DOCSLIB.ORG

Computational Study of Redox Active Centers of Blue Copper Proteins: a Computational DFT Study Matej Pavelka, J.V

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Computational Study of Redox Active Centers of Blue Copper Proteins: a Computational DFT Study Matej Pavelka, J.V Computational Study of Redox Active Centers of Blue Copper Proteins: A Computational DFT Study Matej Pavelka, J.V. Burda To cite this version: Matej Pavelka, J.V. Burda. Computational Study of Redox Active Centers of Blue Copper Proteins: A Computational DFT Study. Molecular Physics, Taylor & Francis, 2009, 106 (24), pp.2733-2748. 10.1080/00268970802672684. hal-00513245 HAL Id: hal-00513245 https://hal.archives-ouvertes.fr/hal-00513245 Submitted on 1 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Molecular Physics For Peer Review Only Computational Study of Redox Active Centers of Blue Copper Proteins: A Computational DFT Study Journal: Molecular Physics Manuscript ID: TMPH-2008-0332.R1 Manuscript Type: Full Paper Date Submitted by the 07-Dec-2008 Author: Complete List of Authors: Pavelka, Matej; Charles University, Chemical Physics and Optics Burda, J.V.; Charles University, Czech Republic, Department of Chemical physics and optics DFT calculations, plastocyanin, blue copper proteins, copper Keywords: complexes URL: http://mc.manuscriptcentral.com/tandf/tmph Page 1 of 45 Molecular Physics 1 2 3 4 5 Computational Study of Redox Active Centers of Blue Copper 6 7 Proteins: A Computational DFT Study 8 9 10 11 Mat ěj Pavelka and Jaroslav V. Burda* 12 13 14 Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, 15 16 For Peer Review Only 17 Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic 18 19 20 *Corresponding author, e-mail: [email protected] 21 22 23 24 Abstract 25 26 27 Active sites of blue copper proteins in both reduced and oxidized states were studied 28 29 at the Density Functional Theory (DFT) level. Two families of these redox sites were 30 31 examined: the Type A centers with methionine ligand as 4 th residue and the Type B 32 33 34 with Glutamine residue. Constrained and full optimizations were performed on the 35 36 protein data bank structures in vacuo and in implicit solvent model simulating protein 37 38 and water environments. It was found that the redox sites do not possess optimum 39 40 41 geometries regardless of the oxidation state. The axial Cu-ligand bond 42 43 elongates/shortens in the fully optimized Cu(I)/Cu(II) complexes. The reduced centers 44 45 have a tendency to decrease the coordination number, while a trend to form four 46 47 48 “equivalent” bonds is preferred in the oxidized centers. Comparison of the full and 49 50 constrained optimizations also revealed that the A centers exhibit lower relaxation 51 52 53 energies. In the constrained structures, a higher ionization potential was predicted for 54 55 the A centers when compared to the B centers regardless of the influence of 56 57 environment. The calculated relative difference of the redox potentials between 58 59 60 various A and B centers is in good agreement with the experimental data. In the fully optimized complexes, the redox properties are dependent on the environment but URL: http://mc.manuscriptcentral.com/tandf/tmph Molecular Physics Page 2 of 45 1 2 3 usually higher IP for the B centers is predicted. Partial charges, MO’s, and spin 4 5 6 density distributions (obtained by natural population analysis) were analyzed together 7 8 with calculated electron paramagnetic resonance (EPR) spectra for deeper 9 10 11 understanding of the obtained results. 