for their use in such processes is that most thermophilic enzymes are nearly inactive at moderate and low temperatures. We have previously proposed that modulation of the coenzyme-binding pocket of thermophilic dehydrogenases can produce mutated proteins with enhanced low-temperature activities. In the current study, we produced and characterized mutants of an NADP-dependent glucose-1-dehydrogenase from the hyperthermophile Sulfolobus tokodaii in which a predicted coenzyme-binding, non-polar residue was replaced by another non-polar residue. Detailed analyses of the kinetic properties of the wild-type enzyme and its mutants showed that one of the mutants (V254I) had improved kcat and kcat/Km values at both 25°C and 80°C. Temperature-induced unfolding experiments showed that the thermal stability of the mutant enzyme was comparable to that of the wild-type enzyme. Calculation of the energetic contribution of the V254I mutation for the dehydrogenase reaction revealed that the mutation destabilizes the enzyme-NADP(+)-glucose ternary complex and reduces the transition-state energy, thus enhancing catalysis.
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Affiliation(s)
- Taisuke Sugii
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Akanuma
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Sota Yagi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kazuki Yagyu
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yukiko Shimoda
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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32
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Dempsey DR, Bond JD, Carpenter AM, Rodriguez Ospina S, Merkler DJ. Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expr Purif 2014; 97:23-8. [PMID: 24576660 DOI: 10.1016/j.pep.2014.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/14/2014] [Accepted: 02/16/2014] [Indexed: 11/24/2022]
Abstract
Glycine N-acyltransferase (GLYAT) is a phase II metabolic detoxification enzyme for exogenous (xenobiotic) and endogenous carboxylic acids; consisting of fatty acids, benzoic acid, and salicylic acid. GLYAT catalyzes the formation of hippurate (N-benzoylglycine) from the corresponding glycine and benzoyl-CoA. Herein, we report the successful expression, purification, and characterization of recombinant mouse GLYAT (mGLYAT). A 34kDa mGLYAT protein was expressed in Escherichia coli and purified to homogeneity by nickel affinity chromatography to a final yield of 2.5mg/L culture. Characterization for both amino donors and amino acceptors were completed, with glycine serving as the best amino donor substrate, (kcat/Km)app=(5.2±0.20)×10(2)M(-1)s(-1), and benzoyl-CoA serving as the best the amino acceptor substrate, (kcat/Km)app=(4.5±0.27)×10(5)M(-1)s(-1). Our data demonstrate that mGLYAT will catalyzed the chain length specific (C2-C6) formation of N-acylglycines. The steady-state kinetic constants determined for recombinant mGLYAT for the substrates benzoyl-CoA and glycine, were shown to be consistent with other reported species (rat, human, bovine, ovine, and rhesus monkey). The successful recombinant expression and purification of mGLYAT can lead to solve unanswered questions associated with this enzyme, consisting of what is the chemical mechanism and what catalytic residues are essential for the how this phase II metabolic detoxification enzyme conjugates glycine to xenobiotic and endogenous carboxylic acids.
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33
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Dempsey DR, Jeffries KA, Anderson RL, Carpenter AM, Rodriquez Opsina S, Merkler DJ. Identification of an arylalkylamine N-acyltransferase from Drosophila melanogaster that catalyzes the formation of long-chain N-acylserotonins. FEBS Lett 2014; 588:594-9. [PMID: 24444601 DOI: 10.1016/j.febslet.2013.12.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/11/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022]
Abstract
Arylalkylamine N-acyltransferase-like 2(2) (AANATL2) from Drosophila melanogaster was expressed and shown to catalyze the formation of long-chain N-acylserotonins and N-acydopamines. Subsequent identification of endogenous amounts of N-acylserotonins and colocalization of these fatty acid amides and AANATL2 transcripts gives supporting evidence that AANATL2 has a role in the biosynthetic formation of these important cell signalling lipids.
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Affiliation(s)
- Daniel R Dempsey
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Kristen A Jeffries
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Ryan L Anderson
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | | | | | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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34
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Miller JM, Lucius AL. ATPγS competes with ATP for binding at Domain 1 but not Domain 2 during ClpA catalyzed polypeptide translocation. Biophys Chem 2013; 185:58-69. [PMID: 24362308 DOI: 10.1016/j.bpc.2013.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 11/30/2022]
Abstract
ClpAP is an ATP-dependent protease that assembles through the association of hexameric rings of ClpA with the cylindrically-shaped protease ClpP. ClpA contains two nucleotide binding domains, termed Domain 1 (D1) or 2 (D2). We have proposed that D1 or D2 limits the rate of ClpA catalyzed polypeptide translocation when ClpP is either absent or present, respectively. Here we show that the rate of ClpA catalyzed polypeptide translocation depends on [ATPγS] in the absence of ClpP, but not in the presence of ClpP. We observe that ATPγS non-cooperatively binds to ClpA during polypeptide translocation with an apparent affinity of ~6 μM, but that introduction of ClpP shifts this affinity such that translocation is not affected. Interpreting these data with our proposed model for translocation catalyzed by ClpA vs. ClpAP suggests that ATPγS competes for binding at D1 but not at D2.
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Affiliation(s)
- Justin M Miller
- Department of Chemistry, The University of Alabama at Birmingham, 1530 3rd Ave S, Birmingham, AL 35294-1240, United States
| | - Aaron L Lucius
- Department of Chemistry, The University of Alabama at Birmingham, 1530 3rd Ave S, Birmingham, AL 35294-1240, United States.
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