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Blumenthal DK, Cheng X, Fajer M, Ho KY, Rohrer J, Gerlits O, Taylor P, Juneja P, Kovalevsky A, Radić Z. Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects. J Biol Chem 2021; 297:101007. [PMID: 34324828 PMCID: PMC8384907 DOI: 10.1016/j.jbc.2021.101007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/26/2022] Open
Abstract
Acetylcholinesterase (EC 3.1.1.7), a key acetylcholine-hydrolyzing enzyme in cholinergic neurotransmission, is present in a variety of states in situ, including monomers, C-terminally disulfide-linked homodimers, homotetramers, and up to three tetramers covalently attached to structural subunits. Could oligomerization that ensures high local concentrations of catalytic sites necessary for efficient neurotransmission be affected by environmental factors? Using small-angle X-ray scattering (SAXS) and cryo-EM, we demonstrate that homodimerization of recombinant monomeric human acetylcholinesterase (hAChE) in solution occurs through a C-terminal four-helix bundle at micromolar concentrations. We show that diethylphosphorylation of the active serine in the catalytic gorge or isopropylmethylphosphonylation by the RP enantiomer of sarin promotes a 10-fold increase in homodimer dissociation. We also demonstrate the dissociation of organophosphate (OP)-conjugated dimers is reversed by structurally diverse oximes 2PAM, HI6, or RS194B, as demonstrated by SAXS of diethylphosphoryl-hAChE. However, binding of oximes to the native ligand-free hAChE, binding of high-affinity reversible ligands, or formation of an SP-sarin-hAChE conjugate had no effect on homodimerization. Dissociation monitored by time-resolved SAXS occurs in milliseconds, consistent with rates of hAChE covalent inhibition. OP-induced dissociation was not observed in the SAXS profiles of the double-mutant Y337A/F338A, where the active center gorge volume is larger than in wildtype hAChE. These observations suggest a key role of the tightly packed acyl pocket in allosterically triggered OP-induced dimer dissociation, with the potential for local reduction of acetylcholine-hydrolytic power in situ. Computational models predict allosteric correlated motions extending from the acyl pocket toward the four-helix bundle dimerization interface 25 Å away.
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Affiliation(s)
- Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Mikolai Fajer
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Kwok-Yiu Ho
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Jacqueline Rohrer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, Tennessee, USA
| | - Palmer Taylor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Puneet Juneja
- Cryo-EM Facility, Iowa State University, Ames, Iowa, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.
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Németh E, Nagy Z, Pécsváradi A. Corrigendum: Chloroplast Glutamine Synthetase, the Key Regulator of Nitrogen Metabolism in Wheat, Performs Its Role by Fine Regulation of Enzyme Activity via Negative Cooperativity of Its Subunits. Front Plant Sci 2018; 9:466. [PMID: 29722357 PMCID: PMC5928443 DOI: 10.3389/fpls.2018.00466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/23/2018] [Indexed: 05/28/2023]
Abstract
[This corrects the article on p. 191 in vol. 9, PMID: 29520285.].
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Affiliation(s)
- Edit Németh
- Department of Plant Biology, University of Szeged, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Zoltán Nagy
- Cereal Research Non-profit Ltd., Szeged, Hungary
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Németh E, Nagy Z, Pécsváradi A. Chloroplast Glutamine Synthetase, the Key Regulator of Nitrogen Metabolism in Wheat, Performs Its Role by Fine Regulation of Enzyme Activity via Negative Cooperativity of Its Subunits. Front Plant Sci 2018; 9:191. [PMID: 29520285 PMCID: PMC5827528 DOI: 10.3389/fpls.2018.00191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/01/2018] [Indexed: 05/24/2023]
Abstract
Glutamine synthetase (GS) is of central interest as the main route of ammonia assimilation in plants, and as a connection point between the organic and inorganic worlds. Even though GS activity is critical for producing high yields of crop plants, the autoregulation of substrate consumption of wheat GS remained unknown until now. Here we show kinetic evidence, that the chloroplast localized GS isoform (GS2) of wheat (Triticum aestivum L. cv. Jubilejnaja-50) takes place at the carbon-nitrogen metabolic branch point, where it is a mediator, and its enzymatic activity is regulated in a negatively cooperative allosteric manner. We have discovered that GS2 activity is described by a tetraphasic kinetic curve in response to increasing levels of glutamate supply. We constructed a model that explains the kinetic properties of glutamate consumption and this unique allosteric behavior. We also studied the subunit composition of both wheat leaf GS isoenzymes by a combination of two dimensional gel electrophoresis and protein blotting. Both leaf isozymes have homogeneous subunit composition. Glutamate is both a substrate, and an allosteric regulator of the biosynthetic reaction. We have concluded on the basis of our results and previous reports, that wheat GS2 is probably a homooctamer, and that it processes its substrate in a well-regulated, concentration dependent way, as a result of its negatively cooperative, allosteric activity. Thus, GS2 has a central role as a regulator between the nitrogen and the carbon cycles via maintaining glutamine-glutamate pool in the chloroplast on the level of substrates, in addition to its function in ammonia assimilation.
