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Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep 2019; 9:18035. [PMID: 31792294 PMCID: PMC6889508 DOI: 10.1038/s41598-019-54564-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
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Klimanova EA, Sidorenko SV, Tverskoi AM, Shiyan AA, Smolyaninova LV, Kapilevich LV, Gusakova SV, Maksimov GV, Lopina OD, Orlov SN. Search for Intracellular Sensors Involved in the Functioning of Monovalent Cations as Secondary Messengers. BIOCHEMISTRY (MOSCOW) 2019; 84:1280-1295. [DOI: 10.1134/s0006297919110063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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53
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Gottschalk J, Zaun H, Eisele A, Kuballa J, Elling L. Key Factors for A One-Pot Enzyme Cascade Synthesis of High Molecular Weight Hyaluronic Acid. Int J Mol Sci 2019; 20:ijms20225664. [PMID: 31726754 PMCID: PMC6888640 DOI: 10.3390/ijms20225664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
In the last decades, interest in medical or cosmetic applications of hyaluronic acid (HA) has increased. Size and dispersity are key characteristics of biological function. In contrast to extraction from animal tissue or bacterial fermentation, enzymatic in vitro synthesis is the choice to produce defined HA. Here we present a one-pot enzyme cascade with six enzymes for the synthesis of HA from the cheap monosaccharides glucuronic acid (GlcA) and N-acetylglucosamine (GlcNAc). The combination of two enzyme modules, providing the precursors UDP–GlcA and UDP–GlcNAc, respectively, with hyaluronan synthase from Pasteurella multocida (PmHAS), was optimized to meet the kinetic requirements of PmHAS for high HA productivity and molecular weight. The Mg2+ concentration and the pH value were found as key factors. The HA product can be tailored by different conditions: 25 mM Mg2+ and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid (HEPES)-NaOH pH 8 result into an HA product with high Mw HA (1.55 MDa) and low dispersity (1.05). Whereas with 15 mM Mg2+ and HEPES–NaOH pH 8.5, we reached the highest HA concentration (2.7 g/L) with a yield of 86.3%. Our comprehensive data set lays the basis for larger scale enzymatic HA synthesis.
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Affiliation(s)
- Johannes Gottschalk
- Laboratory for Biomaterials, Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (J.G.); (A.E.)
| | - Henning Zaun
- Research and Development Department, GALAB Laboratories GmbH, Am Schleusengraben 7, 21029 Hamburg, Germany; (H.Z.); (J.K.)
| | - Anna Eisele
- Laboratory for Biomaterials, Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (J.G.); (A.E.)
| | - Jürgen Kuballa
- Research and Development Department, GALAB Laboratories GmbH, Am Schleusengraben 7, 21029 Hamburg, Germany; (H.Z.); (J.K.)
| | - Lothar Elling
- Laboratory for Biomaterials, Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (J.G.); (A.E.)
- Correspondence: ; Tel.: +49-241-80-28350
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Live cell imaging of signaling and metabolic activities. Pharmacol Ther 2019; 202:98-119. [DOI: 10.1016/j.pharmthera.2019.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
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56
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Bischof H, Burgstaller S, Vujic N, Madl T, Kratky D, Graier WF, Malli R. Purification and Application of Genetically Encoded Potassium Ion Indicators for Quantification of Potassium Ion Concentrations within Biological Samples. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2019; 11:e71. [PMID: 31483097 PMCID: PMC6927797 DOI: 10.1002/cpch.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Vital cells maintain a steep potassium ion (K+ ) gradient across the plasma membrane. Intracellular potassium ion concentrations ([K+ ]) and especially the [K+ ] within the extracellular matrix are strictly regulated, the latter within a narrow range of ∼3.5 to 5.0 mM. Alterations of the extracellular K+ homeostasis are associated with severe pathological alterations and systemic diseases including hypo- or hypertension, heart rate alterations, heart failure, neuronal damage or abnormal skeleton muscle function. In higher eukaryotic organisms, the maintenance of the extracellular [K+ ] is mainly achieved by the kidney, responsible for K+ excretion and reabsorption. Thus, renal dysfunctions are typically associated with alterations in serum- or plasma [K+ ]. Generally, [K+ ] quantifications within bodily fluids are performed using ion selective electrodes. However, tracking such alterations in experimental models such as mice features several difficulties, mainly due to the small blood volume of these animals, hampering the repetitive collection of sample volumes required for measurements using ion selective electrodes. We have recently developed highly sensitive, genetically encoded potassium ion indicators, the GEPIIs, applicable for in vitro determinations of [K+ ]. In addition to the determination of [K+ ] within bodily fluids, GEPIIs proved suitable for the real-time visualization of cell viability over time and the exact determination of the number of dead cells. © 2019 The Authors.
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Affiliation(s)
- H Bischof
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - S Burgstaller
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - N Vujic
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - T Madl
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - D Kratky
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - W F Graier
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - R Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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57
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Kale D, Spurny P, Shamayeva K, Spurna K, Kahoun D, Ganser D, Zayats V, Ludwig J. The S. cerevisiae cation translocation protein Trk1 is functional without its “long hydrophilic loop” but LHL regulates cation translocation activity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1476-1488. [DOI: 10.1016/j.bbamem.2019.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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58
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Gatenby RA. The Role of Cell Membrane Information Reception, Processing, and Communication in the Structure and Function of Multicellular Tissue. Int J Mol Sci 2019; 20:ijms20153609. [PMID: 31344783 PMCID: PMC6696332 DOI: 10.3390/ijms20153609] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/18/2019] [Indexed: 01/12/2023] Open
Abstract
Investigations of information dynamics in eukaryotic cells focus almost exclusively on heritable information in the genome. Gene networks are modeled as “central processors” that receive, analyze, and respond to intracellular and extracellular signals with the nucleus described as a cell’s control center. Here, we present a model in which cellular information is a distributed system that includes non-genomic information processing in the cell membrane that may quantitatively exceed that of the genome. Within this model, the nucleus largely acts a source of macromolecules and processes information needed to synchronize their production with temporal variations in demand. However, the nucleus cannot produce microsecond responses to acute, life-threatening perturbations and cannot spatially resolve incoming signals or direct macromolecules to the cellular regions where they are needed. In contrast, the cell membrane, as the interface with its environment, can rapidly detect, process, and respond to external threats and opportunities through the large amounts of potential information encoded within the transmembrane ion gradient. Our model proposes environmental information is detected by specialized protein gates within ion-specific transmembrane channels. When the gate receives a specific environmental signal, the ion channel opens and the received information is communicated into the cell via flow of a specific ion species (i.e., K+, Na+, Cl−, Ca2+, Mg2+) along electrochemical gradients. The fluctuation of an ion concentration within the cytoplasm adjacent to the membrane channel can elicit an immediate, local response by altering the location and function of peripheral membrane proteins. Signals that affect a larger surface area of the cell membrane and/or persist over a prolonged time period will produce similarly cytoplasmic changes on larger spatial and time scales. We propose that as the amplitude, spatial extent, and duration of changes in cytoplasmic ion concentrations increase, the information can be communicated to the nucleus and other intracellular structure through ion flows along elements of the cytoskeleton to the centrosome (via microtubules) or proteins in the nuclear membrane (via microfilaments). These dynamics add spatial and temporal context to the more well-recognized information communication from the cell membrane to the nucleus following ligand binding to membrane receptors. Here, the signal is transmitted and amplified through transduction by the canonical molecular (e.g., Mitogen Activated Protein Kinases (MAPK) pathways. Cytoplasmic diffusion allows this information to be broadly distributed to intracellular organelles but at the cost of loss of spatial and temporal information also contained in ligand binding.
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Affiliation(s)
- Robert A Gatenby
- Departments of Radiology and Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA.
