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Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kühlbrandt W, Michel H. Active site rearrangement and structural divergence in prokaryotic respiratory oxidases. Science 2019; 366:100-104. [DOI: 10.1126/science.aay0967] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/04/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome bd–type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of theEscherichia colicytochrome bd-I oxidase by single-particle cryo–electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily–specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.
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Affiliation(s)
- S. Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - A. Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - D. J. Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - M. Radloff
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - M. L. Eisinger
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - A. Nikolaev
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - J. Meier-Credo
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - F. Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - H. Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - R. B. Gennis
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - J. Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
| | - J. D. Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - P. Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
- University of Strasbourg Institute for Advanced Study, Strasbourg, France
| | - W. Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
| | - H. Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany
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Esmaeili N, Ebrahimzadeh H, Abdi K, Safarian S. Determination of some phenolic compounds in Crocus sativus L. corms and its antioxidant activities study. Pharmacogn Mag 2011; 7:74-80. [PMID: 21472084 PMCID: PMC3065162 DOI: 10.4103/0973-1296.75906] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/23/2010] [Accepted: 01/20/2011] [Indexed: 11/21/2022] Open
Abstract
It is well known that phenolic compounds are constituents of many plants. In this study, the total phenolics content in Crocus sativus L. corms in dormancy and waking stages were determined by the Folin-Ciocalteu method. Analysis was carried out by gas chromatography-mass spectrometry (GC-MS) after silylation by N-methyl-N-trimethylsilyl trifluroacetamide (MSTFA) + %1 trimethyl iodosilane (TMIS). Numerous compounds were detected and 11 compounds were identified. The highest phenolics content in waking corms was observed for gentisic acid (5.693 ± 0.057 μg/g) and the lowest for gallic acid (0.416 ± 0.006 μg/g); also these two phenolic compounds are the highest (0.929 ± 0.015 μg/g) and lowest (0.017 ± 0.001 μg/g) phenolics in dormant corms, respectively. The results from quantization and GC-MS analysis showed a high concentration of phenolic compounds in waking corms than the dormant stage. Furthermore, the radical scavenging activities of saffron corms were studied by 1,1-diphenyl-2-pycrylhydrazyl (DPPH) test and EC (50)values were determined about 2055 ppm and 8274 ppm for waking and dormant corms, respectively.
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Affiliation(s)
- N Esmaeili
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - H Ebrahimzadeh
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - K Abdi
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - S Safarian
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Moosavi-Movahedi Z, Safarian S, Zahedi M, Sadeghi M, Saboury AA, Chamani J, Bahrami H, Ashraf-Modarres A, Moosavi-Movahedi AA. Calorimetric and Binding Dissections of HSA Upon Interaction with Bilirubin. Protein J 2006; 25:193-201. [PMID: 16721655 DOI: 10.1007/s10930-006-9002-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interactions between bilirubin and human serum albumin (HSA) were studied by isothermal titration calorimetry (ITC) and UV-vis spectrophotometry at 27 degrees C in 100 mM phosphate buffer pH 7.4 containing 1 mM EDTA. The biphasic shape of the HSA-bilirubin binding curve depicted the existence of two bilirubin binding sets on the HSA structure which had distinct binding interactions. Each binding set contained one or more bilirubin binding site. The first binding set at subdomain IIA included one binding site and had a more hydrophobic microenvironment than the other two binding sites in the second bilirubin binding set (subdomain IIIA). With our method of analysis, the calculated dissociation constant of the first binding site is 1.28 x 10(-6) M and 4.80 x 10(-4) M for the second and third binding sites. Here, the typical Boltzmann's equation was used with a new approach to calculate the dissociation constants as well as the standard free energy changes for the HSA-bilirubin interactions. Interestingly, our calculations obtained using the Wyman binding potential theory confirmed that our analysis method had been correct (especially for the second binding phase). The molar extinction coefficient determined for the first bound bilirubin molecule depicted that the bilirubin molecules (in low concentrations) should interact with the nonpolar microenvironment of the first high affinity binding site. Binding of the bilirubin molecules to the first binding site was endothermic (deltaH > 0) and occurred through the large increase in the binding entropy established when the hydrophobic bilirubin molecules escaped from their surrounding polar water molecules and into the hydrophobic medium of the first binding site. On the other hand, the calculated molar extinction coefficient illustrated that the microenvironment of the second binding set (especially for the third binding site) was less hydrophobic than the first one but still more hydrophobic than the buffer medium. The binding of the third bilirubin molecule to the HSA molecule was established more through exothermic (electrostatic) interactions.
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Affiliation(s)
- Z Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Ataie G, Safarian S, Divsalar A, Saboury AA, Moosavi-Movahedi AA, Ranjbar B, Cristalli G, Mardanian S. Kinetic and structural analysis of the inhibition of adenosine deaminase by acetaminophen. J Enzyme Inhib Med Chem 2004; 19:71-8. [PMID: 15202496 DOI: 10.1080/14756360310001632741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Kinetic and thermodynamic studies have been made on the effect of acetaminophen on the activity and structure of adenosine deaminase in 50 mM sodium phosphate buffer pH 7.5, at two temperatures of 27 and 37 degrees C using UV spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. Acetaminophen acts as a competitive inhibitor at 27 degrees C (Ki = 126 microM) and an uncompetitive inhibitor at 37 degrees C (Ki = 214 microM). Circular dichroism studies do not show any considerable effect on the secondary structure of adenosine deaminase by increasing the temperature from 27 to 37 degrees C. However, the secondary structure of the protein becomes more compact at 37 degrees C in the presence of acetaminophen. Fluorescence spectroscopy studies show considerable change in the tertiary structure of the protein by increasing the temperature from 27 to 37 degrees C. Also, the fluorescence spectrum of the protein incubated with different concentrations of acetaminophen show different inhibition behaviors by the effector at the two temperatures.