12 13 14 15 1. Introduction 16 For Peer Review Only 17 18 Every sixth entry in the protein data bank (PDB) contains a metal cofactor. Such 19 20 statistics demonstrate the importance of the metal ions for catalytic processes in a 21 22 23 living cell. Hence, investigation of metal sites – such as copper redox centers – is 24 25 essential for determination of molecular mechanisms in biochemistry. The Cu ions 26 27 often exhibit interesting spectral properties, which originate from the unusual 28 29 30 geometric and electronic structures that are imposed through their interactions with 31 32 protein environment. Such proteins provide many functions: electron transfer, 33 34 35 oxidation-reduction processes, oxygen transport and insertion, and so forth. 36 37 Blue copper proteins forms the so-called Type 1 Cu proteins[1,2]. These Cu 38 39 proteins have an intense absorption band near 600 nm in the oxidized Cu(II) state. 40 41 42 This transition is assigned with the S(cysteine)-Cu Ligand-to-Metal-Charge-Transfer 43 44 (LMCT). Structures of the active sites usually contain a 4-coordinated Cu ion, though 45 46 a coordination number of five was found in azurins. Structural motif consists of the 47 48 49 arrangement Cu(I)/Cu(II):(His)2CysX, where X is Met or Gln. Examples of this motif 50 51 can be found in pseudoazurin, rusticyanin, plastocyanin, mavicyanin, auracyanin, 52 53 stellacyanin, umecyanin, and amicyanin. Interestingly, reduction of the Cu(II) ion to 54 55 56 Cu(I) in type 1 proteins causes minimal structural changes. It results in a low 57 58 activation barrier for the Cu(I) →Cu(II) redox process and thus a rapid electron 59 60 2 URL: http://mc.manuscriptcentral.com/tandf/tmph Page 3 of 45 Molecular Physics 1 2 3 transfer. Very interesting review on these complexes was published recently by 4 5 6 Solomon[3]. 7 8 There is a large number of works investigating biological activity of the 9 10 11 copper proteins using both experimental and theoretical approaches. By means of UV- 12 13 VIS and EPR spectroscopy, Cu-center of azurin was studied[4]. Spectroscopic tools in 14 15 combination with DFT calculations were used to investigate the role of amino acid in 16 For Peer Review Only 17 18 axial position to the copper complex and its influence on a reduction potential[5]. 19 20 Published experimental works include a vast range of techniques, e.g. fluorescence 21 22 spectroscopy[6], X-ray absorption near-edge structure (XANES) spectra[7][8], 23 24 25 combination of EPR and electron-nuclear double resonance (ENDOR) techniques[9], 26 27 EPR and UV-VIS spectra[10], and many other. The basic aspects of a copper 28 29 coordination in the protein environment are summarized in reviews[11-14]. Charge 30 31 32 transfer (CT) dynamics of the blue copper proteins was investigated using a pump- 33 34 probe[15] and resonance Raman spectroscopy[16]. Some other experimental studies 35 36 37 dealing with these proteins should be also mentioned[17-19]. Theoretical studies of 38 39 the copper interactions with amino acids have been reported recently[20-30]. A lot of 40 41 computational effort was devoted to the examination of copper proteins[31-40]. The 42 43 44 first theoretical spectra of plastocyanin were computed by Solomon’s group[41,42] 45 46 and many studies were reported recently, e.g.[43-49]. Calculation of the EPR 47 48 parameters were published for aqua-ligated Cu(II) complexes at the modified B3LYP 49 50 51 level[50]. Similarly also azurin and some other blue copper proteins were 52 53 explored[51]. In the case of plastocyanin, QM/MM method was successfully 54 55 applied[43]. Force-field potentials were developed for Cu-ligand interactions in 56 57 58 plastocyanin[52] and applied in the study of LMCT dynamics for this protein[53]. An 59 60 analogous attempt to construct an empirical force-field for the oxidized form of blue 3 URL: http://mc.manuscriptcentral.com/tandf/tmph Molecular Physics Page 4 of 45 1 2 3 copper proteins was made earlier based on DFT calculations[54]. Same authors 4 5 6 studied coordination bonds in amicyanin and rusticyanin using QM/MM (IMOMM) 7 8 method[55]. 