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59
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Live-Cell Imaging of Physiologically Relevant Metal Ions Using Genetically Encoded FRET-Based Probes. Cells 2019; 8:cells8050492. [PMID: 31121936 PMCID: PMC6562680 DOI: 10.3390/cells8050492] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 01/02/2023] Open
Abstract
Essential biochemical reactions and processes within living organisms are coupled to subcellular fluctuations of metal ions. Disturbances in cellular metal ion homeostasis are frequently associated with pathological alterations, including neurotoxicity causing neurodegeneration, as well as metabolic disorders or cancer. Considering these important aspects of the cellular metal ion homeostasis in health and disease, measurements of subcellular ion signals are of broad scientific interest. The investigation of the cellular ion homeostasis using classical biochemical methods is quite difficult, often even not feasible or requires large cell numbers. Here, we report of genetically encoded fluorescent probes that enable the visualization of metal ion dynamics within individual living cells and their organelles with high temporal and spatial resolution. Generally, these probes consist of specific ion binding domains fused to fluorescent protein(s), altering their fluorescent properties upon ion binding. This review focuses on the functionality and potential of these genetically encoded fluorescent tools which enable monitoring (sub)cellular concentrations of alkali metals such as K+, alkaline earth metals including Mg2+ and Ca2+, and transition metals including Cu+/Cu2+ and Zn2+. Moreover, we discuss possible approaches for the development and application of novel metal ion biosensors for Fe2+/Fe3+, Mn2+ and Na+.
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60
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Huang LK, Liao YY, Lin WH, Lin SM, Liu TY, Lee CH, Pan RL. Potassium Stimulation of IAA Transport Mediated by the Arabidopsis Importer AUX1 Investigated in a Heterologous Yeast System. J Membr Biol 2019; 252:183-194. [PMID: 31053903 DOI: 10.1007/s00232-019-00065-6] [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: 08/19/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
Abstract
Auxin regulates diverse processes involved in plant growth and development. AUX1 is the first identified and most widely investigated auxin importer, and plays an important role in root gravitropism and the development of lateral root and root hair. However, the regulation of auxin transport by AUX1 is still not well understood. In this study, we examined the effect of metal ions on AUX1 transport function and found that the activity could be specifically stimulated four times by K+. Further experiments revealed the preference of KF on the enhancement of transport activity of AUX1 over KCl, KBr, and KI. In addition, the interaction between K+ and AUX1 confers AUX1 more resistant to thermal stress but more vulnerable to proteolysis. Conventional chemical modification indicated that the extracellular acidic amino acids of AUX1 play a key role in the K+ stimulation. Site-specific mutagenesis showed that the replacement of Asp166, Asp293, and Asp312 of AUX1 to alanine deteriorated the K+-stimulated auxin transport. By contrast, when these residues were mutated to glutamate, lysine, or asparagine, only the D312E variant restored the IAA transport activity to the wild-type level. It is thus convinced that D312 is presumably the most promising residue for the K+ stimulation on AUX1.
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Affiliation(s)
- Li-Kun Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China
| | - Ya-Yun Liao
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China
| | - Wei-Hua Lin
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China
| | - Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China
| | - Ching-Hung Lee
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China.
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China.
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61
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Frieden BR, Gatenby RA. Signal transmission through elements of the cytoskeleton form an optimized information network in eukaryotic cells. Sci Rep 2019; 9:6110. [PMID: 30992457 PMCID: PMC6467984 DOI: 10.1038/s41598-019-42343-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/25/2019] [Indexed: 11/23/2022] Open
Abstract
Multiple prior empirical and theoretical studies have demonstrated wire-like flow of electrons and ions along elements of the cytoskeleton but this has never been linked to a biological function. Here we propose that eukaryotes use this mode of signal transmission to convey spatial and temporal environmental information from the cell membrane to the nucleus. The cell membrane, as the interface between intra- and extra-cellular environments, is the site at which much external information is received. Prior studies have demonstrated that transmembrane ion gradients permit information acquisition when an environmental signal interacts with specialized protein gates in membrane ion channels and producing specific ions to flow into or out of the cell along concentration gradients. The resulting localized change in cytoplasmic ion concentrations and charge density can alter location and enzymatic function of peripheral membrane proteins. This allows the cell to process the information and rapidly deploy a local response. Here we investigate transmission of information received and processed in and around the cell membrane by elements of the cytoskeleton to the nucleus to alter gene expression. We demonstrate signal transmission by ion flow along the cytoskeleton is highly optimized. In particular, microtubules, with diameters of about 30 nm, carry coarse-grained Shannon information to the centrosome adjacent to the nucleus with minimum loss of input source information. And, microfilaments, with diameters of about 4 nm, transmit maximum Fisher (fine-grained) information to protein complexes in the nuclear membrane. These previously unrecognized information dynamics allow continuous integration of spatial and temporal environmental signals with inherited information in the genome.
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Affiliation(s)
- B R Frieden
- College of Optical Science, University of Arizona, Tucson, AZ, USA
| | - R A Gatenby
- Department of Integrated Mathematical Biology, Moffitt Cancer Center, Tampa, FL, USA.
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62
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Wineman-Fisher V, Al-Hamdani Y, Addou I, Tkatchenko A, Varma S. Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields. J Chem Theory Comput 2019; 15:2444-2453. [PMID: 30830778 PMCID: PMC6598712 DOI: 10.1021/acs.jctc.8b01198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols. Both water and alcohols use hydroxyls for ion-coordination, and, therefore, this set of molecules constitutes the simplest possible case of transferability. We obtain gas phase reference data systematically from "gold-standard" quantum Monte Carlo and CCSD(T) methods, followed by benchmarked vdW-corrected DFT. We learn that the original polarizable model yields large gas phase water → alcohol transferability errors - the RMS and maximum errors are 2.3 and 5.1 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are overstabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low- and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly - the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Additionally, predictions of condensed phase transfer free energies also improve. Nevertheless, within the limits of the extrathermodynamic assumptions necessary to separate experimental estimates of salt dissolution into constituent cationic and anionic contributions, we note that the error in the condensed phase is systematic, which we attribute, at least, partially to the parametrization in long-range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and nonpolarizable models.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Yasmine Al-Hamdani
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Fïancerie , Luxembourg City , L-1511 , Luxembourg
| | - Iqbal Addou
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Fïancerie , Luxembourg City , L-1511 , Luxembourg
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
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63
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Korte AR, Morris NJ, Vertes A. High Throughput Complementary Analysis and Quantitation of Metabolites by MALDI- and Silicon Nanopost Array-Laser Desorption/Ionization-Mass Spectrometry. Anal Chem 2019; 91:3951-3958. [PMID: 30786207 DOI: 10.1021/acs.analchem.8b05074] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K - H]+ species accounting for as much as 97% of the total metabolite ion signal in positive mode. The capability of NAPA-MS for targeted quantitation of endogenous metabolites in urine via addition of isotopically labeled standards was also examined. Both NAPA-MS and MALDI-MS provided quantitative results in good agreement with one another and the concentrations reported in the literature, as well as good sample-to-sample reproducibility (RSD < 10%).