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Affiliation(s)
- G Ataie
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Moosavi-Movahedi AA, Safarian S, Hakimelahi GH, Ataei G, Ajloo D, Panjehpour S, Riahi S, Mousavi MF, Mardanyan S, Soltani N, Khalafi-Nezhad A, Sharghi H, Moghadamnia H, Saboury AA. QSAR analysis for ADA upon interaction with a series of adenine derivatives as inhibitors. Nucleosides Nucleotides Nucleic Acids 2004; 23:613-24. [PMID: 15113027 DOI: 10.1081/ncn-120030719] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The kinetic parameters of adenosine deaminase such as Km and Ki were determined in the absence and presence of adenine derivatives (R1-R24) in sodium phosphate buffer (50 mM; pH 7.5) solution at 27 degrees C. These kinetic parameters were used for QSAR analysis. As such, we found some theoretical descriptors to which the binding affinity of adenosine deaminase (ADA) towards several adenine nucleosides as inhibitors is correlated. QSAR analysis has revealed that binding affinity of the adenine nucleosides upon interaction with ADA depends on the molecular volume, dipole moment of the molecule, electric charge around the N1 atom, and the highest of positive charge for the related molecules.
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Affiliation(s)
- A A Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, Faculty of Science, University of Tehran, Tehran, Iran.
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Abstract
The interaction between n-octyl-beta-D-glucopyranoside (octyl glucoside) and bovine liver glutamate dehydrogenase (GDH) was studied using techniques including equilibrium dialysis, UV-spectrophotometry, circular dichroism (CD), fluorescence energy transfer and extrinsic spectrofluorometry in 50 mM sodium phosphate buffer solution (pH 7.6). The equilibrium dialysis experiment showed a higher binding of octyl glucoside to GDH that induces up to 80% enzyme inhibition in 20 mM octyl glucoside solution. The CD study indicated that GDH retains its secondary structure in the presence of octyl glucoside, but loses a degree of its tertiary structure by acquiring a more extended tertiary structure. Measurement of the binding of a hydrophobic fluorescent probe, 1-anilino-naphthalene-8-sulfonate (ANS), to GDH revealed that the binding of ANS to GDH is increased in the presence of octyl glucoside, a finding that may be interpreted in terms of the increment of surface hydrophobic patch(es) of GDH because of its binding to octyl glucoside. Fluorescence energy transfer studies also showed more binding of the reduced coenzyme (NADH) to GDH and the Lineweaver-Burk plots (with respect to NADH) indicate the existence of substrate inhibition in the presence of octyl glucoside. These observations are aimed at explaining the formation of the molten globule-like structure of GDH, which is induced by a non-ionic detergent such as octyl glucoside.
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Affiliation(s)
- S Ghobadi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Abstract
Kinetics and binding studies of RNase A and its natural polymeric substrate (RNA), as well as the natural mixture of free 3'-ribonucleotides, were performed by difference spectrophotometry. The obtained kinetic saturation curve, with an anomalous nonhyperbolic shape and a distinct transition point, showed the interchange between the two conformational forms of the enzyme. This occurred in a narrow range of substrate concentration. At low substrate concentration, in spite of the existence of one catalytic cleft, RNase A behaves as a cooperative system, perhaps due to the interactions among the four cooperative binding subsites in the active cleft. At high substrate concentration, the conformational change did occur and was accompanied by a decrease in cooperativity and increment of the catalytic constant. The multiphasic shape of the binding curve, which, in the presence of the enzyme, produced 3'-ribonucleotides (as the ligand molecules), shows four binding subsites. The first three subsites are specific for the attachment of phosphate, ribose, and base moieties belonging to the first bound 3'-ribonucleotide in the direction of 3'-phosphate --> ribose --> base-5'. The fourth subsite relates to the second phosphate group of the second bound 3'-ribonucleotide. The binding direction also converts to 5'-phosphate --> ribose --> base-3' for the ribonucleotide monomers in the RNA structure.
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Affiliation(s)
- S Safarian
- Institute of Biochemistry and Biophysics, University of Tehran, Iran
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Gruol DJ, Wolfe KA, Safarian S. Analysis of glucocorticoid receptor subspecies binding to DNA-cellulose and isolated nuclei. J Steroid Biochem 1989; 34:319-23. [PMID: 2626025 DOI: 10.1016/0022-4731(89)90101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Conversion of the glucocorticoid receptor into a DNA-binding protein results in the generation of several distinct receptor subspecies (peaks A-E) which can be resolved by anion exchange chromatography. In vitro, the fraction of the receptor population (approx. 40%) which gains a capacity to bind DNA-cellulose is preferentially transformed into the peak A species by a process that was enhanced by the presence of KCl. At 0.4 M KCl, virtually all of the DNA-binding receptor was in the peak A form. Isolated nuclei also exhibit a receptor binding profile similar to that observed with DNA-cellulose.
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Affiliation(s)
- D J Gruol
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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