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Demir M, Koepping L, Li Y, Fujimoto L, Bobkov A, Zhao J, Hitosugi T, Sergienko E. Structural Basis for Substrate Binding, Catalysis and Inhibition of Breast Cancer Target Mitochondrial Creatine Kinase by Covalent Inhibitor via Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.598884. [PMID: 38948784 PMCID: PMC11213005 DOI: 10.1101/2024.06.18.598884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mitochondrial creatine kinases are key players in maintaining energy homeostasis in cells by working in conjunction with cytosolic creatine kinases for energy transport from mitochondria to cytoplasm. High levels of MtCK observed in Her2+ breast cancer and inhibition of breast cancer cell growth by substrate analog, cyclocreatine, indicate dependence of cancer cells on the 'energy shuttle' for cell growth and survival. Hence, understanding the key mechanistic features of creatine kinases and their inhibition plays an important role in the development of cancer therapeutics. Herein, we present the mutational and structural investigation on understudied ubiquitous mitochondrial creatine kinase (uMtCK). Our cryo-EM structures and biochemical data on uMtCK showed closure of the loop comprising residue His61 is specific to and relies on creatine binding and the reaction mechanism of phosphoryl transfer depends on electrostatics in the active site. In addition, the previously identified covalent inhibitor CKi showed inhibition in breast cancer BT474 cells, however our biochemical and structural data indicated that CKi is not a potent inhibitor for breast cancer due to strong dependency on the covalent link formation and inability to induce conformational changes upon binding.
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2
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Gasper WC, Gardner S, Ross A, Oppelt SA, Allen KN, Tolan DR. Michaelis-like complex of mouse ketohexokinase isoform C. Acta Crystallogr D Struct Biol 2024; 80:377-385. [PMID: 38805243 DOI: 10.1107/s2059798324003723] [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: 02/27/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Over the past forty years there has been a drastic increase in fructose-related diseases, including obesity, heart disease and diabetes. Ketohexokinase (KHK), the first enzyme in the liver fructolysis pathway, catalyzes the ATP-dependent phosphorylation of fructose to fructose 1-phosphate. Understanding the role of KHK in disease-related processes is crucial for the management and prevention of this growing epidemic. Molecular insight into the structure-function relationship in ligand binding and catalysis by KHK is needed for the design of therapeutic inhibitory ligands. Ketohexokinase has two isoforms: ketohexokinase A (KHK-A) is produced ubiquitously at low levels, whereas ketohexokinase C (KHK-C) is found at much higher levels, specifically in the liver, kidneys and intestines. Structures of the unliganded and liganded human isoforms KHK-A and KHK-C are known, as well as structures of unliganded and inhibitor-bound mouse KHK-C (mKHK-C), which shares 90% sequence identity with human KHK-C. Here, a high-resolution X-ray crystal structure of mKHK-C refined to 1.79 Å resolution is presented. The structure was determined in a complex with both the substrate fructose and the product of catalysis, ADP, providing a view of the Michaelis-like complex of the mouse ortholog. Comparison to unliganded structures suggests that KHK undergoes a conformational change upon binding of substrates that places the enzyme in a catalytically competent form in which the β-sheet domain from one subunit rotates by 16.2°, acting as a lid for the opposing active site. Similar kinetic parameters were calculated for the mouse and human enzymes and indicate that mice may be a suitable animal model for the study of fructose-related diseases. Knowledge of the similarity between the mouse and human enzymes is important for understanding preclinical efforts towards targeting this enzyme, and this ground-state, Michaelis-like complex suggests that a conformational change plays a role in the catalytic function of KHK-C.
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Affiliation(s)
- William C Gasper
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sarah Gardner
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Adam Ross
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Sarah A Oppelt
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Karen N Allen
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Dean R Tolan
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
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3
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Buchachenko AL. Does Biological Longevity Depend on the Magnetic Fields? RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2023. [DOI: 10.1134/s1990793123010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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4
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Magnetic field and nuclear spin influence on the DNA synthesis rate. Sci Rep 2023; 13:465. [PMID: 36627313 PMCID: PMC9832033 DOI: 10.1038/s41598-022-26744-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
The rate of a chemical reaction can be sensitive to the isotope composition of the reactants, which provides also for the sensitivity of such "spin-sensitive" reactions to the external magnetic field. Here we demonstrate the effect of the external magnetic field on the enzymatic DNA synthesis together with the effect of the spin-bearing magnesium ions ([Formula: see text]Mg). The rate of DNA synthesis monotonously decreased with the external magnetic field induction increasing in presence of zero-spin magnesium ions ([Formula: see text]Mg). On the contrary, in the presence of the spin-bearing magnesium ions, the dependence of the reaction rate on the magnetic field induction was non-monotonous and possess a distinct minimum at 80-100 mT. To describe the observed effect, we suggested a chemical scheme and biophysical mechanism considering a competition between Zeeman and Fermi interactions in the external magnetic field.
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The characterization of novel monomeric creatine kinases in the early branching Alveolata species, Perkinsus marinus: Implications for phosphagen kinase evolution. Comp Biochem Physiol B Biochem Mol Biol 2022; 262:110758. [PMID: 35598705 DOI: 10.1016/j.cbpb.2022.110758] [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: 03/07/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
The genome of the unicellular molluscan parasite Perkinsus marinus contains at least five genes coding for putative creatine kinases (CK), a phosphoryl transfer enzyme which plays a key role in cellular energy transactions. Expression and kinetic analyses of three of the P. marinus CKs revealed them to be true CKs with catalytic properties in the range of typical metazoan CKs. A sequence comparison of the P. marinus CKs with a range of CK dimers and other dimeric phosphoryl transfer enzymes in this family (phosphagen kinases) showed that the P. marinus CKs lacked some of the critical residues involved in dimer stabilization, a trait all previously characterized CKs share. Size exclusion chromatography of all three expressed P. marinus CK constructs indicated they are monomeric, consistent with the observed lack of some critical dimer stabilizing residues. Phylogenetic analyses of the P. marinus CKs and putative dinoflagellate CKs with a broad range of monomeric and dimeric phosphagen kinases revealed that the Perkinsus CKs form a distinct, well-supported clade with dinoflagellate CKs which also lack the dimer stabilizing residues. Analysis of the genomic data for P. marinus showed the presence of putative genes for the two enzymes associated with creatine biosynthesis. CK in higher organisms plays a critical role in energy buffering in cell types displaying high and variable rates of ATP turnover. The presence of multiple CKs and the creatine biosynthetic pathway in P. marinus indicates that this unicellular parasite has the full complement of molecular machinery for CK-mediated energy buffering.
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Mandal PK, Dwivedi D, Shukla D, Samkaria A, Roy RG, Arora Y, Jindal K. Interplay Between Hippocampal Glutathione Depletion and pH Increment in Alzheimer’s Disease. J Alzheimers Dis 2022; 88:1-6. [DOI: 10.3233/jad-215729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Oxidative stress (OS) is a critical factor in the pathogenesis of Alzheimer’s disease (AD). Elevated OS in AD lowers the level of glutathione (GSH), a brain antioxidant. Currently, GSH is under examination in the clinical population for understanding its association with oxidative load in AD research. Significant depletion in hippocampal GSH, as observed using in vivo magnetic resonance spectroscopy (MRS), reportedly correlates with cognitive impairment in AD. Alterations in cellular-energy metabolism and increased hippocampal pH have also been reported in AD. Hence, this combined molecular interplay between hippocampal GSH and pH must be studied longitudinally for advancing AD research. Herein, we propose a schematic model depicting the molecular events in AD pathogenesis and provide a possible link between OS, GSH depletion, and pH alterations in the hippocampus. The model would further potentiate the need for in vivo longitudinal studies to confirm the interlinked mechanism between OS, hippocampal GSH depletion, and pH increment in an AD patient brain.
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Affiliation(s)
- Pravat K. Mandal
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
- Florey Institute of Neuroscience and Mental Health, Melbourne School of Medicine Campus, Melbourne, Australia
| | - Divya Dwivedi
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
| | - Deepika Shukla
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
| | - Avantika Samkaria
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
| | - Rimil Guha Roy
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
| | - Yashika Arora
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
| | - Komal Jindal
- Neuroimaging and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon, India
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7
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Buchachenko AL. Compressed Molecules and Enzymes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793122010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kalic T, Radauer C, Lopata AL, Breiteneder H, Hafner C. Fish Allergy Around the World—Precise Diagnosis to Facilitate Patient Management. FRONTIERS IN ALLERGY 2021; 2:732178. [PMID: 35387047 PMCID: PMC8974716 DOI: 10.3389/falgy.2021.732178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/17/2021] [Indexed: 02/03/2023] Open
Abstract
The accurate and precise diagnosis of IgE-mediated fish allergy is one of the biggest challenges in allergy diagnostics. A wide range of fish species that belong to evolutionary distant classes are consumed globally. Moreover, each fish species may contain multiple isoforms of a given allergen that often differ in their allergenicity. Recent studies indicated that the cross-reactivity between different fish species is limited in some cases and depends on the evolutionary conservation of the involved allergens. Fish allergens belong to several protein families with different levels of stability to food processing. Additionally, different preparation methods may contribute to specific sensitization patterns to specific fish species and allergens in different geographic regions. Here, we review the challenges and opportunities for improved diagnostic approaches to fish allergy. Current diagnostic shortcomings include the absence of important region-specific fish species in commercial in vitro and in vivo tests as well as the lack of their standardization as has been recently demonstrated for skin prick test solutions. These diagnostic shortcomings may compromise patients' safety by missing some of the relevant species and yielding false negative test results. In contrast, the avoidance of all fish as a common management approach is usually not necessary as many patients may be only sensitized to specific species and allergens. Although food challenges remain the gold standard, other diagnostic approaches are investigated such as the basophil activation test. In the context of molecular allergy diagnosis, we discuss the usefulness of single allergens and raw and heated fish extracts. Recent developments such as allergen microarrays offer the possibility to simultaneously quantify serum IgE specific to multiple allergens and allergen sources. Such multiplex platforms may be used in the future to design diagnostic allergen panels covering evolutionary distant fish species and allergens relevant for particular geographic regions.