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Affiliation(s)
- Andrew R Korte
- Department of Chemistry , George Washington University , Washington , D.C. 20052 , United States
| | | | - Akos Vertes
- Department of Chemistry , George Washington University , Washington , D.C. 20052 , United States
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64
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Xiao J, Salsbury FR. Na +-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. Phys Chem Chem Phys 2019; 21:4320-4330. [PMID: 30724273 PMCID: PMC6993936 DOI: 10.1039/c8cp07293k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The monovalent sodium ion (Na+) is a critical modulator of thrombin. However, the mechanism of thrombin's activation by Na+ has been widely debated for more than twenty years. Details of the linkage between thrombin and Na+ remain vague due to limited temporal and spatial resolution in experiments. In this work, we combine microsecond scale atomic-detailed molecular dynamics simulations with correlation network analyses and hidden Markov modeling to probe the detailed thermodynamic and kinetic picture of Na+-binding events and their resulting allosteric responses in thrombin. We reveal that ASP189 and ALA190 comprise a stable Na+-binding site (referred as "inner" Na+-binding site) along with the previously known one (referred as "outer" Na+-binding site). The corresponding newly identified Na+-binding mode introduces significant allosteric responses in thrombin's regulatory regions by stabilizing selected torsion angles of residues responsive to Na+-binding. Our Markov model indicates that the bound Na+ prefers to transfer between the two Na+-binding sites when an unbinding event takes place. These results suggest a testable hypothesis of a substrate-driven Na+ migration (ΔG ∼ 1.7 kcal mol-1) from the "inner" Na+-binding site to the "outer" one during thrombin's catalytic activities. The binding of a Na+ ion at the "inner" Na+-binding site should be inferred as a prerequisite for thrombin's efficient recognition to the substrate, which opens a new angle for our understanding of Na+-binding's allosteric activation on thrombin and sheds light on detailed processes in thrombin's activation.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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65
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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66
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Sediqi H, Wray A, Jones C, Jones M. Application of Spectral Phasor analysis to sodium microenvironments in myoblast progenitor cells. PLoS One 2018; 13:e0204611. [PMID: 30379959 PMCID: PMC6209149 DOI: 10.1371/journal.pone.0204611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
Sodium ions (Na+) are key regulators of molecular events in many cellular processes, yet the dynamics of this ion remain poorly defined. Developing approaches to identify and characterise Na+ microenvironments will enable more detailed elucidation of the mechanisms of signal transduction. Here we report the application of Spectral Phasor analysis to the Na+ fluorophore, CoroNa Green, to identify and spatially map spectral emissions that report Na+ microenvironments. We use differentiating stem cells where Na+ fluxes were reported as an antecedent. Myoblast stem cells were induced to differentiate by serum starvation and then fixed at intervals between 0 and 40-minutes of differentiation prior to addition of CoroNa Green. The fluorescent intensity was insufficient to identify discrete Na+ microenvironments. However, using Spectral Phasor analysis we identified spectral shifts in CoroNa Green fluorescence which is related to the Na+ microenvironment. Further, spectral-heterogeneity appears to be contingent on the distance of Na+ from the nucleus in the early stages of differentiation. Spectral Phasor analysis of CoroNa Green in fixed stem cells demonstrates for the first time that CoroNa Green has unique spectral emissions depending on the nature of the Na+ environment in differentiating stem cells. Applying Spectral Phasor analysis to CoroNa Green in live stem cells is likely to further elucidate the role of Na+ microenvironments in the differentiation process.
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Affiliation(s)
- Hamid Sediqi
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Alex Wray
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Christopher Jones
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Mark Jones
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
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67
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Aparicio D, Torres-Puig S, Ratera M, Querol E, Piñol J, Pich OQ, Fita I. Mycoplasma genitalium adhesin P110 binds sialic-acid human receptors. Nat Commun 2018; 9:4471. [PMID: 30367053 PMCID: PMC6203739 DOI: 10.1038/s41467-018-06963-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023] Open
Abstract
Adhesion of pathogenic bacteria to target cells is a prerequisite for colonization and further infection. The main adhesins of the emerging sexually transmitted pathogen Mycoplasma genitalium, P140 and P110, interact to form a Nap complex anchored to the cell membrane. Herein, we present the crystal structures of the extracellular region of the virulence factor P110 (916 residues) unliganded and in complex with sialic acid oligosaccharides. P110 interacts only with the neuraminic acid moiety of the oligosaccharides and experiments with human cells demonstrate that these interactions are essential for mycoplasma cytadherence. Additionally, structural information provides a deep insight of the P110 antigenic regions undergoing programmed variation to evade the host immune response. These results enlighten the interplay of M. genitalium with human target cells, offering new strategies to control mycoplasma infections. How the Mycoplasma genitalium cytadhesins P140 and P110 promote host cell invasion remains poorly understood. Here, combining structural analysis with functional assays, Aparicio et al. identify the P110 domain that binds to sialylated receptors essential for mycoplasma cytadherence.
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Affiliation(s)
- David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sergi Torres-Puig
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mercè Ratera
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Oscar Q Pich
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
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68
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Immobilization of β-galactosidase in glutaraldehyde-chitosan and its application to the synthesis of lactulose using cheese whey as feedstock. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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69
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Li Y, Sun L, Lu C, Gong Y, Li M, Sun S. Promising Antifungal Targets Against Candida albicans Based on Ion Homeostasis. Front Cell Infect Microbiol 2018; 8:286. [PMID: 30234023 PMCID: PMC6131588 DOI: 10.3389/fcimb.2018.00286] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
In recent decades, invasive fungal infections have been increasing significantly, contributing to high incidences and mortality in immunosuppressed patients. Candida albicans (C. albicans) is the most prevalent opportunistic fungal pathogen in humans that can cause severe and often fatal bloodstream infections. Current antifungal agents have several limitations, including that only a small number of classes of antifungals are available, certain of which have severe toxicity and high cost. Moreover, the emergence of drug resistance is a new limitation to successful patient outcomes. Therefore, the development of antifungals with novel targets is an essential strategy for the efficient management of C. albicans infections. It is widely recognized that ion homeostasis is crucial for all living cells. Many studies have identified that ion-signaling and transduction networks are central to fungal survival by regulating gene expression, morphological transition, host invasion, stress response, and drug resistance. Dysregulation of ion homeostasis rapidly mediates cell death, forming the mechanistic basis of a growing number of compounds that elicit antifungal activity. Most of the potent antifungals have been widely used in the clinic, and certain of them have low toxicity, meaning that they may be expected to be used as antifungal drugs in the future. Hence, we briefly summarize the homeostasis regulation of several important ions, potential antifungal targets based on these ion-signaling networks, and antifungal compounds based on the disruption of ion homeostasis. This summary will help in designing effective drugs and identifying new targets for combating fungal diseases.
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Affiliation(s)
- Yiman Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Licui Sun
- Department of Pharmacy, Feicheng Mining Central Hospital, Feicheng, China
| | - Chunyan Lu
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
| | - Ying Gong
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Min Li
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
| | - Shujuan Sun
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
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70
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Banerjee I, Behl B, Mendonca M, Shrivastava G, Russo AJ, Menoret A, Ghosh A, Vella AT, Vanaja SK, Sarkar SN, Fitzgerald KA, Rathinam VAK. Gasdermin D Restrains Type I Interferon Response to Cytosolic DNA by Disrupting Ionic Homeostasis. Immunity 2018; 49:413-426.e5. [PMID: 30170814 DOI: 10.1016/j.immuni.2018.07.006] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/18/2018] [Accepted: 07/12/2018] [Indexed: 10/28/2022]
Abstract
Inflammasome-activated caspase-1 cleaves gasdermin D to unmask its pore-forming activity, the predominant consequence of which is pyroptosis. Here, we report an additional biological role for gasdermin D in limiting cytosolic DNA surveillance. Cytosolic DNA is sensed by Aim2 and cyclic GMP-AMP synthase (cGAS) leading to inflammasome and type I interferon responses, respectively. We found that gasdermin D activated by the Aim2 inflammasome suppressed cGAS-driven type I interferon response to cytosolic DNA and Francisella novicida in macrophages. Similarly, interferon-β (IFN-β) response to F. novicida infection was elevated in gasdermin D-deficient mice. Gasdermin D-mediated negative regulation of IFN-β occurred in a pyroptosis-, interleukin-1 (IL-1)-, and IL-18-independent manner. Mechanistically, gasdermin D depleted intracellular potassium (K+) via membrane pores, and this K+ efflux was necessary and sufficient to inhibit cGAS-dependent IFN-β response. Thus, our findings have uncovered an additional interferon regulatory module involving gasdermin D and K+ efflux.
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Affiliation(s)
- Ishita Banerjee
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Bharat Behl
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Morena Mendonca
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA; Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Ashley J Russo
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Antoine Menoret
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Arundhati Ghosh
- Cancer Virology Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Anthony T Vella
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Sivapriya Kailasan Vanaja
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Saumendra N Sarkar
- Cancer Virology Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Centre for Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, NTNU, 7491 Trondheim, Norway
| | - Vijay A K Rathinam
- Department of Immunology, UConn Health School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA.