9 10 11 A great attention was also paid to examination of the “small inorganic 12 13 complexes” in order to determine coordination geometries and electronic properties of 14 15 various copper compounds. Investigation of these small models can provide a deeper 16 For Peer Review Only 17 18 insight into and an easier interpretation of the Cu(I)/Cu(II) behavior. Interactions of 19 20 the both Cu cations with molecules like water, ammonia, or hydrogen-sulfide were 21 22 intensively studied by many researchers[56-76]. A more detailed literature discussion 23 24 25 on this topics can be found in our previous papers where these complexes were 26 27 inspected[77-79]. 28 29 This study focuses on models of active mononuclear centers, which are 30 31 32 present in blue copper proteins (e.g. plastocyanin in Figure 1). This study gives a 33 34 comparison of electronic properties for general tetra-coordinated complexes with the 35 36 37 active centers of blue copper proteins (within the fixed-geometry from pdb 38 39 structures). 40 41 42 43 44 2. Computational Details 45 46 Active sites of the blue copper proteins (Scheme 1 ) were studied at the DFT level of 47 48 49 theory. In the Type A family of the blue proteins (with Met residue), the following 50 51 protein structures from the PDB database[80] were considered: amicyanin (1AAC), 52 53 auracyanin (1QHQ), plastocyanin (1KDI and 1KDJ), and rusticyanin (1A3Z and 54 55 56 1RCY).
Load more

Recommended publications
  • A Copper Protein and a Cytochrome Bind at the Same Site on Bacterial Cytochrome C Peroxidase† Sofia R
    14566 Biochemistry 2004, 43, 14566-14576 A Copper Protein and a Cytochrome Bind at the Same Site on Bacterial Cytochrome c Peroxidase† Sofia R. Pauleta,‡,§ Alan Cooper,⊥ Margaret Nutley,⊥ Neil Errington,| Stephen Harding,| Francoise Guerlesquin,3 Celia F. Goodhew,‡ Isabel Moura,§ Jose J. G. Moura,§ and Graham W. Pettigrew‡ Veterinary Biomedical Sciences, Royal (Dick) School of Veterinary Studies, UniVersity of Edinburgh, Summerhall, Edinburgh EH9 1QH, U.K., Department of Chemistry, UniVersity of Glasgow, Glasgow G12 8QQ, U.K., Centre for Macromolecular Hydrodynamics, UniVersity of Nottingham, Sutton Bonington, Nottingham LE12 5 RD, U.K., Unite de Bioenergetique et Ingenierie des Proteines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseilles cedex 20, France, Requimte, Departamento de Quimica, CQFB, UniVersidade NoVa de Lisboa, 2829-516 Monte de Caparica, Portugal ReceiVed July 5, 2004; ReVised Manuscript ReceiVed September 9, 2004 ABSTRACT: Pseudoazurin binds at a single site on cytochrome c peroxidase from Paracoccus pantotrophus with a Kd of 16.4 µMat25°C, pH 6.0, in an endothermic reaction that is driven by a large entropy change. Sedimentation velocity experiments confirmed the presence of a single site, although results at higher pseudoazurin concentrations are complicated by the dimerization of the protein. Microcalorimetry, ultracentrifugation, and 1H NMR spectroscopy studies in which cytochrome c550, pseudoazurin, and cytochrome c peroxidase were all present could be modeled using a competitive binding algorithm. Molecular docking simulation of the binding of pseudoazurin to the peroxidase in combination with the chemical shift perturbation pattern for pseudoazurin in the presence of the peroxidase revealed a group of solutions that were situated close to the electron-transferring heme with Cu-Fe distances of about 14 Å.