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Affiliation(s)
- Tanja Kalic
- Department of Dermatology, University Hospital St. Poelten, Karl Landsteiner University of Health Sciences, St. Poelten, Austria
- Center for Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Christian Radauer
- Center for Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Andreas L. Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Heimo Breiteneder
- Center for Pathophysiology, Infectiology and Immunology, Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Christine Hafner
- Department of Dermatology, University Hospital St. Poelten, Karl Landsteiner University of Health Sciences, St. Poelten, Austria
- Karl Landsteiner Institute for Dermatological Research, Karl Landsteiner Society, St. Poelten, Austria
- *Correspondence: Christine Hafner
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Steinritz D, Lüling R, Siegert M, Mückter H, Popp T, Reinemer P, Gudermann T, Thiermann H, John H. Alkylation of rabbit muscle creatine kinase surface methionine residues inhibits enzyme activity in vitro. Arch Toxicol 2021; 95:3253-3261. [PMID: 34396457 PMCID: PMC8448711 DOI: 10.1007/s00204-021-03137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022]
Abstract
Creatine kinase (CK) catalyzes the formation of phosphocreatine from adenosine triphosphate (ATP) and creatine. The highly reactive free cysteine residue in the active site of the enzyme (Cys283) is considered essential for the enzymatic activity. In previous studies we demonstrated that Cys283 is targeted by the alkylating chemical warfare agent sulfur mustard (SM) yielding a thioether with a hydroxyethylthioethyl (HETE)-moiety. In the present study, the effect of SM on rabbit muscle CK (rmCK) activity was investigated with special focus on the alkylation of Cys283 and of reactive methionine (Met) residues. For investigation of SM-alkylated amino acids in rmCK, micro liquid chromatography-electrospray ionization high-resolution tandem-mass spectrometry measurements were performed using the Orbitrap technology. The treatment of rmCK with SM resulted in a decrease of enzyme activity. However, this decrease did only weakly correlate to the modification of Cys283 but was conclusive for the formation of Met70-HETE and Met179-HETE. In contrast, the activity of mutants of rmCK produced by side-directed mutagenesis that contained substitutions of the respective Met residues (Met70Ala, Met179Leu, and Met70Ala/Met179Leu) was highly resistant against SM. Our results point to a critical role of the surface exposed Met70 and Met179 residues for CK activity.
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Affiliation(s)
- Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany. .,Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität Munich (LMU), Goethestraße 33, 80366, Munich, Germany. .,Bundeswehr Medical Service Academy, Ingolstädter Straße 240, 80939, Munich, Germany.
| | - Robin Lüling
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.,Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität Munich (LMU), Goethestraße 33, 80366, Munich, Germany
| | - Markus Siegert
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.,Proteros Biostructures GmbH, Bunsenstraße 7a, 82152, Planegg, Germany
| | - Harald Mückter
- Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität Munich (LMU), Goethestraße 33, 80366, Munich, Germany
| | - Tanja Popp
- Bundeswehr Institute of Radiobiology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Peter Reinemer
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.,AM1 Ventures GmbH, Fasanenstraße 27a, 81247, Munich, Germany
| | - Thomas Gudermann
- Walther-Straub-Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität Munich (LMU), Goethestraße 33, 80366, Munich, Germany
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Harald John
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
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Yano D, Suzuki T. Phosphagen kinases from five groups of eukaryotic protists (Choanomonada, Alveolate, Stramenopiles, Haptophyta, and Cryptophyta): Diverse enzyme activities and phylogenetic relationship with metazoan enzymes. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110663. [PMID: 34364990 DOI: 10.1016/j.cbpb.2021.110663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/25/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022]
Abstract
Among 28 groups of eukaryotes, apart from Metazoa, phosphagen kinase (PKs) is distributed in only a few protist groups, including the Choanomonada with the closest affinity to metazoans. To clarify the origin of metazoan PKs, we performed a database search and focused on 11 sequences of PK homologs from five groups of protists: the Choanomonada, Alveolata, Haptophyta, Stramenopiles, and Cryptophyta. The recombinant enzymes were prepared to determine their substrate specificity. Emiliania (Haptophyta), Anophryoides, Pseudocohnilembus, Vitrella and Chromera (Alveolata), and Monosiga (Choanomonada) all contained a gene for arginine kinase (AK). In contrast, Aphanomyces, Albugo and Ectocarpus (Stramenopiles), and Guillardia (Cryptophyta) possessed a gene for taurocyamine kinase (TK). The Guillardia TK enzyme exhibited rather strong substrate inhibition toward taurocyamine, which was analyzed using the most likely kinetic model. This was the first report of substrate inhibition in a TK. Together with the research results from other groups, the AK, TK, or creatine kinase (CK) activities have been observed sporadically in at least six groups of protists. However, it is not clear the three enzyme activities were emerged early in the evolution and divergence of protist groups, or some of enzyme activities were introduced to the protists by horizontal gene transfer. In addition, we found that seven protist enzymes examined in this study possess a myristoylation signaling sequence at the N-terminus. The amino-acid sequence around the guanidine-specificity region and the key residue at 89th position of the protist AK and CK were homologous to those of the metazoan enzymes, but those for protist TKs were different indicating that the latter evolved independently.
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Affiliation(s)
- Daichi Yano
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan.
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11
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Yano D, Uda K, Nara M, Suzuki T. Diversity of phosphagen kinases in annelids: The first sequence report for a putative opheline kinase. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110662. [PMID: 34371154 DOI: 10.1016/j.cbpb.2021.110662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Opheline kinase (OK) is one of the phosphagen kinases (PKs) restricted to annelids, but the amino acid sequence has not been determined yet. The OK enzyme was isolated in 1966 from the polychaete Ophelia neglecta (Opheliidae) and shown to have somewhat broader activities for the various substrates opheline, lombricine and taurocyamine. To determine the OK sequence, we analyzed the RNA sequencing data for Ophelina sp. and Thoracophelia sp., belonging to Opheliidae. Four PK sequences, namely, taurocyamine kinase (TK), creatine kinase (CK), mitochondrial CK (MiCK) and putative OK, were identified in both species, and the recombinant Ophelina enzymes were expressed in E. coli and purified. Since the substrate opheline was not commercially available, we used the partial activity toward taurocyamine to infer the enzyme specificity. The putative Ophelina OK showed lower activity to taurocyamine with a Vmax/Km nearly identical to a previously published value for an OK from a related species Ophelia neglecta. Under the same conditions, the true Ophelina TK showed much higher activity. Thus, the putative Ophelina enzyme was determined to be OK. The amino acid sequence alignment indicated that Ophelina and Thoracophelia OKs have five amino acid deletions in the GS region, like those of LKs and AKs, and the guanidino substrate specific residue was Lys, the same as LKs. In the phylogenetic tree constructed from annelid PK amino acid sequences, the OK sequences formed a distinct cluster, and it was placed near the TK and lombricine kinase (LK) clusters. This is the first report of the amino acid sequence for the OK enzyme.
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Affiliation(s)
- Daichi Yano
- Laboratories of Comparative Biochemistry, Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan
| | - Kouji Uda
- Laboratories of Comparative Biochemistry, Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan
| | - Masakazu Nara
- Paleontology, Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan
| | - Tomohiko Suzuki
- Laboratories of Comparative Biochemistry, Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi 780-8520, Japan.
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Buchachenko AL, Kuznetsov DA. Genes and Cancer under Magnetic Control. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [PMCID: PMC8064421 DOI: 10.1134/s1990793121010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A. L. Buchachenko
- Semenov Federal Research Center of Chemical Physics Russian Academy of Sciences, 119991 Moscow, Russia
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, 142432 Chernogolovka, Russia
- Scientific Center of the Russian Academy of Sciences, 142432 Chernogolovka, Russia
- Moscow State University, 119992 Moscow, Russia
| | - D. A. Kuznetsov
- Semenov Federal Research Center of Chemical Physics Russian Academy of Sciences, 119991 Moscow, Russia
- Russian National Research Medical University, 119997 Moscow, Russia
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Vraneš M, Ostojić S, Podlipnik Č, Tot A. Molecular docking and density functional theory studies on creatine, guanidinoacetic acid, and their phosphorylated analogues binding to muscle creatine kinase. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820978583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Comparative molecular docking studies on creatine and guanidinoacetic acid, as well as their phosphorylated analogues, creatine phosphate, and phosphorylated guanidinoacetic acid, are investigated. Docking and density functional theory studies are carried out for muscle creatine kinase. The changes in the geometries of the ligands before and after binding to the enzyme are investigated to explain the better binding of guanidinoacetic acid and phosphorylated guanidinoacetic acid compared to creatine and creatine phosphate.