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71
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Adenosine Kinase couples sensing of cellular potassium depletion to purine metabolism. Sci Rep 2018; 8:11988. [PMID: 30097648 PMCID: PMC6086891 DOI: 10.1038/s41598-018-30418-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023] Open
Abstract
Adenosine Kinase (ADK) regulates the cellular levels of adenosine (ADO) by fine-tuning its metabolic clearance. The transfer of γ-phosphate from ATP to ADO by ADK involves regulation by the substrates and products, as well as by Mg2+ and inorganic phosphate. Here we present new crystal structures of mouse ADK (mADK) binary (mADK:ADO; 1.2 Å) and ternary (mADK:ADO:ADP; 1.8 Å) complexes. In accordance with the structural demonstration of ADO occupancy of the ATP binding site, kinetic studies confirmed a competitive model of auto-inhibition of ADK by ADO. In the ternary complex, a K+ ion is hexacoordinated between loops adjacent to the ATP binding site, where Asp310 connects the K+ coordination sphere to the ATP binding site through an anion hole structure. Nuclear Magnetic Resonance 2D 15N-1H HSQC experiments revealed that the binding of K+ perturbs Asp310 and residues of adjacent helices 14 and 15, engaging a transition to a catalytically productive structure. Consistent with the structural data, the mutants D310A and D310P are catalytically deficient and loose responsiveness to K+. Saturation Transfer Difference spectra of ATPγS provided evidence for an unfavorable interaction of the mADK D310P mutant for ATP. Reductions in K+ concentration diminish, whereas increases enhance the in vitro activity of mADK (maximum of 2.5-fold; apparent Kd = 10.4 mM). Mechanistically, K+ increases the catalytic turnover (Kcat) but does not affect the affinity of mADK for ADO or ATP. Depletion of intracellular K+ inhibited, while its restoration was accompanied by a full recovery of cellular ADK activity. Together, this novel dataset reveals the molecular basis of the allosteric activation of ADK by K+ and highlights the role of ADK in connecting depletion of intracellular K+ to the regulation of purine metabolism.
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72
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Vibrio parahaemolyticus Senses Intracellular K + To Translocate Type III Secretion System 2 Effectors Effectively. mBio 2018; 9:mBio.01366-18. [PMID: 30042203 PMCID: PMC6058294 DOI: 10.1128/mbio.01366-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many Gram-negative bacterial symbionts and pathogens employ a type III secretion system (T3SS) to live in contact with eukaryotic cells. Because T3SSs inject bacterial proteins (effectors) directly into host cells, the switching of secretory substrates between translocators and effectors in response to host cell attachment is a crucial step for the effective delivery of effectors. Here, we show that the protein secretion switch of Vibrio parahaemolyticus T3SS2, which is a main contributor to the enteropathogenicity of a food poisoning bacterium, is regulated by two gatekeeper proteins, VgpA and VgpB. In the absence of these gatekeepers, effector secretion was activated, but translocator secretion was abolished, causing the loss of virulence. We found that the K+ concentration, which is high inside the host cell but low outside, is a key factor for VgpA- and VgpB-mediated secretion switching. Exposure of wild-type bacteria to K+ ions provoked both gatekeeper and effector secretions but reduced the level of secretion of translocators. The secretion protein profile of wild-type bacteria cultured with 0.1 M KCl was similar to that of gatekeeper mutants. Furthermore, depletion of K+ ions in host cells diminished the efficiency of T3SS2 effector translocation. Thus, T3SS2 senses the high intracellular concentration of K+ of the host cell so that T3SS2 effectors can be effectively injected. The pathogenesis of many Gram-negative bacterial pathogens arises from a type III secretion system (T3SS), whereby bacterial proteins (effectors) are directly injected into host cells. The injected effectors then modify host cell functions. For effective delivery of effector proteins, bacteria need to both recognize host cell attachment and switch the type of secreted proteins. Here, we identified gatekeeper proteins that play important roles in a T3SS2 secretion switch of Vibrio parahaemolyticus, a causative agent of food-borne gastroenteritis. We also found that K+, which is present in high concentrations inside the host cell but in low concentrations outside, is a key factor for the secretion switch. Thus, V. parahaemolyticus senses the high intracellular K+ concentration, triggering the effective injection of effectors.
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73
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Rorsman NJG, Ta CM, Garnett H, Swietach P, Tammaro P. Defining the ionic mechanisms of optogenetic control of vascular tone by channelrhodopsin-2. Br J Pharmacol 2018; 175:2028-2045. [PMID: 29486056 PMCID: PMC5979753 DOI: 10.1111/bph.14183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/16/2018] [Accepted: 02/14/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE Optogenetic control of electromechanical coupling in vascular smooth muscle cells (VSMCs) is emerging as a powerful research tool with potential applications in drug discovery and therapeutics. However, the precise ionic mechanisms involved in this control remain unclear. EXPERIMENTAL APPROACH Cell imaging, patch-clamp electrophysiology and muscle tension recordings were used to define these mechanisms over a wide range of light stimulations. KEY RESULTS Transgenic mice expressing a channelrhodopsin-2 variant [ChR2(H134R)] selectively in VSMCs were generated. Isolated VSMCs obtained from these mice demonstrated blue light-induced depolarizing whole-cell currents. Fine control of artery tone was attained by varying the intensity of the light stimulus. This arterial response was sufficient to overcome the endogenous, melanopsin-mediated, light-evoked, arterial relaxation observed in the presence of contractile agonists. Ca2+ entry through voltage-gated Ca2+ channels, and opening of plasmalemmal depolarizing channels (TMEM16A and TRPM) and intracellular IP3 receptors were involved in the ChR2(H134R)-dependent arterial response to blue light at intensities lower than ~0.1 mW·mm-2 . Light stimuli of greater intensity evoked a significant Ca2+ influx directly through ChR2(H134R) and produced marked intracellular alkalinization of VSMCs. CONCLUSIONS AND IMPLICATIONS We identified the range of light intensity allowing optical control of arterial tone, primarily by means of endogenous channels and without substantial alteration to intracellular pH. Within this range, mice expressing ChR2(H134R) in VSMCs are a powerful experimental model for achieving accurate and tuneable optical voltage-clamp of VSMCs and finely graded control of arterial tone, offering new approaches to the discovery of vasorelaxant drugs.
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Affiliation(s)
- Nils J G Rorsman
- Department of PharmacologyUniversity of OxfordOxfordUK
- OXION Initiative in Ion Channels and DiseaseUniversity of OxfordOxfordUK
| | - Chau M Ta
- Department of PharmacologyUniversity of OxfordOxfordUK
| | | | - Pawel Swietach
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Paolo Tammaro
- Department of PharmacologyUniversity of OxfordOxfordUK
- OXION Initiative in Ion Channels and DiseaseUniversity of OxfordOxfordUK
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74
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Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M. Evolution of chemokine receptors is driven by mutations in the sodium binding site. PLoS Comput Biol 2018; 14:e1006209. [PMID: 29912865 PMCID: PMC6037435 DOI: 10.1371/journal.pcbi.1006209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/09/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022] Open
Abstract
Chemokines and their receptors (members of the GPCR super-family) are involved in a wide variety of physiological processes and diseases; thus, understanding the specificity of the chemokine receptor family could help develop new receptor specific drugs. Here, we explore the evolutionary mechanisms that led to the emergence of the chemokine receptors. Based on GPCR hierarchical classification, we analyzed nested GPCR sets with an eigen decomposition approach of the sequence covariation matrix and determined three key residues whose mutation was crucial for the emergence of the chemokine receptors and their subsequent divergence into homeostatic and inflammatory receptors. These residues are part of the allosteric sodium binding site. Their structural and functional roles were investigated by molecular dynamics simulations of CXCR4 and CCR5 as prototypes of homeostatic and inflammatory chemokine receptors, respectively. This study indicates that the three mutations crucial for the evolution of the chemokine receptors dramatically altered the sodium binding mode. In CXCR4, the sodium ion is tightly bound by four protein atoms and one water molecule. In CCR5, the sodium ion is mobile within the binding pocket and moves between different sites involving from one to three protein atoms and two to five water molecules. Analysis of chemokine receptor evolution reveals that a highly constrained sodium binding site characterized most ancient receptors, and that the constraints were subsequently loosened during the divergence of this receptor family. We discuss the implications of these findings for the evolution of the chemokine receptor functions and mechanisms of action.
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Affiliation(s)
- Bruck Taddese
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Madeline Deniaud
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Antoine Garnier
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Asma Tiss
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hervé Abdi
- The University of Texas at Dallas, School of Behavioral and Brain Sciences, Dallas, Texas, United States of America
| | - Daniel Henrion
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Marie Chabbert
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
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Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Rep 2018; 20:2666-2677. [PMID: 28903046 DOI: 10.1016/j.celrep.2017.08.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/05/2017] [Accepted: 08/19/2017] [Indexed: 12/21/2022] Open
Abstract
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.
