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Rao Z, Kim SY, Li X, Kim DS, Kim YJ, Park JH. Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase. Mol Cells 2020; 43:784-792. [PMID: 32863281 PMCID: PMC7528679 DOI: 10.14348/molcells.2020.0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 11/27/2022] Open
Abstract
Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna (DmAK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in DmAK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of DmAK.
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Affiliation(s)
- Zhili Rao
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- These authors contributed equally to this work
| | - So Young Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- These authors contributed equally to this work
| | - Xiaotong Li
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Yong Ju Kim
- Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
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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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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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Seafood allergy: A comprehensive review of fish and shellfish allergens. Mol Immunol 2018; 100:28-57. [PMID: 29858102 DOI: 10.1016/j.molimm.2018.04.008] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/23/2022]
Abstract
Seafood refers to several distinct groups of edible aquatic animals including fish, crustacean, and mollusc. The two invertebrate groups of crustacean and mollusc are, for culinary reasons, often combined as shellfish but belong to two very different phyla. The evolutionary and taxonomic diversity of the various consumed seafood species poses a challenge in the identification and characterisation of the major and minor allergens critical for reliable diagnostics and therapeutic treatments. Many allergenic proteins are very different between these groups; however, some pan-allergens, including parvalbumin, tropomyosin and arginine kinase, seem to induce immunological and clinical cross-reactivity. This extensive review details the advances in the bio-molecular characterisation of 20 allergenic proteins within the three distinct seafood groups; fish, crustacean and molluscs. Furthermore, the structural and biochemical properties of the major allergens are described to highlight the immunological and subsequent clinical cross-reactivities. A comprehensive list of purified and recombinant allergens is provided, and the applications of component-resolved diagnostics and current therapeutic developments are discussed.
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Zuo H, Chen L, Kong M, Yang Y, Lü P, Qiu L, Wang Q, Ma S, Chen K. The toxic effect of sodium fluoride on Spodoptera frugiperda 9 cells and differential protein analysis following NaF treatment of cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 236:313-323. [PMID: 29414353 DOI: 10.1016/j.envpol.2018.01.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Accumulation of excess fluoride has a destructive effect on the environment, endangering human health, affecting organism growth and development, and leading to damage to the biological chain, thereby affecting ecological environment balance. In recent years, numerous studies focused on the molecular mechanisms associated with fluoride toxicity; however, fluoride-toxicity mechanisms in insect cells remain unclear. This study explored the toxic impact of sodium fluoride (NaF) on Spodoptera frugiperda 9 (Sf9) insect cells. High concentrations of NaF (10-4 M, 10-3 M and 10-2 M) resulted in cell enlargement, cell membrane blurring and breakage, and release of cellular contents. Dose-response curves indicated that NaF-specific inhibition rates on Sf9-cell activity increased along with increases in NaF concentration, with a half-inhibitory concentration (IC50) for NaF of 5.919 × 10-3 M at 72 h. Compared with controls, the percentages of early and late apoptotic and necrotic cells clearly increased based on observed increases in NaF concentrations. Two-dimensional gel electrophoresis combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to detect differentially expressed proteins in Sf9 cells treated with IC50 NaF, identifying 17 proteins, seven of which were upregulated and 10 downregulated. These results demonstrated that Sf9 cells showed signs of NaF-mediated toxicity through alterations in cell morphology, apoptosis rates, and protein expression.
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Affiliation(s)
- Huan Zuo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Liang Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ming Kong
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Peng Lü
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lipeng Qiu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Qiang Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shangshang Ma
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Godsey MH, Davulcu O, Nix JC, Skalicky JJ, Brüschweiler RP, Chapman MS. The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase. Structure 2016; 24:1658-1667. [PMID: 27594681 DOI: 10.1016/j.str.2016.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 01/26/2023]
Abstract
Arginine kinase provides a model for functional dynamics, studied through crystallography, enzymology, and nuclear magnetic resonance. Structures are now solved, at ambient temperature, for the transition state analog (TSA) complex. Analysis of quasi-rigid sub-domain displacements show that differences between the two TSA structures average about 5% of changes between substrate-free and TSA forms, and they are nearly co-linear. Small backbone hinge rotations map to sites that also flex on substrate binding. Anisotropic atomic displacement parameters (ADPs) are refined using rigid-body TLS constraints. Consistency between crystal forms shows that they reflect intrinsic molecular properties more than crystal lattice effects. In many regions, the favored directions of thermal/static displacement are appreciably correlated with movements on substrate binding. Correlation between ADPs and larger substrate-associated movements implies that the latter approximately follow paths of low-energy intrinsic motions.
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Affiliation(s)
- Michael H Godsey
- Department of Math/Science, Concordia University, Portland, OR 97211, USA
| | - Omar Davulcu
- Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jay C Nix
- Molecular Biology Consortium, Lawrence Berkeley Natl. Lab., Berkeley, CA 94720, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 8412, USA
| | - Rafael P Brüschweiler
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael S Chapman
- Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
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Valera Vera EA, Sayé M, Reigada C, Damasceno FS, Silber AM, Miranda MR, Pereira CA. Resveratrol inhibits Trypanosoma cruzi arginine kinase and exerts a trypanocidal activity. Int J Biol Macromol 2016; 87:498-503. [DOI: 10.1016/j.ijbiomac.2016.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
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Noh S, Marshall JL. Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets. PeerJ 2016; 4:e1678. [PMID: 26893965 PMCID: PMC4756749 DOI: 10.7717/peerj.1678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK) and apolipoprotein A-1 binding protein (APBP). These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of conspecific males to induce oviposition in females.
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Affiliation(s)
- Suegene Noh
- Department of Biology, Washington University in St. Louis , St. Louis, MO , United States
| | - Jeremy L Marshall
- Department of Entomology, Kansas State University , Manhattan, KS , United States
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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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Proteomic approach for identifying gonad differential proteins in the oyster (Crassostrea angulata) following food-chain contamination with HgCl2. J Proteomics 2013; 94:37-53. [DOI: 10.1016/j.jprot.2013.08.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/17/2013] [Accepted: 08/20/2013] [Indexed: 12/17/2022]
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