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Affiliation(s)
- M Vraneš
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Novi Sad, Serbia
| | - S Ostojić
- Faculty of Sport and Physical Education, University of Novi Sad, Novi Sad, Serbia
| | - Č Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - A Tot
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Novi Sad, Serbia
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14
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Terekhov SS, Mokrushina YA, Nazarov AS, Zlobin A, Zalevsky A, Bourenkov G, Golovin A, Belogurov A, Osterman IA, Kulikova AA, Mitkevich VA, Lou HJ, Turk BE, Wilmanns M, Smirnov IV, Altman S, Gabibov AG. A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. SCIENCE ADVANCES 2020; 6:eaaz9861. [PMID: 32637600 PMCID: PMC7314540 DOI: 10.1126/sciadv.aaz9861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.
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Affiliation(s)
- Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton S. Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zlobin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | | | - Andrey Golovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Arizona State University, Tempe, AZ, USA
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
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15
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Buchachenko AL, Bukhvostov AA, Ermakov KV, Kuznetsov DA. A specific role of magnetic isotopes in biological and ecological systems. Physics and biophysics beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 155:1-19. [PMID: 32224188 DOI: 10.1016/j.pbiomolbio.2020.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/17/2019] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
Abstract
The great diversity of molecular processes in chemistry, physics, and biology exhibits universal property: they are controlled by powerful factor, angular momentum. Conservation of angular momentum (electron spin) is a fundamental and universal principle: all molecular processes are spin selective, they are allowed only for those spin states of reactants whose total spin is identical to that of products. Magnetic catalysis induced by magnetic interactions is a powerful and universal means to overcome spin prohibition and to control physical, chemical and biochemical processes. Contributing almost nothing in total energy, being negligibly small, magnetic interactions are the only ones which are able to change electron spin of reactants and switch over the processes between spin-allowed and spin-forbidden channels, controlling pathways and chemical reactivity in molecular processes. The main source of magnetic and electromagnetic effects in biological systems is now generally accepted and demonstrated in this paper to be radical pair mechanism which implies pairwise generation of radicals in biochemical reactions. This mechanism was convincingly established for enzymatic adenosine triphosphate (ATP) and desoxynucleic acid (DNA) synthesis by using catalyzing metal ions with magnetic nuclei (25Mg, 43Ca, 67Zn) and supported by magnetic field effects on these reactions. The mechanism, is shown to function in medicine as a medical remedy or technology (trans-cranial magnetic stimulation, nuclear magnetic control of the ATP synthesis in heart muscle, the killing of cancer cells by suppression of DNA synthesis). However, the majority of magnetic effects in biology remain to be irreproducible, contradictory, and enigmatic. Three sources of such a state are shown in this paper to be: the presence of paramagnetic metal ions as a component of enzymatic site or as an impurity in an uncontrollable amount; the property of the radical pair mechanism to function at a rather high concentration of catalyzing metal ions, when at least two ions enter into the catalytic site; and the kinetic restrictions, which imply compatibility of chemical and spin dynamics in radical pair. The purpose of the paper is to analyze the reliable sources of magnetic effects, to elucidate the reasons of their inconsistency, to show how and at what conditions magnetic effects exhibit themselves and how they may be controlled, switched on and off, taking into account not only biological and madical but some geophysical and environmental aspects as well.
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Affiliation(s)
- Anatoly L Buchachenko
- Institute of Chemical Physics, Russian Academy of Sciences, 119991, Moscow, Russian Federation; Institute of Problems of Chemical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Russian Federation; Scientific Center of the Russian Academy of Sciences, 142432, Chernogolovka, Russian Federation; Moscow State University, 119992, Moscow, Russian Federation
| | | | - Kirill V Ermakov
- Russian National Research Medical University, 119997, Moscow, Russian Federation
| | - Dmitry A Kuznetsov
- Institute of Chemical Physics, Russian Academy of Sciences, 119991, Moscow, Russian Federation; Russian National Research Medical University, 119997, Moscow, Russian Federation.
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16
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Buchachenko A, Bukhvostov A, Ermakov K, Kuznetsov D. Nuclear spin selectivity in enzymatic catalysis: A caution for applied biophysics. Arch Biochem Biophys 2019; 667:30-35. [PMID: 31029686 DOI: 10.1016/j.abb.2019.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 10/27/2022]
Abstract
Nuclear magnetic ions 25Mg2+, 43Ca2+, and 67Zn2+ suppress DNA synthesis by 3-5 times with respect to ions with nonmagnetic nuclei. This observation unambiguously evidences that the DNA synthesis occurs by radical pair mechanism, which is well known in chemistry and implies pairwise generation of radicals by electron transfer between reaction partners. This mechanism coexists with generally accepted nucleophilic one; it is switched on, when at least two ions enter into the catalytic site. It is induced by both sorts of ions, magnetic and nonmagnetic but it functions by 3-5 times more efficiently with magnetic ions stimulating radical pair mechanism. Decreasing catalytic activity of polymerases by 3-5 times, nuclear magnetic ions 25Mg2+, 43Ca2+, and 67Zn2+ even more strongly, by 30-50 times, increase mortality of cancer cells. The two reasons of this unique phenomenon are suggested: first, the high concentration of nuclear magnetic ions delivered by specific nano-container into the cancer cells, and, second, generation of short DNA fragments by polymerases loaded with nuclear magnetic ions, which is known to activate protein p53, efficiently stimulating apoptosis of cancer cells.
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Affiliation(s)
- Anatoly Buchachenko
- Institute of Chemical Physics, Russian Academy of Sciences, 119991, Moscow, Russian Federation; Institute of Problems of Chemical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Russian Federation; Scientific Center of the Russian Academy of Sciences, 142432, Chernogolovka, Russian Federation; Moscow State University, Russian Federation
| | - Alexander Bukhvostov
- Russian National Research Medical University, Moscow, 119997, Russian Federation.
| | - Kirill Ermakov
- Russian National Research Medical University, Moscow, 119997, Russian Federation
| | - Dmitry Kuznetsov
- Institute of Chemical Physics, Russian Academy of Sciences, 119991, Moscow, Russian Federation; Russian National Research Medical University, Moscow, 119997, Russian Federation
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17
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Adessi TG, Borioni JL, Pigni NB, Bastida J, Cavallaro V, Murray AP, Puiatti M, Oberti JC, Leiva S, Nicotra VE, Garcia ME. Clinanthus microstephium, an Amaryllidaceae Species with Cholinesterase Inhibitor Alkaloids: Structure-Activity Analysis of Haemanthamine Skeleton Derivatives. Chem Biodivers 2019; 16:e1800662. [PMID: 30801949 DOI: 10.1002/cbdv.201800662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/22/2019] [Indexed: 12/14/2022]
Abstract
Plants of the Amaryllidaceae family are well-known (not only) for their ornamental value but also for the alkaloids that they produce. In this report, the first phytochemical study of Clinanthus genus was carried out. The chemical composition of alkaloid fractions from Clinanthus microstephium was analyzed by GC/MS and NMR. Seven known compounds belonging to three structural types of Amaryllidaceae alkaloids were identified. An epimeric mixture of a haemanthamine-type compound (6-hydroxymaritidine) was tested as an inhibitor against acetyl- and butyrylcholinesterase enzymes (AChE and BChE, respectively), two enzymes relevant in the treatment of Alzheimer's disease, with good results. Structure-activity relationships through molecular docking studies with this alkaloid and other structurally related compounds were discussed.