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Affiliation(s)
- Ed Reznik
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Emma Briars
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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76
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Wang J, Jackson DG, Dahl G. Cationic control of Panx1 channel function. Am J Physiol Cell Physiol 2018; 315:C279-C289. [PMID: 29719168 DOI: 10.1152/ajpcell.00303.2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The sequence and predicted membrane topology of pannexin1 (Panx1) places it in the family of gap junction proteins. However, rather than forming gap junction channels, Panx1 forms channels in the nonjunctional membrane. Panx1 operates in two distinct open states, depending on the mode of stimulation. The exclusively voltage-gated channel has a small conductance (<100 pS) and is highly selective for the flux of chloride ions. The Panx1 channel activated by various physiological stimuli or by increased concentrations of extracellular potassium ions has a large conductance (~500 pS, however, with multiple, long-lasting subconductance states) and is nonselectively permeable to small molecules, including ATP. To test whether the two open conformations also differ pharmacologically, the effects of di-and trivalent cations on the two Panx1 channel conformations were investigated. The rationale for this venture was that, under certain experimental conditions, ATP release from cells can be inhibited by multivalent cations, yet the literature indicates that the ATP release channel Panx1 is not affected by these ions. Consistent with previous reports, the Panx1 channel was not activated by removal of extracellular Ca2+ and the currents through the voltage-activated channel were not altered by Ca2+, Zn2+, Ba2+, or Gd3+. In contrast, the Panx1 channel activated to the large channel conformation by extracellular K+, osmotic stress, or low oxygen was inhibited by the multivalent cations in a dose-dependent way. Thus, monovalent cations activated the Panx1 channel from the closed state to the "large" conformation, while di- and trivalent cations exclusively inhibited this large channel conformation.
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Affiliation(s)
- Junjie Wang
- Department of Physiology and Biophysics, University of Miami School of Medicine , Miami, Florida
| | - David George Jackson
- Department of Physiology and Biophysics, University of Miami School of Medicine , Miami, Florida
| | - Gerhard Dahl
- Department of Physiology and Biophysics, University of Miami School of Medicine , Miami, Florida
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Ajewole E, Santamaria‐Kisiel L, Pajak A, Jaskolski M, Marsolais F. Structural basis of potassium activation in plant asparaginases. FEBS J 2018; 285:1528-1539. [DOI: 10.1111/febs.14428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/07/2018] [Accepted: 02/27/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Ebenezer Ajewole
- Department of Biology University of Western Ontario London Canada
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
| | | | - Agnieszka Pajak
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
- Department of Crystallography Faculty of Chemistry A. Mickiewicz University Poznan Poland
| | - Frédéric Marsolais
- Department of Biology University of Western Ontario London Canada
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
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78
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Marshall AC, Bond CS, Bruning JB. Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew C. Marshall
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Charles S. Bond
- School
of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John B. Bruning
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Chrysargyris A, Michailidi E, Tzortzakis N. Physiological and Biochemical Responses of Lavandula angustifolia to Salinity Under Mineral Foliar Application. FRONTIERS IN PLANT SCIENCE 2018; 9:489. [PMID: 29731759 PMCID: PMC5920160 DOI: 10.3389/fpls.2018.00489] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/29/2018] [Indexed: 05/10/2023]
Abstract
Saline water has been proposed as a solution to partially cover plant water demands due to scarcity of irrigation water in hot arid areas. Lavender (Lavandula angustifolia Mill.) plants were grown hydroponically under salinity (0-25-50-100 mM NaCl). The overcome of salinity stress was examined by K, Zn, and Si foliar application for the plant physiological and biochemical characteristics. The present study indicated that high (100 mM NaCl) salinity decreased plant growth, content of phenolics and antioxidant status and essential oil (EO) yield, while low-moderate salinity levels maintained the volatile oil profile in lavender. The integrated foliar application of K and Zn lighten the presumable detrimental effects of salinity in terms of fresh biomass, antioxidant capacity, and EO yield. Moderate salinity stress along with balanced concentration of K though foliar application changed the primary metabolites pathways in favor of major volatile oil constituents biosynthesis and therefore lavender plant has the potential for cultivation under prevalent semi-saline conditions. Zn and Si application, had lesser effects on the content of EO constituents, even though altered salinity induced changings. Our results have demonstrated that lavender growth/development and EO production may be affected by saline levels, whereas mechanisms for alteration of induced stress are of great significance considering the importance of the oil composition, as well.
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80
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Jeanne Dit Fouque K, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers. Analyst 2018; 143:2323-2333. [DOI: 10.1039/c8an00138c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.
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Affiliation(s)
| | - Javier Moreno
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms
- National Museum of Natural History
- Sorbonne Univ
- 75005 Paris
- France
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81
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Bischof H, Rehberg M, Stryeck S, Artinger K, Eroglu E, Waldeck-Weiermair M, Gottschalk B, Rost R, Deak AT, Niedrist T, Vujic N, Lindermuth H, Prassl R, Pelzmann B, Groschner K, Kratky D, Eller K, Rosenkranz AR, Madl T, Plesnila N, Graier WF, Malli R. Novel genetically encoded fluorescent probes enable real-time detection of potassium in vitro and in vivo. Nat Commun 2017; 8:1422. [PMID: 29127288 PMCID: PMC5681659 DOI: 10.1038/s41467-017-01615-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 01/01/2023] Open
Abstract
Changes in intra- and extracellular potassium ion (K+) concentrations control many important cellular processes and related biological functions. However, our current understanding of the spatiotemporal patterns of physiological and pathological K+ changes is severely limited by the lack of practicable detection methods. We developed K+-sensitive genetically encoded, Förster resonance energy transfer-(FRET) based probes, called GEPIIs, which enable quantitative real-time imaging of K+ dynamics. GEPIIs as purified biosensors are suitable to directly and precisely quantify K+ levels in different body fluids and cell growth media. GEPIIs expressed in cells enable time-lapse and real-time recordings of global and local intracellular K+ signals. Hitherto unknown Ca2+-triggered, organelle-specific K+ changes were detected in pancreatic beta cells. Recombinant GEPIIs also enabled visualization of extracellular K+ fluctuations in vivo with 2-photon microscopy. Therefore, GEPIIs are relevant for diverse K+ assays and open new avenues for live-cell K+ imaging. K+ plays an important role in physiology and disease, but the lack of high specificity K+ sensors limits our understanding of its spatiotemporal dynamics. Here the authors develop genetically-encoded FRET-based probes able to quantify K+ concentration in body fluids, cells and specific organelles.
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Affiliation(s)
- Helmut Bischof
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Markus Rehberg
- Ludwig-Maximilians University (LMU), Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Sarah Stryeck
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Katharina Artinger
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Emrah Eroglu
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Markus Waldeck-Weiermair
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Benjamin Gottschalk
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Rene Rost
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Andras T Deak
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Tobias Niedrist
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Nemanja Vujic
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Hanna Lindermuth
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Ruth Prassl
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Brigitte Pelzmann
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Klaus Groschner
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010, Graz, Austria
| | - Dagmar Kratky
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Kathrin Eller
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Alexander R Rosenkranz
- Clinical Division of Nephrology, Medical University of Graz, Auenbruggerplatz 27, 8036, Graz, Austria
| | - Tobias Madl
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Nikolaus Plesnila
- Ludwig-Maximilians University (LMU), Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Feodor-Lynen-Straße 17, 81377, Munich, Germany
| | - Wolfgang F Graier
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Roland Malli
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria. .,BioTechMed-Graz, Graz, Austria.