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Affiliation(s)
- Edit Németh
- Department of Plant Biology, University of Szeged, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Zoltán Nagy
- Cereal Research Non-profit Ltd., Szeged, Hungary
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Machado ATP, Fonseca EMB, Reis MAD, Saraiva AM, Santos CAD, de Toledo MAS, Polikarpov I, de Souza AP, Aparicio R, Iulek J. Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis. Proteins 2017; 85:1931-1943. [PMID: 28677327 DOI: 10.1002/prot.25347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/07/2017] [Accepted: 07/02/2017] [Indexed: 11/05/2022]
Abstract
Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein.
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Affiliation(s)
| | | | - Marcelo Augusto Dos Reis
- Institute of Chemistry, University of Campinas, São Paulo, Brazil.,Federal Institute of Education, Science and Technology of South of Minas Gerais, Inconfidentes, Minas Gerais, Brazil
| | - Antonio Marcos Saraiva
- Molecular Biology and Genetic Engineering Centre, University of Campinas, São Paulo, Brazil
| | | | | | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Centre, University of Campinas, São Paulo, Brazil.,Department of Plant Biology, Biology Institute, University of Campinas, São Paulo, Brazil
| | - Ricardo Aparicio
- Institute of Chemistry, University of Campinas, São Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Brazil
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Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins 2009; 76:403-17. [PMID: 19173312 PMCID: PMC4101808 DOI: 10.1002/prot.22355] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An unresolved question about GPCR function is the role of membrane components in receptor stability and activation. In particular, cholesterol is known to affect the function of membrane proteins, but the details of its effect on GPCRs are still elusive. Here, we describe how cholesterol modulates the behavior of the TM1-TM2-TM7-helix 8(H8) functional network that comprises the highly conserved NPxxY(x)(5,6)F motif, through specific interactions with the receptor. The inferences are based on the analysis of microsecond length molecular dynamics (MD) simulations of rhodopsin in an explicit membrane environment. Three regions on the rhodopsin exhibit the highest cholesterol density throughout the trajectory: the extracellular end of TM7, a location resembling the high-density sterol area from the electron microscopy data; the intracellular parts of TM1, TM2, and TM4, a region suggested as the cholesterol binding site in the recent X-ray crystallography data on beta(2)-adrenergic GPCR; and the intracellular ends of TM2-TM3, a location that was categorized as the high cholesterol density area in multiple independent 100 ns MD simulations of the same system. We found that cholesterol primarily affects specific local perturbations of the helical TM domains such as the kinks in TM1, TM2, and TM7. These local distortions, in turn, relate to rigid-body motions of the TMs in the TM1-TM2-TM7-H8 bundle. The specificity of the effects stems from the nonuniform distribution of cholesterol around the protein. Through correlation analysis we connect local effects of cholesterol on structural perturbations with a regulatory role of cholesterol in the structural rearrangements involved in GPCR function.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA.
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Edwards BF, Evans DR, Warren SG, Monaco HL, Landfear SM, Eisele G, Crawford JL, Wiley DC, Lipscomb WN. Complex of aspartate carbamoyltransferase from Escherichia coli with its allosteric inhibitor, cytidine triphosphate: electron density at 5.9-angstroms resolution. Proc Natl Acad Sci U S A 1974; 71:4437-41. [PMID: 4612518 PMCID: PMC433901 DOI: 10.1073/pnas.71.11.4437] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Following our earlier determination of the three-dimensional structure of aspartate carbamoyltransferase (EC 2.1.3.2; carbamoylphosphate: L-aspartate carbamoyltransferase) to 5.5-A resolution [S. G. Warren, B. F. P. Edwards, D. R. Evans, D. C. Wiley & W. N. Lipscomb (1973) Proc. Nat. Acad. Sci. USA 70, 1117-1121], we report here, from a different crystal form, the three-dimensional structure at 5.9 A of this enzyme complexed with its allosteric inhibitor, cytidine triphosphate. Location of the major binding site of this inhibitor within each of the six regulatory chains is made secure by comparison of these results with those obtained upon binding of 5-iodocytidine triphosphate to the enzyme. Conformational changes in the aspartate carbamoyltransferase molecule when this inhibitor binds are described briefly at 5.9-A resolution.
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