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Affiliation(s)
- Tonino G Adessi
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Instituto Multidisciplinario de Biología Vegetal, IMBIV-CONICET, Córdoba, XUA5000, Argentina
| | - José L Borioni
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, M5502JMA, Argentina
| | - Natalia B Pigni
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Instituto de Ciencia y Tecnología de Alimentos Córdoba, ICYTAC-CONICET, Córdoba, XUA5000, Argentina
| | - Jaume Bastida
- Departamento de Biología, Sanidad y Medio Ambiente, Facultad de Farmacia y Ciencias de la Alimentación, Universidad de Barcelona, 08028, Barcelona, España
| | - Valeria Cavallaro
- INQUISUR-CONICET, Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, B8000CPB, Argentina
| | - Ana P Murray
- INQUISUR-CONICET, Departamento de Química, Universidad Nacional del Sur, Bahía Blanca, B8000CPB, Argentina
| | - Marcelo Puiatti
- Instituto de Investigaciones en Físico-Química de Córdoba, INFIQC-CONICET, Córdoba, XUA5000, Argentina
| | - Juan C Oberti
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Instituto Multidisciplinario de Biología Vegetal, IMBIV-CONICET, Córdoba, XUA5000, Argentina
| | - Segundo Leiva
- Museo de Historia Natural, Universidad Privada Antenor Orrego de Trujillo, Trujillo, 13006, Perú
| | - Viviana E Nicotra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Instituto Multidisciplinario de Biología Vegetal, IMBIV-CONICET, Córdoba, XUA5000, Argentina
| | - Manuela E Garcia
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, XUA5000, Argentina.,Instituto Multidisciplinario de Biología Vegetal, IMBIV-CONICET, Córdoba, XUA5000, Argentina
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18
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Chen F, Zhu K, Chen L, Ouyang L, Chen C, Gu L, Jiang Y, Wang Z, Lin Z, Zhang Q, Shao X, Dai J, Zhao Y. Protein target identification of ginsenosides in skeletal muscle tissues: discovery of natural small-molecule activators of muscle-type creatine kinase. J Ginseng Res 2019; 44:461-474. [PMID: 32372868 PMCID: PMC7195589 DOI: 10.1016/j.jgr.2019.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Background Ginseng effectively reduces fatigue in both animal models and clinical trials. However, the mechanism of action is not completely understood, and its molecular targets remain largely unknown. Methods By screening for proteins that interact with the primary components of ginseng (ginsenosides) in an affinity chromatography assay, we have identified muscle-type creatine kinase (CK-MM) as a potential target in skeletal muscle tissues. Results Biolayer interferometry analysis showed that ginsenoside metabolites, instead of parent ginsenosides, had direct interaction with recombinant human CK-MM. Subsequently, 20(S)-protopanaxadiol (PPD), which is a ginsenoside metabolite and displayed the strongest interaction with CK-MM in the study, was selected as a representative to confirm direct binding and its biological importance. Biolayer interferometry kinetics analysis and isothermal titration calorimetry assay demonstrated that PPD specifically bound to human CK-MM. Moreover, the mutation of key amino acids predicted by molecular docking decreased the affinity between PPD and CK-MM. The direct binding activated CK-MM activity in vitro and in vivo, which increased the levels of tissue phosphocreatine and strengthened the function of the creatine kinase/phosphocreatine system in skeletal muscle, thus buffering cellular ATP, delaying exercise-induced lactate accumulation, and improving exercise performance in mice. Conclusion Our results suggest a cellular target and an initiating molecular event by which ginseng reduces fatigue. All these findings indicate PPD as a small molecular activator of CK-MM, which can help in further developing better CK-MM activators based on the dammarane-type triterpenoid structure.
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Affiliation(s)
- Feiyan Chen
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Kexuan Zhu
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Hanlin College, Nanjing University of Chinese Medicine, Taizhou, China
| | - Lin Chen
- Department of Physiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liufeng Ouyang
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Laboratory of Pathological Sciences, College of Medicine, Yan'an University, Yan'an, China
| | - Cuihua Chen
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Gu
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yucui Jiang
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhongli Wang
- School of Nursing, Jiujiang University, Jiujiang, China
| | - Zixuan Lin
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiang Zhang
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao Shao
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianguo Dai
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Corresponding author. Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, 210046, China.
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19
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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20
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Abstract
Isoforms of creatine kinase (CK) generate and use phosphocreatine, a concentrated and highly diffusible cellular "high energy" intermediate, for the main purpose of energy buffering and transfer in order to maintain cellular energy homeostasis. The mitochondrial CK isoform (mtCK) localizes to the mitochondrial intermembrane and cristae space, where it assembles into peripherally membrane-bound, large cuboidal homooctamers. These are part of proteolipid complexes wherein mtCK directly interacts with cardiolipin and other anionic phospholipids, as well as with the VDAC channel in the outer membrane. This leads to a stabilization and cross-linking of inner and outer mitochondrial membrane, forming so-called contact sites. Also the adenine nucleotide translocator of the inner membrane can be recruited into these proteolipid complexes, probably mediated by cardiolipin. The complexes have functions mainly in energy transfer to the cytosol and stimulation of oxidative phosphorylation, but also in restraining formation of reactive oxygen species and apoptosis. In vitro evidence indicates a putative role of mtCK in mitochondrial phospholipid distribution, and most recently a role in thermogenesis has been proposed. This review summarizes the essential structural and functional data of these mtCK complexes and describes in more detail the more recent advances in phospholipid interaction, thermogenesis, cancer and evolution of mtCK.
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21
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Ji T, Zhang C, Zheng L, Dunaway-Mariano D, Allen KN. Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions. Biochemistry 2018; 57:3480-3492. [PMID: 29695157 DOI: 10.1021/acs.biochem.8b00223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human phosphomannomutases PMM1 and PMM2 catalyze the interconversion of hexose 6-phosphates and hexose 1-phosphates. The two isoforms share 66% sequence identity and have kinetic properties similar to those of mutases in vitro but differ in their functional roles in vivo. Though the physiological role of PMM2 is catalysis of the mutase reaction that provides the mannose 1-phosphate (Man-1-P) essential for protein glycosylation, PMM1 is thought to provide a phosphohydrolase activity in the presence of inosine monophosphate (IMP), converting glucose 1,6-bisphosphate (Glu-1,6-P2) to glucose 6-phosphate (Glu-6-P), rescuing glycolysis during brain ischemia. To uncover the structural basis of how IMP binding converts PMM1 from a mutase to a phosphatase, the 1.93 Å resolution structure of PMM1 complexed with IMP was determined. The structure reveals IMP bound at the substrate recruitment site, thus inhibiting the mutase activity while simultaneously activating a phosphatase activity (IMP Kact = 1.5 μM) resulting from the hydrolysis of the phospho-enzyme. The bound structure and site-directed mutagenesis confirm that the long-range electrostatic interactions provided by Arg180 and Arg183 conserved in PMM1 are the major contributors to IMP binding, and their oblation removes phosphatase but not mutase activity. These residues are not present in the PMM2 isoform, which consequently lacks significant phosphatase activity in the presence of IMP. T2 relaxation nuclear magnetic resonance and small angle X-ray scattering together support the hypothesis that binding of IMP to PMM1 favors an enzyme conformation that is catalytically competent for water attack at the phosphoaspartyl intermediate. Such a mechanism may be generalizable to other enzymes that act through covalent intermediates.
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Affiliation(s)
- Tianyang Ji
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Chunchun Zhang
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Li Zheng
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Karen N Allen
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
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22
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Selimoglu SM, Kasap M, Akpinar G, Karadenizli A, Wis AM, Gormus U. Improved Production of Highly Active and Pure Human Creatine Kinase MB. J Mol Microbiol Biotechnol 2018. [PMID: 29539608 DOI: 10.1159/000486716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human creatine kinase MB (hCKMB) is one of the most preferred biomarkers used for the diagnosis of acute coronary syndrome due to its high sensitivity and specificity. The increasing need for highly purified and biologically active hCKMB in the field of diagnostics makes its production valuable. Currently, the production of hCKMB is mainly achieved in methylotrophic yeast, Pichia pastoris, because the production in Escherichia coli is challenging and generally yields an inactive enzyme with a low quantity. With the aim of finding the best way for the high-yield production of active hCKMB in E. coli, an efficient strategy was developed using a construct allowing tandem expression of each subunit with 2 different tags. The strategy allowed the efficient expression and separate characterization of each subunit and 1-step purification of the heterodimeric protein into homogeneity. The heterodimeric protein displayed more than 11-fold greater specific activity than the commercially available one. The production strategy described in this study shows a clear advantage over the currently used ones and can be made available not only for laboratory scale production but also for commercial production. Our study is also a well-suited example for the studies in which novel protein expression strategies are needed to achieve greater yields with higher purities.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Aynur Karadenizli
- Department of Medical Microbiology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Abdul Mounem Wis
- Department of Chemical Engineering, School of Engineering, Kocaeli University, Kocaeli, Turkey
| | - Uzay Gormus
- Department of Medical Biochemistry, Faculty of Medicine, Biruni University, Kocaeli, Turkey
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23
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Wu QY, Wei F, Zhu YY, Tong YX, Cao J, Zhou P, Li ZY, Zeng LY, Li F, Wang XY, Xu KL. Roles of amino acid residues H66 and D326 in the creatine kinase activity and structural stability. Int J Biol Macromol 2017; 107:512-520. [PMID: 28916380 DOI: 10.1016/j.ijbiomac.2017.09.020] [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: 07/18/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 11/24/2022]
Abstract
Creatine kinase (CK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphocreatine to ADP in vertebrates. CK contains a pair of highly conserved amino acids (H66 and D326) which might play an important role in sustaining the compact structure of CK by linking its N- and C- terminal domains; however the mechanism is still unclear. In this study, spectroscopic, structural modeling and protein folding experiments suggested that D326A, H66P and H66P/D326A mutations led to disruption of the hydrogen bond between those two amino acid residues and form the partially unfolded state which made it easier to be inactivated and unfolded under environmental stresses, and more prone to form insoluble aggregates. The formation of insoluble aggregates would decrease levels of active CKs which may provide clues in CK deficiency disease. Moreover, these results indicated that the degree of synergism had closely relationship to the conformational changes of CK. Thus, our results provided clues for understanding the mechanism of amino acid residues outside the active site in regulating substrate synergism.