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82
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Cellular information dynamics through transmembrane flow of ions. Sci Rep 2017; 7:15075. [PMID: 29118414 PMCID: PMC5678125 DOI: 10.1038/s41598-017-15182-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022] Open
Abstract
We propose cells generate large transmembrane ion gradients to form information circuits that detect, process, and respond to environmental perturbations or signals. In this model, the specialized gates of transmembrane ion channels function as information detectors that communicate to the cell through rapid and (usually) local pulses of ions. Information in the ion "puffs" is received and processed by the cell through resulting changes in charge density and/or mobile cation (and/or anion) concentrations alter the localization and function of peripheral membrane proteins. The subsequent changes in protein binding to the membrane or activation of K+, Ca2+ or Mg2+-dependent enzymes then constitute a cellular response to the perturbation. To test this hypothesis we analyzed ion-based signal transmission as a communication channel operating with coded inputs and decoded outputs. By minimizing the Kullback-Leibler cross entropy [Formula: see text] between concentrations of the ion species inside [Formula: see text] and outside [Formula: see text] the cell membrane, we find signal transmission through transmembrane ion flow forms an optimal Shannon information channel that minimizes information loss and maximizes transmission speed. We demonstrate the ion dynamics in neuronal action potentials described by Hodgkin and Huxley (including the equations themselves) represent a special case of these general information principles.
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83
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Pesci L, Gurikov P, Liese A, Kara S. Amine-Mediated Enzymatic Carboxylation of Phenols Using CO 2 as Substrate Increases Equilibrium Conversions and Reaction Rates. Biotechnol J 2017; 12. [PMID: 28862371 DOI: 10.1002/biot.201700332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Indexed: 01/08/2023]
Abstract
A variety of strategies is applied to alleviate thermodynamic and kinetic limitations in biocatalytic carboxylation of metabolites in vivo. A key feature to consider in enzymatic carboxylations is the nature of the cosubstrate: CO2 or its hydrated form, bicarbonate. The substrate binding and activation mechanism determine what the actual carboxylation agent is. Dihydroxybenzoic acid (de)carboxylases catalyze the reversible regio-selective ortho-(de)carboxylation of phenolics. These enzymes have attracted considerable attention in the last 10 years due to their potential in substituting harsh conditions typical of chemical carboxylations (100-200 °C, 5-100 bar) with, ideally, greener ones (20-40 °C, 1 bar). They are reported to use bicarbonate as substrate, needed in large excess to overcome thermodynamic and kinetic limitations. Therefore, CO2 can be used as substrate by these enzymes only if it is converted into bicarbonate in situ. In this contribution, we report the simultaneous amine-mediated conversion of CO2 into bicarbonate and the ortho-carboxylation of different phenolic molecules catalyzed by 2,3-dihydroxybenzoic acid (de)carboxylase from Aspergillus oryzae. Our results show that under the newly developed conditions a significant thermodynamic (up to twofold increase in conversion) and kinetic improvement (up to approx. fivefold increase in rate) of the biocatalytic carboxylation of catechol is achieved.
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Affiliation(s)
- Lorenzo Pesci
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Pavel Gurikov
- Institute of Thermal Separation Processes, Hamburg University of Technology, Hamburg, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
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84
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Shisler KA, Hutcheson RU, Horitani M, Duschene KS, Crain AV, Byer AS, Shepard EM, Rasmussen A, Yang J, Broderick WE, Vey JL, Drennan CL, Hoffman BM, Broderick JB. Monovalent Cation Activation of the Radical SAM Enzyme Pyruvate Formate-Lyase Activating Enzyme. J Am Chem Soc 2017; 139:11803-11813. [PMID: 28768413 PMCID: PMC5579537 DOI: 10.1021/jacs.7b04883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Pyruvate formate-lyase
activating enzyme (PFL-AE) is a radical S-adenosyl-l-methionine (SAM) enzyme that installs
a catalytically essential glycyl radical on pyruvate formate-lyase.
We show that PFL-AE binds a catalytically essential monovalent cation
at its active site, yet another parallel with B12 enzymes,
and we characterize this cation site by a combination of structural,
biochemical, and spectroscopic approaches. Refinement of the PFL-AE
crystal structure reveals Na+ as the most likely ion present
in the solved structures, and pulsed electron nuclear double resonance
(ENDOR) demonstrates that the same cation site is occupied by 23Na in the solution state of the as-isolated enzyme. A SAM
carboxylate-oxygen is an M+ ligand, and EPR and circular
dichroism spectroscopies reveal that both the site occupancy and the
identity of the cation perturb the electronic properties of the SAM-chelated
iron–sulfur cluster. ENDOR studies of the PFL-AE/[13C-methyl]-SAM complex show that the target sulfonium positioning
varies with the cation, while the observation of an isotropic hyperfine
coupling to the cation by ENDOR measurements establishes its intimate,
SAM-mediated interaction with the cluster. This monovalent cation
site controls enzyme activity: (i) PFL-AE in the absence of any simple
monovalent cations has little–no activity; and (ii) among monocations,
going down Group 1 of the periodic table from Li+ to Cs+, PFL-AE activity sharply maximizes at K+, with
NH4+ closely matching the efficacy of K+. PFL-AE is thus a type I M+-activated enzyme whose
M+ controls reactivity by interactions with the cosubstrate,
SAM, which is bound to the catalytic iron–sulfur cluster.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Rachel U Hutcheson
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Kaitlin S Duschene
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Adam V Crain
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Ashley Rasmussen
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jian Yang
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Jessica L Vey
- Department of Chemistry and Biochemistry, California State University Northridge , Northridge, California 91330, United States.,Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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85
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Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nat Commun 2017; 8:15959. [PMID: 28722007 PMCID: PMC5524983 DOI: 10.1038/ncomms15959] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/12/2017] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ∼1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function. The large and complex HIV-1 capsid modulates several molecular events during HIV-1’s infective cycle. Here the authors use all-atom molecular dynamic simulations to probe the biophysical properties of the genome-free HIV-1 capsid.
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86
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Guerrero-Mendiola C, García-Trejo JJ, Encalada R, Saavedra E, Ramírez-Silva L. The contribution of two isozymes to the pyruvate kinase activity of Vibrio cholerae: One K+-dependent constitutively active and another K+-independent with essential allosteric activation. PLoS One 2017; 12:e0178673. [PMID: 28686591 PMCID: PMC5501398 DOI: 10.1371/journal.pone.0178673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 11/18/2022] Open
Abstract
In a previous phylogenetic study of the family of pyruvate kinase EC (2.7.1.40), a cluster with Glu117 and another with Lys117 were found (numbered according to the rabbit muscle enzyme). The sequences with Glu117 have been found to be K+-dependent, whereas those with Lys117 were K+-independent. Interestingly, only γ-proteobacteria exhibit sequences in both branches of the tree. In this context, it was explored whether these phylogenetically distinct pyruvate kinases were both expressed and contribute to the pyruvate kinase activity in Vibrio cholerae. The main findings of this work showed that the isozyme with Glu117 is an active K+-dependent enzyme. At the same substrate concentration, its Vmax in the absence of fructose 1,6 bisphosphate was 80% of that with its effector. This result is in accordance with the non-essential activation described by allosteric ligands for most pyruvate kinases. In contrast, the pyruvate kinase with Lys117 was a K+-independent enzyme displaying an allosteric activation by ribose 5-phosphate. At the same substrate concentration, its activity without the effector was 0.5% of the one obtained in the presence of ribose 5-phosphate, indicating that this sugar monophosphate is a strong activator of this enzyme. This absolute allosteric dependence is a novel feature of pyruvate kinase activity. Interestingly, in the K+-independent enzyme, Mn2+ may "mimic" the allosteric effect of Rib 5-P. Despite their different allosteric behavior, both isozymes display a rapid equilibrium random order kinetic mechanism. The intracellular concentrations of fructose 1,6-bisphosphate and ribose 5-phosphate in Vibrio cholerae have been experimentally verified to be sufficient to induce maximal activation of both enzymes. In addition, Western blot analysis indicated that both enzymes were co-expressed. Therefore, it is concluded that VcIPK and VcIIPK contribute to the activity of pyruvate kinase in this γ-proteobacterium.
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Affiliation(s)
- Carlos Guerrero-Mendiola
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ignacio Chávez, Ciudad de México, México
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Ignacio Chávez, Ciudad de México, México
| | - Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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87
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Dilger JM, Glover MS, Clemmer DE. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1293-1303. [PMID: 28357817 DOI: 10.1007/s13361-016-1592-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/17/2016] [Accepted: 12/18/2016] [Indexed: 05/18/2023]
Abstract
Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
- Spectrum Warfare Systems Department, Naval Surface Warfare Center, Crane Division, Crane, IN, 47522, USA.