    [Show full text]
  • Chapter 3 the Title and Subtitle of This Chapter Convey a Dual Meaning
    3.1. Introduction Chapter 3 The title and subtitle of this chapter convey a dual meaning. At first reading, the subtitle Photosynthetic Reaction might seem to indicate that the topic of the structure, function and organization of Centers: photosynthetic reaction centers is So little time, so much to do exceedingly complex and that there is simply insufficient time or space in this brief article to cover the details. While this is John H. Golbeck certainly the case, the subtitle is Department of Biochemistry additionally meant to convey the idea that there is precious little time after the and absorption of a photon to accomplish the Molecular Biology task of preserving the energy in the form of The Pennsylvania State University stable charge separation. University Park, PA 16802 USA The difficulty is there exists a fundamental physical limitation in the amount of time available so that a photochemically induced excited state can be utilized before the energy is invariably wasted. Indeed, the entire design philosophy of biological reaction centers is centered on overcoming this physical, rather than chemical or biological, limitation. In this chapter, I will outline the problem of conserving the free energy of light-induced charge separation by focusing on the following topics: 3.2. Definition of the problem: the need to stabilize a charge-separated state. 3.3. The bacterial reaction center: how the cofactors and proteins cope with this problem in a model system. 3.4. Review of Marcus theory: what governs the rate of electron transfer in proteins? 3.5. Photosystem II: a variation on a theme of the bacterial reaction center.
    [Show full text]
  • The New Face of Protein-Bound Copper: the Type Zero Copper Site
    Science Highlight – February 2010 The New Face of Protein-bound Copper: The Type Zero Copper Site Nature adapts copper ions to a multitude of tasks, yet in doing so forces the metal into only a few different electronic structures [1]. Mononuclear copper sites observed in native proteins either adopt the type 1 (T1) or type 2 (T2) electronic structure. T1 sites exhibit intense charge-transfer absorption giving rise to their alternate title, blue copper sites, due to highly covalent coordination by a thiol ligand donated by a cysteine sidechain in their host proteins. This interaction has consequences for the spectroscopic features of the protein, but more importantly gives rise to dramatic enhancement of electron transfer activity. T2 sites on the other hand resemble more closely aqueous copper(II) ions, and are found in catalytic domains rather than electron transfer sites. While investigating the factors that tune reduction potentials in the T2 C112D variant of Pseudomonas aeruginosa azurin [2], Kyle M. Lancaster, under the guidance of Harry B. Gray and John H. Richards at the California Institute of Technology, discovered a copper(II) coordination mode that did not easily fit either of the two classifications for a mononuclear copper(II) site. The C112D/M121L azurin variant displayed one of the fingerprinting features of T1 copper: namely, a narrow axial hyperfine (A||) in its EPR spectrum. However, the removal of C112 obviated any possibility for an intense charge transfer band in the spectrum. Finally, electrochemical measurements by Keiko Yokoyama demonstrated that this hard-ligand copper(II) site could attain a copper(II/I) reduction potential typical for a T1 copper protein.
    [Show full text]
  • Stellacyanin. Studies of the Metal-Binding Site Using X-Ray
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector STELLACYANIN Studies of the Metal-binding Site using X-ray Absorption Spectroscopy J. PEISACH Departments ofMolecular Pharmacology and Molecular Biology, Albert Einstein College ofMedicine, Bronx, New York 10461 L. POWERS AND W. E. BLUMBERG Bell Laboratories, Murray Hill, New Jersey 07974 B. CHANCE Johnson Research Foundation, University ofPennsylvania Medical School, Philadelphia, Pennsylvania 19104 ABSTRACT Stellacyanin is a mucoprotein of molecular weight -20,000 containing one copper atom in a blue or type I site. The metal ion can exist in both the Cu(II) and Cu(I) redox states. The metal binding site in plastocyanin, another blue copper protein, contains one cysteinyl, one methionyl, and two imidazoyl residues (Colman et al. 1978. Nature [Lond.l. 272:319-324.), but an exactly analogous site cannot exist in stellacyanin as it lacks methionine. The copper coordination in stellacyanin has been studied by x-ray edge absorption and extended k-ray absorption fine structure (EXAFS) analysis. A new, very conservative data analysis procedure has been introduced, which suggests that there are two nitrogen atoms in the first coordination shell of the oxidized [Cu(II)] protein and one in the reduced [Cu(I)] protein; these N atoms have normal Cu-N distances: 1.95-2.05 A. In both redox states there are either one or two sulfur atoms coordinating the copper, the exact number being indeterminable from the present data. In the oxidized state the Cu-S distance is intermediate between the short bond found in plastocyanin and those found in near tetragonal copper model compounds.