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Affiliation(s)
- Qing-Yun Wu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Fang Wei
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuan-Yuan Zhu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Xue Tong
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiang Cao
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ping Zhou
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhen-Yu Li
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ling-Yu Zeng
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Li
- Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Xiao-Yun Wang
- College of Life Sciences, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Kai-Lin Xu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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24
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Davulcu O, Peng Y, Brüschweiler R, Skalicky JJ, Chapman MS. Elevated μs-ms timescale backbone dynamics in the transition state analog form of arginine kinase. J Struct Biol 2017; 200:258-266. [PMID: 28495594 DOI: 10.1016/j.jsb.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 10/19/2022]
Abstract
Arginine kinase catalyzes reversible phosphoryl transfer between arginine and ATP. Crystal structures of arginine kinase in an open, substrate-free form and closed, transition state analog (TSA) complex indicate that the enzyme undergoes substantial domain and loop rearrangements required for substrate binding, catalysis, and product release. Nuclear magnetic resonance (NMR) has shown that substrate-free arginine kinase is rigid on the ps-ns timescale (average S2=0.84±0.08) yet quite dynamic on the µs-ms timescale (35 residues with Rex, 12%), and that movements of the N-terminal domain and the loop comprising residues I182-G209 are rate-limiting on catalysis. Here, NMR of the TSA-bound enzyme shows similar rigidity on the ps-ns timescale (average S2=0.91±0.05) and substantially increased μs-ms timescale dynamics (77 residues; 22%). Many of the residues displaying μs-ms dynamics in NMR Carr-Purcell-Meiboom-Gill (CPMG) 15N backbone relaxation dispersion experiments of the TSA complex are also dynamic in substrate-free enzyme. However, the presence of additional dynamic residues in the TSA-bound form suggests that dynamics extend through much of the C-terminal domain, which indicates that in the closed form, a larger fraction of the protein takes part in conformational transitions to the excited state(s). Conformational exchange rate constants (kex) of the TSA complex are all approximately 2500s-1, higher than any observed in the substrate-free enzyme (800-1900s-1). Elevated μs-ms timescale protein dynamics in the TSA-bound enzyme is more consistent with recently postulated catalytic networks involving multiple interconnected states at each step of the reaction, rather than a classical single stabilized transition state.
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Affiliation(s)
- Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Yu Peng
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology and Campus Chemical Instrument Center, The Ohio State University, OH 43210, United States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Michael S Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, United States.
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Godina-Nava JJ, Torres-Vega G, López-Riquelme GO, López-Sandoval E, Samana AR, García Velasco F, Hernández-Aguilar C, Domínguez-Pacheco A. Quantum mechanical model for the anticarcinogenic effect of extremely-low-frequency electromagnetic fields on early chemical hepatocarcinogenesis. Phys Rev E 2017; 95:022416. [PMID: 28297882 DOI: 10.1103/physreve.95.022416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/07/2022]
Abstract
Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.
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Affiliation(s)
| | - Gabino Torres-Vega
- Departamento de Física CINVESTAV-IPN, Ap. Postal 14-740, CdMex, C.P. 07000, Mexico
| | | | - Eduardo López-Sandoval
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rodovia Jorge Amado, Km 16, Bairro Salobrinho, 45662-900 Ilhéus, BA, Brazil
| | - Arturo Rodolfo Samana
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rodovia Jorge Amado, Km 16, Bairro Salobrinho, 45662-900 Ilhéus, BA, Brazil
| | - Fermín García Velasco
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rodovia Jorge Amado, Km 16, Bairro Salobrinho, 45662-900 Ilhéus, BA, Brazil
| | - Claudia Hernández-Aguilar
- National Polytechnic Institute, Sepi-ESIME, Zacatenco, Professional Unit Adolfo López Mateos, Col. Lindavista, Cd Mex, C.P. 07738, Mexico
| | - Arturo Domínguez-Pacheco
- National Polytechnic Institute, Sepi-ESIME, Zacatenco, Professional Unit Adolfo López Mateos, Col. Lindavista, Cd Mex, C.P. 07738, Mexico
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Li Q, Fan S, Li X, Jin Y, He W, Zhou J, Cen S, Yang Z. Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase. Sci Rep 2016; 6:38088. [PMID: 27909311 PMCID: PMC5133464 DOI: 10.1038/srep38088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022] Open
Abstract
Human ubiquitous mitochondrial creatine kinase (uMtCK) is responsible for the regulation of cellular energy metabolism. To investigate the phosphoryl-transfer mechanism catalyzed by human uMtCK, in this work, molecular dynamic simulations of uMtCK∙ATP-Mg2+∙creatine complex and quantum mechanism calculations were performed to make clear the puzzle. The theoretical studies hereof revealed that human uMtCK utilizes a two-step dissociative mechanism, in which the E227 residue of uMtCK acts as the catalytic base to accept the creatine guanidinium proton. This catalytic role of E227 was further confirmed by our assay on the phosphatase activity. Moreover, the roles of active site residues in phosphoryl transfer reaction were also identified by site directed mutagenesis. This study reveals the structural basis of biochemical activity of uMtCK and gets insights into its phosphoryl transfer mechanism.
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Affiliation(s)
- Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Weiqing He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - ZhaoYong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure 2016; 24:1248-1256. [PMID: 27396830 PMCID: PMC4972691 DOI: 10.1016/j.str.2016.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/25/2016] [Accepted: 05/12/2016] [Indexed: 01/14/2023]
Abstract
Cullin-RING E3 ligases (CRLs) are elongated and bowed protein complexes that transfer ubiquitin over 60 Å to proteins targeted for proteasome degradation. One such CRL contains the ankyrin repeat and SOCS box protein 9 (ASB9), which binds to and partially inhibits creatine kinase (CK). While current models for the ASB9-CK complex contain some known interface residues, the overall structure and precise interface of the ASB9-CK complex remains unknown. Through an integrative modeling approach, we report a third-generation model that reveals precisely the interface interactions and also fits the shape of the ASB9-CK complex as determined by small-angle X-ray scattering. We constructed an atomic model for the entire CK-targeting CRL to uncover dominant modes of motion that could permit ubiquitin transfer. Remarkably, only the correctly docked CK-containing E3 ligase and not incorrectly docked structures permitted close approach of ubiquitin to the CK substrate.
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Affiliation(s)
- Jamie M Schiffer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Robert D Malmstrom
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA; National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA
| | - Jonathan Parnell
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Cesar Ramirez-Sarmiento
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Javiera Reyes
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA; National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA.
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA.
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Buchachenko A. Why magnetic and electromagnetic effects in biology are irreproducible and contradictory? Bioelectromagnetics 2015; 37:1-13. [DOI: 10.1002/bem.21947] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/01/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Anatoly Buchachenko
- Institute of Chemical Physics; Russian Academy of Sciences; Moscow Russia
- Institute of Problems of Chemical Physics; Russian Academy of Sciences; Chernogolovka Russia
- Yaroslavl’ State University; Yaroslavl’ Russia
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Okazaki N, Motomura S, Okazoe N, Yano D, Suzuki T. Cooperativity and evolution of Tetrahymena two-domain arginine kinase. Int J Biol Macromol 2015; 79:696-703. [PMID: 26049117 DOI: 10.1016/j.ijbiomac.2015.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/15/2015] [Accepted: 05/24/2015] [Indexed: 11/30/2022]
Abstract
Tetrahymena pyriformis contains two arginine kinases, a 40-kDa enzyme (AK1) with a myristoylation signal sequence at the N-terminus and a two-domain 80-kDa enzyme (AK2). The former is localized mainly in cilia and the latter is in the cytoplasm. AK1 was successfully synthesized using an insect cell-free protein synthesis system and subjected to peptide mass fingerprinting (PMF) analysis. The masses corresponding to unmodified N-terminal tryptic peptide or N-terminal myristoylated peptide were not observed, suggesting that N-terminal peptides were not ionized in this analysis. We performed PMF analyses for two other phosphagen kinases (PKs) with myristoylation signals, an AK from Nematostella vectensis and a PK from Ectocarpus siliculosus. In both cases, the myristoylated, N-terminal peptides were clearly identified. The differences between the experimental and theoretical masses were within 0.0165-0.0583 Da, supporting the accuracy of the identification. Domains 1 and 2 of Tetrahymena two-domain AK2 were expressed separately in Escherichia coli and the extent of cooperativity was estimated on the basis of their kinetic constants. The results suggested that each of the domains functions independently, namely no cooperativity is displayed between the two domains. This is in sharp contrast to the two-domain AK from Anthopleura.
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Affiliation(s)
- Noriko Okazaki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Shou Motomura
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Nanaka Okazoe
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan.