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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88
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Baron F, Bonnassie S, Alabdeh M, Cochet MF, Nau F, Guérin-Dubiard C, Gautier M, Andrews SC, Jan S. Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses. Front Microbiol 2017; 8:829. [PMID: 28553268 PMCID: PMC5428311 DOI: 10.3389/fmicb.2017.00829] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022] Open
Abstract
Chicken egg white protects the embryo from bacterial invaders by presenting an assortment of antagonistic activities that combine together to both kill and inhibit growth. The key features of the egg white anti-bacterial system are iron restriction, high pH, antibacterial peptides and proteins, and viscosity. Salmonella enterica serovar Enteritidis is the major pathogen responsible for egg-borne infection in humans, which is partly explained by its exceptional capacity for survival under the harsh conditions encountered within egg white. However, at temperatures up to 42°C, egg white exerts a much stronger bactericidal effect on S. Enteritidis than at lower temperatures, although the mechanism of egg white-induced killing is only partly understood. Here, for the first time, the impact of exposure of S. Enteritidis to egg white under bactericidal conditions (45°C) is explored by global-expression analysis. A large-scale (18.7% of genome) shift in transcription is revealed suggesting major changes in specific aspects of S. Enteritidis physiology: induction of egg white related stress-responses (envelope damage, exposure to heat and alkalinity, and translation shutdown); shift in energy metabolism from respiration to fermentation; and enhanced micronutrient provision (due to iron and biotin restriction). Little evidence of DNA damage or redox stress was obtained. Instead, data are consistent with envelope damage resulting in cell death by lysis. A surprise was the high degree of induction of hexonate/hexuronate utilization genes, despite no evidence indicating the presence of these substrates in egg white.
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Affiliation(s)
- Florence Baron
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Sylvie Bonnassie
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- Science de la Vie et de la Terre, Université de Rennes IRennes, France
| | - Mariah Alabdeh
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Marie-Françoise Cochet
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Françoise Nau
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Catherine Guérin-Dubiard
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Michel Gautier
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | | | - Sophie Jan
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
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89
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Arimany-Nardi C, Claudio-Montero A, Viel-Oliva A, Schmidtke P, Estarellas C, Barril X, Bidon-Chanal A, Pastor-Anglada M. Identification and Characterization of a Secondary Sodium-Binding Site and the Main Selectivity Determinants in the Human Concentrative Nucleoside Transporter 3. Mol Pharm 2017; 14:1980-1987. [DOI: 10.1021/acs.molpharmaceut.7b00085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Arimany-Nardi
- Departament
de Bioquímica i Biomedicina Molecular, Facultat de Biologia and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Oncology
Program, National Biomedical Research Institute on Liver and Gastrointestinal
Diseases (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - A. Claudio-Montero
- Departament
de Bioquímica i Biomedicina Molecular, Facultat de Biologia and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Oncology
Program, National Biomedical Research Institute on Liver and Gastrointestinal
Diseases (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - A. Viel-Oliva
- Departament
de Bioquímica i Biomedicina Molecular, Facultat de Biologia and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Oncology
Program, National Biomedical Research Institute on Liver and Gastrointestinal
Diseases (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - P. Schmidtke
- Departament
de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica,
Facultat de Farmàcia i Ciències de l′Alimentació
and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - C. Estarellas
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia i Ciències de l′Alimentació
and Institute of Biomedicine (IBUB), Campus de l′Alimentació
de Torribera, Universitat de Barcelona, 08921 Santa Coloma
de Gramenet, Spain
| | - X. Barril
- Departament
de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica,
Facultat de Farmàcia i Ciències de l′Alimentació
and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - A. Bidon-Chanal
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia i Ciències de l′Alimentació
and Institute of Biomedicine (IBUB), Campus de l′Alimentació
de Torribera, Universitat de Barcelona, 08921 Santa Coloma
de Gramenet, Spain
| | - M. Pastor-Anglada
- Departament
de Bioquímica i Biomedicina Molecular, Facultat de Biologia and Institute of Biomedicine (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Oncology
Program, National Biomedical Research Institute on Liver and Gastrointestinal
Diseases (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
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90
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Zhou Y, Liu K, Zhang J, Chu J, He B. Mg2+-induced stabilization of β-galactosidase from Bacillus megaterium and its application in the galactosylation of natural products. Biotechnol Lett 2017; 39:1175-1181. [DOI: 10.1007/s10529-017-2344-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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91
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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92
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Primo C, Ferri-Blázquez A, Loewith R, Yenush L. Reciprocal Regulation of Target of Rapamycin Complex 1 and Potassium Accumulation. J Biol Chem 2016; 292:563-574. [PMID: 27895122 DOI: 10.1074/jbc.m116.746982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/16/2016] [Indexed: 12/19/2022] Open
Abstract
The proper maintenance of potassium homeostasis is crucial for cell viability. Among the major determinants of potassium uptake in the model organism Saccharomyces cerevisiae are the Trk1 high affinity potassium transporter and the functionally redundant Hal4 (Sat4) and Hal5 protein kinases. These kinases are required for the plasma membrane accumulation of not only Trk1 but also several nutrient permeases. Here, we show that overexpression of the target of rapamycin complex 1 (TORC1) effector NPR1 improves hal4 hal5 growth defects by stabilizing nutrient permeases at the plasma membrane. We subsequently found that internal potassium levels and TORC1 activity are linked. Specifically, growth under limiting potassium alters the activities of Npr1 and another TORC1 effector kinase, Sch9; hal4 hal5 and trk1 trk2 mutants display hypersensitivity to rapamycin, and reciprocally, TORC1 inhibition reduces potassium accumulation. Our results demonstrate that in addition to carbon and nitrogen, TORC1 also responds to and regulates potassium fluxes.
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Affiliation(s)
- Cecilia Primo
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
| | - Alba Ferri-Blázquez
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
| | - Robbie Loewith
- the Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Swiss National Centre for Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lynne Yenush
- From the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia, Spain 46022 and
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93
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Kurisaki I, Nagaoka M. Na + Binding Is Ineffective in Forming a Primary Substrate Pocket of Thrombin. J Phys Chem B 2016; 120:11873-11879. [PMID: 27781431 DOI: 10.1021/acs.jpcb.6b07827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thrombin is a serine protease involved in the blood coagulation reaction, and it shows maximum enzymatic activity in the presence of Na+. It has been supposed that Na+ binding promotes conversion from the inactive form, with a collapsed primary substrate pocket (S1 pocket), to the active form, with a properly formed S1 pocket. However, the evidence supporting this activation mechanism was derived from the X-ray crystallographic structures solved under nonphysiological conditions and using thrombin mutants; thus, it still remains elusive whether the activation mechanism is actually attributed to Na+ binding. To address the problem, we employed all-atom molecular dynamics simulations for both active and inactive forms of thrombin in the presence and absence of Na+ binding and examined the effect of Na+ binding on S1-pocket formation. In contrast to the conventional supposition, we revealed that Na+ binding does not prevent S1-pocket collapse virtually, but rather, the bound Na+ can move to the S1 pocket, thus blocking substrate access directly. Additionally, it was clarified that Na+ binding does not promote S1-pocket formation. According to these insights, we concluded that Na+ binding is irrelevant to the interconversion between the inactive and active forms of thrombin.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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94
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Turck D, Bresson JL, Burlingame B, Dean T, Fairweather-Tait S, Heinonen M, Hirsch-Ernst KI, Mangelsdorf I, McArdle H, Neuhäuser-Berthold M, Nowicka G, Pentieva K, Sanz Y, Siani A, Sjödin A, Stern M, Tomé D, Van Loveren H, Vinceti M, Willatts P, Aggett P, Martin A, Przyrembel H, Brönstrup A, Ciok J, Gómez Ruiz JÁ, de Sesmaisons-Lecarré A, Naska A. Dietary reference values for potassium. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.4592] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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95
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Ueda S, Kawamura Y, Iijima H, Nakajima M, Shirai T, Okamoto M, Kondo A, Hirai MY, Osanai T. Anionic metabolite biosynthesis enhanced by potassium under dark, anaerobic conditions in cyanobacteria. Sci Rep 2016; 6:32354. [PMID: 27576448 PMCID: PMC5006033 DOI: 10.1038/srep32354] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/08/2016] [Indexed: 11/09/2022] Open
Abstract
Potassium (K(+)) is an essential macronutrient for all living organisms including cyanobacteria. Cyanobacteria are a group of bacteria performing oxygenic photosynthesis, widely studied in basic and applied sciences. The primary metabolism of the unicellular cyanobacterium Synechocystis sp. PCC 6803 is altered by environmental conditions, and it excretes organic acids and hydrogen under dark, anaerobic conditions. Here we demonstrated that K(+) widely changes the primary carbon metabolism of this cyanobacterium. Succinate and lactate excretion from the cells incubated under dark, anaerobic conditions was enhanced in the presence of K(+), while hydrogen production was repressed. The addition of K(+) and the genetic manipulation of acetate kinase AckA and an RNA polymerase sigma factor SigE additively increased succinate and lactate production to 141.0 and 217.6 mg/L, which are 11 and 46 times, compared to the wild-type strain without K(+), respectively. Intracellular levels of 2-oxoglutarate, succinate, fumarate, and malate increased by K(+) under dark, anaerobic conditions. This study provides the evidence of the considerable effect of K(+) on the biosynthesis of anionic metabolites in a unicellular cyanobacterium.