    [Show full text]
  • Copper Transportion of WD Protein in Hepatocytes from Wilson Disease Patients in Vitro
    PO Box 2345, Beijing 100023, China World J Gastroenterol 2001;7(6):846-851 Fax: +86-10-85381893 World Journal of Gastroenterology E-mail: [email protected] www.wjgnet.com Copyright © 2001 by The WJG Press ISSN 1007-9327 • ORIGINAL RESEARCH • Copper transportion of WD protein in hepatocytes from Wilson disease patients in vitro Guo-Qing Hou1, Xiu-Ling Liang2, Rong Chen2, Lien Tang3, Ying Wang2, Ping-Yi Xu2, Ying-Ru Zhang2, Cui-Hua Ou2 1Department of Neurology, Guangzhou First Municipal People’s Hospital, transportion by promoting the activity of copper Guangzhou Medical College, Guangzhou 510180, Guangdong Province, transportion P-type ATPase. China 2Department of Neurology, First Affiliated Hospital, Sun Yat-Sen CONCLUSION: Copper transportion P-type ATPase plays University of Medical Sciences, Guangzhou 510080, Guangdong an important role in hepatocytic copper metabolism. Province, China Dysfunction of hepatocytic WD protein copper 3Department of Pharmacology, University of Kentucky, Lexington, KY transportion might be one of the most important 40506, USA factors for WD. Supported by Key Clinical Program of Ministry of Ministry of Health (No.37091), “211 Project” of SUMS sponsored by Ministry of Health, Subject headings glucuronosyltranferase/genetics; and Guangdong Provincial Natural Science Foundation, No.990064 glucurono syltranferase/biosynthesis; DNA,complementary/ Correspondence to: Dr. Guo-qing Hou, Department of Neurology, genetics; liver/cytology; hasters; lung/cytology; animal Guangzhou First Municipal People’s Hospital, Guangzhou Medical College, 1 Panfu Rd, Guangzhou 510180, China. [email protected] Hou GQ, Liang XL, Chen R, Tang LW, Wang Y, Xu PY, Zhang YR, Ou Telephone: +86-20-81083090 Ext 596, Fax: +86-20-81094250 CH.
    [Show full text]
  • Glycolysis Citric Acid Cycle Oxidative Phosphorylation Calvin Cycle Light
    Stage 3: RuBP regeneration Glycolysis Ribulose 5- Light-Dependent Reaction (Cytosol) phosphate 3 ATP + C6H12O6 + 2 NAD + 2 ADP + 2 Pi 3 ADP + 3 Pi + + 1 GA3P 6 NADP + H Pi NADPH + ADP + Pi ATP 2 C3H4O3 + 2 NADH + 2 H + 2 ATP + 2 H2O 3 CO2 Stage 1: ATP investment ½ glucose + + Glucose 2 H2O 4H + O2 2H Ferredoxin ATP Glyceraldehyde 3- Ribulose 1,5- Light Light Fx iron-sulfur Sakai-Kawada, F Hexokinase phosphate bisphosphate - 4e + center 2016 ADP Calvin Cycle 2H Stroma Mn-Ca cluster + 6 NADP + Light-Independent Reaction Phylloquinone Glucose 6-phosphate + 6 H + 6 Pi Thylakoid Tyr (Stroma) z Fe-S Cyt f Stage 1: carbon membrane Phosphoglucose 6 NADPH P680 P680* PQH fixation 2 Plastocyanin P700 P700* D-(+)-Glucose isomerase Cyt b6 1,3- Pheophytin PQA PQB Fructose 6-phosphate Bisphosphoglycerate ATP Lumen Phosphofructokinase-1 3-Phosphoglycerate ADP Photosystem II P680 2H+ Photosystem I P700 Stage 2: 3-PGA Photosynthesis Fructose 1,6-bisphosphate reduction 2H+ 6 ADP 6 ATP 6 CO2 + 6 H2O C6H12O6 + 6 O2 H+ + 6 Pi Cytochrome b6f Aldolase Plastoquinol-plastocyanin ATP synthase NADH reductase Triose phosphate + + + CO2 + H NAD + CoA-SH isomerase α-Ketoglutarate + Stage 2: 6-carbonTwo 3- NAD+ NADH + H + CO2 Glyceraldehyde 3-phosphate Dihydroxyacetone phosphate carbons Isocitrate α-Ketoglutarate dehydogenase dehydrogenase Glyceraldehyde + Pi + NAD Isocitrate complex 3-phosphate Succinyl CoA Oxidative Phosphorylation dehydrogenase NADH + H+ Electron Transport Chain GDP + Pi 1,3-Bisphosphoglycerate H+ Succinyl CoA GTP + CoA-SH Aconitase synthetase