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Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P. The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. J Biol Chem 2015; 290:12951-63. [PMID: 25837252 DOI: 10.1074/jbc.m114.628909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The taurocyamine kinase from the blood fluke Schistosoma mansoni (SmTK) belongs to the phosphagen kinase (PK) family and catalyzes the reversible Mg(2+)-dependent transfer of a phosphoryl group between ATP and taurocyamine. SmTK is derived from gene duplication, as are all known trematode TKs. Our crystallographic study of SmTK reveals the first atomic structure of both a TK and a PK with a bilobal structure. The two unliganded lobes present a canonical open conformation and interact via their respective C- and N-terminal domains at a helix-mediated interface. This spatial arrangement differs from that observed in true dimeric PKs, in which both N-terminal domains make contact. Our structures of SmTK complexed with taurocyamine or l-arginine compounds explain the mechanism by which an arginine residue of the phosphagen specificity loop is crucial for substrate specificity. An SmTK crystal was soaked with the dead end transition state analog (TSA) components taurocyamine-NO3 (2-)-MgADP. One SmTK monomer was observed with two bound TSAs and an asymmetric conformation, with the first lobe semiclosed and the second closed. However, isothermal titration calorimetry and enzyme kinetics experiments showed that the two lobes function independently. A small angle x-ray scattering model of SmTK-TSA in solution with two closed active sites was generated.
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Affiliation(s)
- Romain Merceron
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Ayman M Awama
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Roland Montserret
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Olivier Marcillat
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Patrice Gouet
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
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31
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Venter G, Polling S, Pluk H, Venselaar H, Wijers M, Willemse M, Fransen JAM, Wieringa B. Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop. Eur J Cell Biol 2014; 94:114-27. [PMID: 25538032 DOI: 10.1016/j.ejcb.2014.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/20/2022] Open
Abstract
Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323-330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation.
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Affiliation(s)
- Gerda Venter
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Saskia Polling
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Helma Pluk
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Mietske Wijers
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marieke Willemse
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jack A M Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Londergan CH, Baskin R, Bischak CG, Hoffman KW, Snead DM, Reynoso C. Dynamic Asymmetry and the Role of the Conserved Active-Site Thiol in Rabbit Muscle Creatine Kinase. Biochemistry 2014; 54:83-95. [DOI: 10.1021/bi5008063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Rachel Baskin
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Connor G. Bischak
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Kevin W. Hoffman
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - David M. Snead
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Christopher Reynoso
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
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Phosphagen kinase in Schistosoma japonicum: II. Determination of amino acid residues essential for substrate catalysis using site-directed mutagenesis. Mol Biochem Parasitol 2014; 194:56-63. [PMID: 24815317 DOI: 10.1016/j.molbiopara.2014.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Phosphagen kinases (PKs) play major roles in the regulation of energy metabolism in animals. Creatine kinase (CK) is the sole PK in vertebrates, whereas several PKs are present in invertebrates. We previously identified a contiguous dimer taurocyamine kinase (TK) from the trematode Schistosoma japonicum (Sj), a causative agent of schistosomiasis. SjTK contiguous dimer is comprised of domain 1 (D1) and domain 2 (D2). In this study, we used SjTK contiguous dimer (SjTKD1D2) or truncated single-domain constructs (SjTKD1 or SjTKD2) and employed site-directed mutagenesis to investigate the enzymatic properties of TK mutants. Mutation in SjTKD1 or SjTKD2 (D1E222G or D2E225G) caused complete loss of activity for the substrate taurocyamine. Likewise, a double mutant (D1E222GD2E225G) in the contiguous dimer (D1D2) exhibited complete loss of activity for the substrate taurocyamine. However, catalytic activity in the contiguous dimer remained in both of D1 inactive mutant (D1D2D1E222G) and D2 inactive mutant (D1D2D2E225G), suggesting that efficient catalysis of SjTKD1D2 is dependent on the activity of D1 and D2. The catalytic efficiency of the mixture of both single domains (WTD1+WTD2) showed same enzymatic properties (Km(Tauro)=0.68;Vmax/Km(Tauro)=137.04) to WTD1D2 (Km(Tauro)=0.47; Vmax/Km(Tauro)=144.30). This result suggests that the contiguous dimeric structure is not essential for the catalytic efficiencies of both domains of SjTK. Vmax/Km(Tauro) of the mixture of wild-type and inactivated domains (78.02 in WTD1+D2E225G and 128.24 in D1E222G+WTD2) were higher than the corresponding mutants (47.25 in D1D2D1E222G and 46.77 in D1D2D2E225G). To identify amino acid residues that are critical for taurocyamine binding, we performed alanine scanning mutagenesis at positions 57-63 on the guanidino specificity (GS) region of the SjTKD1, which is considered to be involved in guanidino-substrate recognition. R63A and R63Y mutants lost activity for taurocyamine, suggesting that these residues are associated with taurocyamine binding. In addition, we investigated the role of Tyr84 in D1 and found an association with substrate alignment. The Y84 residue was replaced with R, H, K, I, A, and G. Although the activities of each mutant were decreased (Vmax=2.36-67.50μmolPi/min/mgprotein), Y84 mutants possess binding affinity for taurocyamine (Km(Tauro)=3.19-10.04mM). The D1Y84R, D1Y84H, D1Y84K, and D1Y84A mutants exhibited low activity for taurocyamine, whereas the D1Y84I and D1Y84G mutants exhibited slightly decreased activity compared with the other Y84 mutants. The D1Y84K mutant lost substrate synergy between taurocyamine and ATP, suggesting that this mutation moves the position of the GS loop, similar to that of lombricine kinase (LK), and interferes with taurocyamine binding. This is the first comprehensive investigation of essential amino acid residues for substrate catalysis in trematode TK.
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Geng HL, Bian MR, Liu Y, Cao J, Chen C, Wang ZY, Li ZY, Zeng LY, Wang XY, Wu QY, Xu KL. The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding. Int J Biol Macromol 2014; 66:302-10. [DOI: 10.1016/j.ijbiomac.2014.02.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 11/25/2022]
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Xiao JY, Lee JY, Tokuhiro S, Nagataki M, Jarilla BR, Nomura H, Kim TI, Hong SJ, Agatsuma T. Molecular cloning and characterization of taurocyamine kinase from Clonorchis sinensis: a candidate chemotherapeutic target. PLoS Negl Trop Dis 2013; 7:e2548. [PMID: 24278491 PMCID: PMC3836730 DOI: 10.1371/journal.pntd.0002548] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/07/2013] [Indexed: 11/21/2022] Open
Abstract
Background Adult Clonorchis sinensis lives in the bile duct and causes endemic clonorchiasis in East Asian countries. Phosphagen kinases (PK) constitute a highly conserved family of enzymes, which play a role in ATP buffering in cells, and are potential targets for chemotherapeutic agents, since variants of PK are found only in invertebrate animals, including helminthic parasites. This work is conducted to characterize a PK from C. sinensis and to address further investigation for future drug development. Methology/Principal findings A cDNA clone encoding a putative polypeptide of 717 amino acids was retrieved from a C. sinensis transcriptome. This polypeptide was homologous to taurocyamine kinase (TK) of the invertebrate animals and consisted of two contiguous domains. C. sinensis TK (CsTK) gene was reported and found consist of 13 exons intercalated with 12 introns. This suggested an evolutionary pathway originating from an arginine kinase gene group, and distinguished annelid TK from the general CK phylogenetic group. CsTK was found not to have a homologous counterpart in sequences analysis of its mammalian hosts from public databases. Individual domains of CsTK, as well as the whole two-domain enzyme, showed enzymatic activity and specificity toward taurocyamine substrate. Of the CsTK residues, R58, I60 and Y84 of domain 1, and H60, I63 and Y87 of domain 2 were found to participate in binding taurocyamine. CsTK expression was distributed in locomotive and reproductive organs of adult C. sinensis. Developmentally, CsTK was stably expressed in both the adult and metacercariae stages. Recombinant CsTK protein was found to have low sensitivity and specificity toward C. sinensis and platyhelminth-infected human sera on ELISA. Conclusion CsTK is a promising anti-C. sinensis drug target since the enzyme is found only in the C. sinensis and has a substrate specificity for taurocyamine, which is different from its mammalian counterpart, creatine. The food-borne clonorchiasis imposes public health problems on inhabitants in endemic areas. Praziquantel has been employed as an efficacious anthelminthic in large-scale campaigns as well as for individual treatment of Clonorchis sinensis human infections. Although praziquantel continues to have good efficacy, new drug development for this parasite has been recognized as a crucial issue to be investigated intensively. Clonorchis sinensis adults generate energy through glycolysis, actively utilizing exogenous glucose, and produce a large amount of eggs each day. Taurocyamine kinase (CsTK) is distributed abundantly in the locomotive and reproductive organs, and is an important enzyme in energy generation and homeostasis in adult C. sinensis. Enzymes of the glycolytic pathway are also expressed abundantly in these organs and in tegument, implying these organs play central roles which are essential for survival and reproduction of C. sinensis. The TK enzymes, including CsTK, are found only among invertebrate organisms and have substrate specificity for taurocyamine, which are significantly different from phosphagen kinases of vertebrate animals. With these molecular biological, enzymatic, and evolutionary characteristics, we propose here that CsTK could be a target for development of chemotherapeutic agents against C. sinensis and be a biomolecular model for other human-infecting trematodes.