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Affiliation(s)
- Sakiko Ueda
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yuhki Kawamura
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Hiroko Iijima
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Mitsuharu Nakajima
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Tomokazu Shirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mami Okamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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96
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Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem J 2016; 473:2395-411. [DOI: 10.1042/bcj20160336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 01/27/2023]
Abstract
Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity-enhanced Factor IXa variants has demonstrated a delicately balanced bidirectional network. Essential molecular interactions across multiple regions of the Factor IXa molecule co-operate in the maturation of the active site. This maturation is specifically facilitated by long-range communication through the Ile212–Ile213 motif unique to Factor IXa and a flexibility of the 170-loop that is further dependent on the conformation in the Cys168–Cys182 disulfide bond. Ultimately, the network consists of compensatory brakes (Val16 and Ile213) and accelerators (Tyr99 and Phe174) that together allow for a subtle fine-tuning of enzymatic activity.
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97
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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98
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Pirkmajer S, Chibalin AV. Na,K-ATPase regulation in skeletal muscle. Am J Physiol Endocrinol Metab 2016; 311:E1-E31. [PMID: 27166285 DOI: 10.1152/ajpendo.00539.2015] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
Skeletal muscle contains one of the largest and the most dynamic pools of Na,K-ATPase (NKA) in the body. Under resting conditions, NKA in skeletal muscle operates at only a fraction of maximal pumping capacity, but it can be markedly activated when demands for ion transport increase, such as during exercise or following food intake. Given the size, capacity, and dynamic range of the NKA pool in skeletal muscle, its tight regulation is essential to maintain whole body homeostasis as well as muscle function. To reconcile functional needs of systemic homeostasis with those of skeletal muscle, NKA is regulated in a coordinated manner by extrinsic stimuli, such as hormones and nerve-derived factors, as well as by local stimuli arising in skeletal muscle fibers, such as contractions and muscle energy status. These stimuli regulate NKA acutely by controlling its enzymatic activity and/or its distribution between the plasma membrane and the intracellular storage compartment. They also regulate NKA chronically by controlling NKA gene expression, thus determining total NKA content in skeletal muscle and its maximal pumping capacity. This review focuses on molecular mechanisms that underlie regulation of NKA in skeletal muscle by major extrinsic and local stimuli. Special emphasis is given to stimuli and mechanisms linking regulation of NKA and energy metabolism in skeletal muscle, such as insulin and the energy-sensing AMP-activated protein kinase. Finally, the recently uncovered roles for glutathionylation, nitric oxide, and extracellular K(+) in the regulation of NKA in skeletal muscle are highlighted.
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Affiliation(s)
- Sergej Pirkmajer
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; and
| | - Alexander V Chibalin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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99
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Mass spectrometry of oligopeptides in the presence of large amounts of alkali halides using desorption/ionization induced by neutral cluster impact. Biointerphases 2016; 11:02A316. [PMID: 26825286 DOI: 10.1116/1.4940705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Oligopeptides in the presence of large amounts of salt were desorbed and ionized using desorption/ionization induced by neutral clusters (DINeC) for further analysis by means of mass spectrometry (MS). Using oligopeptides in alkali halide solutions as a model system, DINeC was shown to yield clear and fragmentation free mass spectra of the biomolecules even from environments with a large excess of salt. The results were traced back to a phase separation between salt and biomolecules during sample preparation. The ratio between alkali metal complexes [M+A](+) and bare biomolecules [M+H](+) was controlled using different preparation schemes. DINeC was applied to the products of a tryptic digest of bovine serum albumin in the presence of sodium chloride; the results of a mass fingerprint analysis did not show a major difference for the spectra with and without salt in the original solution. The metal-ion/peptide interaction was further investigated by means of tandem-MS.
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100
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Nieves-Cordones M, Al Shiblawi FR, Sentenac H. Roles and Transport of Sodium and Potassium in Plants. Met Ions Life Sci 2016; 16:291-324. [PMID: 26860305 DOI: 10.1007/978-3-319-21756-7_9] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The two alkali cations Na(+) and K(+) have similar relative abundances in the earth crust but display very different distributions in the biosphere. In all living organisms, K(+) is the major inorganic cation in the cytoplasm, where its concentration (ca. 0.1 M) is usually several times higher than that of Na(+). Accumulation of Na(+) at high concentrations in the cytoplasm results in deleterious effects on cell metabolism, e.g., on photosynthetic activity in plants. Thus, Na(+) is compartmentalized outside the cytoplasm. In plants, it can be accumulated at high concentrations in vacuoles, where it is used as osmoticum. Na(+) is not an essential element in most plants, except in some halophytes. On the other hand, it can be a beneficial element, by replacing K(+) as vacuolar osmoticum for instance. In contrast, K(+) is an essential element. It is involved in electrical neutralization of inorganic and organic anions and macromolecules, pH homeostasis, control of membrane electrical potential, and the regulation of cell osmotic pressure. Through the latter function in plants, it plays a role in turgor-driven cell and organ movements. It is also involved in the activation of enzymes, protein synthesis, cell metabolism, and photosynthesis. Thus, plant growth requires large quantities of K(+) ions that are taken up by roots from the soil solution, and then distributed throughout the plant. The availability of K(+) ions in the soil solution, slowly released by soil particles and clays, is often limiting for optimal growth in most natural ecosystems. In contrast, due to natural salinity or irrigation with poor quality water, detrimental Na(+) concentrations, toxic for all crop species, are present in many soils, representing 6 % to 10 % of the earth's land area. Three families of ion channels (Shaker, TPK/KCO, and TPC) and 3 families of transporters (HAK, HKT, and CPA) have been identified so far as contributing to K(+) and Na(+) transport across the plasmalemma and internal membranes, with high or low ionic selectivity. In the model plant Arabidopsis thaliana, these families gather at least 70 members. Coordination of the activities of these systems, at the cell and whole plant levels, ensures plant K(+) nutrition, use of Na(+) as a beneficial element, and adaptation to saline conditions.
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Affiliation(s)
- Manuel Nieves-Cordones
- Laboratory of Plant Biochemistry and Molecular Physiology, UMR BPMP CNRS/INRA/MontpellierSupAgro, University of Montpellier, INRA, Place Viala, F-34060, Montpellier cedex 1, France
| | - Fouad Razzaq Al Shiblawi
- Laboratory of Plant Biochemistry and Molecular Physiology, UMR BPMP CNRS/INRA/MontpellierSupAgro, University of Montpellier, INRA, Place Viala, F-34060, Montpellier cedex 1, France
| | - Hervé Sentenac
- Laboratory of Plant Biochemistry and Molecular Physiology, UMR BPMP CNRS/INRA/MontpellierSupAgro, University of Montpellier, INRA, Place Viala, F-34060, Montpellier cedex 1, France.
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