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Affiliation(s)
- Jing-Ying Xiao
- Department of Environmental Health Sciences, Kochi Medical School, Nankoku, Kochi, Japan ; Department of Parasitology, Basic Medical College, Jiamusi University, Jiamusi, China
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Jarilla BR, Tokuhiro S, Nagataki M, Uda K, Suzuki T, Acosta LP, Agatsuma T. The role of Y84 on domain 1 and Y87 on domain 2 of Paragonimus westermani taurocyamine kinase: Insights on the substrate binding mechanism of a trematode phosphagen kinase. Exp Parasitol 2013; 135:695-700. [PMID: 24184078 DOI: 10.1016/j.exppara.2013.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/18/2013] [Accepted: 10/23/2013] [Indexed: 11/17/2022]
Abstract
The two-domain taurocyamine kinase (TK) from Paragonimus westermani was suggested to have a unique substrate binding mechanism. We performed site-directed mutagenesis on each domain of this TK and compared the kinetic parameters Km(Tc) and Vmax with that of the wild-type to determine putative amino acids involved in substrate recognition and binding. Replacement of Y84 on domain 1 and Y87 on domain 2 with R resulted in the loss of activity for the substrate taurocyamine. Y84E mutant has a dramatic decrease in affinity and activity for taurocyamine while Y87E has completely lost catalytic activity. Substituting H and I on the said positions also resulted in significant changes in activity. Mutation of the residues A59 on the GS region of domain 1 also caused significant decrease in affinity and activity while mutation on the equivalent position on domain 2 resulted in complete loss of activity.
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Affiliation(s)
- Blanca R Jarilla
- Department of Environmental Health Sciences, Kochi University, Kochi 783-8505, Japan; Department of Immunology, Research Institute for Tropical Medicine, Muntinlupa 1781, Philippines
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Rosmilah M, Shahnaz M, Meinir J, Masita A, Noormalin A, Jamaluddin M. Identification of parvalbumin and two new thermolabile major allergens of Thunnus tonggol using a proteomics approach. Int Arch Allergy Immunol 2013; 162:299-309. [PMID: 24193115 DOI: 10.1159/000354544] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 07/12/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The longtail tuna (Thunnus tonggol) is widely consumed in Asia. Parvalbumin, the main major allergen of fish, has been well identified in multiple fish species, yet little is known about the allergenic proteins in T. tonggol. Thus, the aim of this study was to characterize the major allergens of T. tonggol using a proteomics approach. METHODS Raw and boiled extracts of the fish were prepared. Fish proteins were separated by means of SDS-PAGE and two-dimensional (2-DE) electrophoresis. 1-DE immunoblotting of raw extract was performed with sera from fish-allergic patients. Ten sera were further analysed by 2-DE immunoblotting. Selected major allergenic protein spots were excised, trypsin digested and analysed by means of mass spectrometry. RESULTS SDS-PAGE of raw extract revealed 26 protein fractions, while boiled extract demonstrated fewer bands. The 2-DE gel profile of the raw extract further fractionated the protein bands to more than 100 distinct protein spots. 1-DE immunoblotting of raw extract exhibited two thermolabile protein fractions of 42 and 51 kDa as the major allergens, while the boiled extract only revealed a single IgE-binding band at 151 kDa. 2-DE immunoblotting of raw extract further detected numerous major IgE-reactive spots of 11-13, 42 and 51 kDa. Mass spectrometry analysis of the peptides generated from the 12, 42 and 51 kDa digested spots indicated that these spots were parvalbumin, creatine kinase and enolase, respectively. CONCLUSIONS In addition to parvalbumin, two new thermolabile allergens were identified as major allergenic proteins of T. tonggol. This study proved that both thermostable and thermolabile proteins are important in local tuna allergy and should be included in diagnostic strategies.
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Affiliation(s)
- Misnan Rosmilah
- Department of Biology, Faculty of Science and Mathematics, Sultan Idris Education University, Tanjong Malim, Perak, Malaysia
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Palmer A, Begres BN, Van Houten JM, Snider MJ, Fraga D. Characterization of a putative oomycete taurocyamine kinase: Implications for the evolution of the phosphagen kinase family. Comp Biochem Physiol B Biochem Mol Biol 2013; 166:173-81. [PMID: 23978736 DOI: 10.1016/j.cbpb.2013.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/16/2022]
Abstract
Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. Within animal species, these enzymes play a critical role in energy homeostasis by catalyzing the reversible transfer of a high-energy phosphoryl group from Mg⋅ATP to an acceptor molecule containing a guanidinium group. In this work, a putative PK gene was identified in the oomycete Phytophthora sojae that was predicted, based on sequence homology, to encode a multimeric hypotaurocyamine kinase. The recombinant P. sojae enzyme was purified and shown to catalyze taurocyamine phosphorylation efficiently (kcat/KM (taurocyamine) = 2 × 10(5) M(-1) s(-1)) and glycocyamine phosphorylation only weakly (kcat/KM (glycocyamine) = 2 × 10(2) M(-1) s(-1)), but lacked any observable kinase activity with the more ubiquitous guanidinium substrates, creatine or arginine. Additionally, the enzyme was observed to be dimeric but lacked cooperativity between the subunits in forming a transition state analog complex. These results suggest that protozoan PKs may exhibit more diversity in substrate specificity than was previously thought.
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Affiliation(s)
- Allyson Palmer
- Program in Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
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Crystal structure of shrimp arginine kinase in binary complex with arginine—a molecular view of the phosphagen precursor binding to the enzyme. J Bioenerg Biomembr 2013; 45:511-8. [DOI: 10.1007/s10863-013-9521-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/03/2013] [Indexed: 12/20/2022]
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Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP. PLoS One 2013; 8:e64004. [PMID: 23700444 PMCID: PMC3659122 DOI: 10.1371/journal.pone.0064004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/07/2013] [Indexed: 11/19/2022] Open
Abstract
The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK) with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP), was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123–170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.
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Uda K, Hoshijima M, Suzuki T. A novel taurocyamine kinase found in the protist Phytophthora infestans. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:42-8. [PMID: 23499944 DOI: 10.1016/j.cbpb.2013.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/05/2013] [Accepted: 03/05/2013] [Indexed: 11/30/2022]
Abstract
Phosphagen kinase (PK), which is typically in the form of creatine kinase (CK; EC 2.7.3.2) in vertebrates or arginine kinase (AK; EC 2.7.3.3) in invertebrates, plays a key role in ATP buffering systems of tissues and nerves that display high and variable rates of ATP turnover. The enzyme is also found with intermittent occurrence as AK in unicellular organisms, protist and bacteria species, suggesting an ancient origin of AK. Through a database search, we identified two novel PK genes, coding 40- and 80-kDa (contiguous dimer) enzymes in the protist Phytophthora infestans. Both enzymes showed strong activity for taurocyamine and, in addition, we detected taurocyamine in cell extracts of P. infestans. Thus, the enzyme was identified to be taurocyamine kinase (TK; EC 2.7.3.4). This was the first phosphagen kinase, other than AK, to be found in unicellular organisms. Their position on the phylogenetic tree indicates that P. infestans TKs evolved uniquely at an early stage of evolution. Occurrence of TK in protists suggests that PK enzymes show flexible substrate specificity.
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Affiliation(s)
- Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
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42
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Varga A, Gráczer E, Chaloin L, Liliom K, Závodszky P, Lionne C, Vas M. Selectivity of kinases on the activation of tenofovir, an anti-HIV agent. Eur J Pharm Sci 2012. [PMID: 23201309 DOI: 10.1016/j.ejps.2012.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nucleoside analogues, used in HIV-therapy, need to be phosphorylated by cellular enzymes in order to become potential substrates for HIV reverse transcriptase. After incorporation into the viral DNA chain, because of lacking of their 3'-hydroxyl groups, they stop the elongation process and lead to the death of the virus. Phosphorylation of the HIV-drug derivative, tenofovir monophosphate was tested with the recombinant mammalian nucleoside diphosphate kinase (NDPK), 3-phosphoglycerate kinase (PGK), creatine kinase (CK) and pyruvate kinase (PK). Among them, only CK was found to phosphorylate tenofovir monophosphate with a reasonable rate (about 45-fold lower than with its natural substrate, ADP), while PK exhibits even lower, but still detectable activity (about 1000-fold lower compared to the value with ADP). On the other hand, neither NDPK nor PGK has any detectable activity on tenofovir monophosphate. The absence of activity with PGK is surprising, since the drug tenofovir competitively inhibits both CK and PGK towards their nucleotide substrates, with similar inhibitory constants, K(I) of 2.9 and 4.8mM, respectively. Computer modelling (docking) of tenofovir mono- or diphosphate forms to these four kinases suggests that the requirement of large-scale domain closure for functioning (as for PGK) may largely restrict their applicability for phosphorylation/activation of pro-drugs having a structure similar to tenofovir monophosphate.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary.
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Clark SA, Davulcu O, Chapman MS. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Biochem Biophys Res Commun 2012; 427:212-7. [PMID: 22995310 DOI: 10.1016/j.bbrc.2012.09.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/09/2012] [Indexed: 11/29/2022]
Abstract
Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and l-arginine and is a monomeric homolog of the human enzyme creatine kinase. Arginine and creatine kinases belongs to the phosphagen kinase family of enzymes, which consists of eight known members, each of which is specific for its own phosphagen. Here, the source of phosphagen specificity in arginine kinase is investigated through the use of phosphagen analogs. Crystal structures have been determined for Limulus polyphemus arginine kinase with one of four arginine analogs bound in a transition state analog complex: l-ornithine, l-citrulline, imino-l-ornithine, and d-arginine. In all complexes, the enzyme achieves a closed conformation very similar to that of the cognate transition state analog complex, but differences are observed in the configurations of bound ligands. Arginine kinase exhibits no detectable activity towards ornithine, citrulline, or imino-l-ornithine, and only trace activity towards d-arginine. The crystal structures presented here demonstrate that phosphagen specificity is derived neither from a lock-and-key mechanism nor a modulation of induced-fit conformational changes, but potentially from subtle distortions in bound substrate configurations.
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Affiliation(s)
- Shawn A Clark
- Institute of Molecular Biophysics, Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306-4380, USA
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44
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Rivière G, Hologne M, Marcillat O, Lancelin JM. Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits. FEBS J 2012; 279:2863-75. [PMID: 22715856 DOI: 10.1111/j.1742-4658.2012.08667.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Muscle creatine kinase (MCK; EC2.7.3.2) is a 86 kDa homodimer that belongs to the family of guanidino kinases. MCK has been intensively studied for several decades, but it is still not known why it is a dimer because this quaternary structure does not translate into obvious structural or functional advantages over the homologous monomeric arginine kinase. In particular, it remains to be demonstrated whether MCK subunits are independent. Here, we describe NMR chemical-shift perturbation and relaxation experiments designed to study the active site 320s flexible loop of this enzyme. The analysis was performed with the enzyme in its ligand-free and MgADP-complexed forms, as well as with the transition-state analogue abortive complex (MCK-Mg-ADP-creatine-nitrate ion). Our data indicate that each subunit can bind substrates independently.
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Affiliation(s)
- Gwladys Rivière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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45
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Lopez-Zavala AA, Sotelo-Mundo RR, Garcia-Orozco KD, Isac-Martinez F, Brieba LG, Rudiño-Piñera E. Crystallization and X-ray diffraction studies of arginine kinase from the white Pacific shrimp Litopenaeus vannamei. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:783-5. [PMID: 22750864 PMCID: PMC3388921 DOI: 10.1107/s1744309112020180] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/04/2012] [Indexed: 11/10/2022]
Abstract
Crystals of an unligated monomeric arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei (LvAK) were successfully obtained using the microbatch method. Crystallization conditions and preliminary X-ray diffraction analysis to 1.25 Å resolution are reported. Data were collected at 100 K on NSLS beamline X6A. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.5, b = 70.2, c = 81.7 Å. One monomer per asymmetric unit was found, with a Matthews coefficient (V(M)) of 2.05 Å(3) Da(-1) and 40% solvent content. Initial phases were determined by molecular replacement using a homology model of LvAK as the search model. Refinement was performed with PHENIX, with final R(work) and R(free) values of 0.15 and 0.19, respectively. Biological analysis of the structure is currently in progress.
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Affiliation(s)
- Alonso A. Lopez-Zavala
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Karina D. Garcia-Orozco
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Felipe Isac-Martinez
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, 36500 Irapuato, GTO, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avernida Universidad #2001, Col. Chamilpa, 62210 Cuernavaca, MOR, Mexico
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Crotty D, Silkstone G, Poddar S, Ranson R, Prina-Mello A, Wilson MT, Coey JMD. Reexamination of magnetic isotope and field effects on adenosine triphosphate production by creatine kinase. Proc Natl Acad Sci U S A 2012; 109:1437-42. [PMID: 22198842 PMCID: PMC3277194 DOI: 10.1073/pnas.1117840108] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The influence of isotopically enriched magnesium on the creatine kinase catalyzed phosphorylation of adenosine diphosphate is examined in two independent series of experiments where adenosine triphosphate (ATP) concentrations were determined by a luciferase-linked luminescence end-point assay or a real-time spectrophotometric assay. No increase was observed between the rates of ATP production with natural Mg, (24)Mg, and (25)Mg, nor was any significant magnetic field effect observed in magnetic fields from 3 to 1,000 mT. Our results are in conflict with those reported by Buchachenko et al. [J Am Chem Soc 130:12868-12869 (2008)], and they challenge these authors' general claims that a large (two- to threefold) magnetic isotope effect is "universally observable" for ATP-producing enzymes [Her Russ Acad Sci 80:22-28 (2010)] and that "enzymatic phosphorylation is an ion-radical, electron-spin-selective process" [Proc Natl Acad Sci USA 101:10793-10796 (2005)].
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Affiliation(s)
- Darragh Crotty
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College, Dublin 2, Ireland
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland; and
| | - Gary Silkstone
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Soumya Poddar
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College, Dublin 2, Ireland
| | - Richard Ranson
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Adriele Prina-Mello
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College, Dublin 2, Ireland
| | - Michael T. Wilson
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - J. M. D. Coey
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College, Dublin 2, Ireland
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Uda K, Ellington WR, Suzuki T. A diverse array of creatine kinase and arginine kinase isoform genes is present in the starlet sea anemone Nematostella vectensis, a cnidarian model system for studying developmental evolution. Gene 2012; 497:214-27. [PMID: 22305986 DOI: 10.1016/j.gene.2012.01.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 01/16/2012] [Accepted: 01/19/2012] [Indexed: 11/25/2022]
Abstract
Phosphagen (guanidino) kinases (PK) constitute a family of homologous phosphotransferases catalyzing the reversible transfer of the high-energy phosphoryl group of ATP to naturally occurring guanidine compounds. Prior work has shown that PKs can be phylogenetically separated into two distinct groups- an arginine kinase (AK) subfamily and a creatine kinase (CK) subfamily. The latter includes three CK isoforms- cytoplasmic CK (CyCK), mitochondrial CK (MiCK) and three-domain flagellar CK (fCK). In the present study we identified six unique PK genes from the draft genome sequence of the starlet sea anemone Nematostella vectensis, a well-known model organism for understanding metazoan developmental evolution. Using reverse transcription polymerase chain reaction (RTPCR) methods, full length cDNAs were amplified for all of these PKs. These cDNAs were cloned and expressed in Escherichia coli as 6x His-tagged fusion proteins. The six PKs were identified as the three typical CK isoforms (CyCK, MiCK and fCK), two unusual AKs (a two-domain AK (2DAK) and a three-domain AK (3DAK)) and a PK which phosphorylated arginine. The latter enzyme had a very low AK activity (its apparent V(max) value being less than 0.2% that of 3DAK), lacks several key residues necessary for AK enzyme activity, and was tentatively designated as AK1. As far as we know, this constitutes the first report of an AK with the three fused AK domains. The Bayesian tree suggested that the third domain of 3DAK likely evolved from the gene for domain 2 of typical two-domain AK found widely in cnidarians. Construction of phylogenetic trees and comparison of exon-intron organizations of their respective genes indicated that the N. vectensis three-domain fCK and 3DAK evolved independently, and both enzymes are likely to be targeted to cell membranes since they have a myristoylation signal at their respective N-termini. These results complement prior work on other basal invertebrates showing that multiple CK and AK isoform genes were present at the dawn of the radiation of metazoans. The presence of isoform diversity in an organism lacking in structural complexity reflects an early imperative for targeting of PKs to particular cellular contexts such as muscle fibers, neurons, ciliated/flagellated epithelia and spermatozoa.
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Buchachenko AL, Kuznetsov DA, Breslavskaya NN. Chemistry of enzymatic ATP synthesis: an insight through the isotope window. Chem Rev 2012; 112:2042-58. [PMID: 22277055 DOI: 10.1021/cr200142a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anatoly L Buchachenko
- N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, 119991 Moscow, Russian Federation.
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49
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Impact of intra-subunit interactions on the dimeric arginine kinase activity and structural stability. Int J Biol Macromol 2011; 49:822-31. [DOI: 10.1016/j.ijbiomac.2011.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/23/2011] [Accepted: 07/26/2011] [Indexed: 11/22/2022]
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50
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Slow skeletal muscle myosin-binding protein-C (MyBPC1) mediates recruitment of muscle-type creatine kinase (CK) to myosin. Biochem J 2011; 436:437-45. [PMID: 21426302 DOI: 10.1042/bj20102007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Muscle contraction requires high energy fluxes, which are supplied by MM-CK (muscle-type creatine kinase) which couples to the myofibril. However, little is known about the detailed molecular mechanisms of how MM-CK participates in and is regulated during muscle contraction. In the present study, MM-CK is found to physically interact with the slow skeletal muscle-type MyBPC1 (myosin-binding protein C1). The interaction between MyBPC1 and MM-CK depended on the creatine concentration in a dose-dependent manner, but not on ATP, ADP or phosphocreatine. The MyBPC1-CK interaction favoured acidic conditions, and the two molecules dissociated at above pH 7.5. Domain-mapping experiments indicated that MM-CK binds to the C-terminal domains of MyBPC1, which is also the binding site of myosin. The functional coupling of myosin, MyBPC1 and MM-CK is further corroborated using an ATPase activity assay in which ATP expenditure accelerates upon the association of the three proteins, and the apparent K(m) value of myosin is therefore reduced. The results of the present study suggest that MyBPC1 acts as an adaptor to connect the ATP consumer (myosin) and the regenerator (MM-CK) for efficient energy metabolism and homoeostasis.
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