    [Show full text]
  • Plastocyanin Redox Kinetics in Spinach Chloroplasts: Evidence for Disequilibrium in the High Potential Chain
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1659 (2004) 63–72 http://www.elsevier.com/locate/bba Plastocyanin redox kinetics in spinach chloroplasts: evidence for disequilibrium in the high potential chain Helmut Kirchhoff*, Mark Aurel Schfttler, Julia Maurer, Engelbert Weis Institut fu¨r Botanik, Schlossgarten 3, D-48149 Mu¨nster, Germany Received 24 May 2004; received in revised form 9 August 2004; accepted 12 August 2004 Available online 26 August 2004 Abstract Reduction kinetics of cytochrome f, plastocyanin (PC) and P700 (dhigh-potential chainT) in thylakoids from spinach were followed after pre-oxidation by a saturating light pulse. We describe a novel approach to follow PC redox kinetics from deconvolution of 810–860 nm absorption changes. The equilibration between the redox-components was analyzed by plotting the redox state of cytochrome f and PC against that of P700. In thylakoids with (1) diminished electron transport rate (adjusted with a cytochrome bf inhibitor) or (2) de-stacked grana, cytochrome f and PC relaxed close to their thermodynamic equilibriums with P700. In stacked thylakoids with non-inhibited electron transport, the equilibration plots were complex and non-hyperbolic, suggesting that during fast electron flux, the dhigh-potential chainT does not homogeneously equilibrate throughout the membrane. Apparent equilibrium constants b5 were calculated, which are below the thermodynamic equilibrium known for the dhigh potential chainT. The disequilibrium found in stacked thylakoids with high electron fluxes is explained by restricted long-range PC diffusion. We develop a model assuming that about 30% of Photosystem I mainly located in grana end- membranes and margins rapidly equilibrate with cytochrome f via short-distance transluminal PC diffusion, while long-range lateral PC migration between grana cores and distant stroma lamellae is restricted.
    [Show full text]
  • Toxicological Profile for Copper
    TOXICOLOGICAL PROFILE FOR COPPER U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES Public Health Service Agency for Toxic Substances and Disease Registry September 2004 COPPER ii DISCLAIMER The use of company or product name(s) is for identification only and does not imply endorsement by the Agency for Toxic Substances and Disease Registry. COPPER iii UPDATE STATEMENT A Toxicological Profile for Copper, Draft for Public Comment was released in September 2002. This edition supersedes any previously released draft or final profile. Toxicological profiles are revised and republished as necessary. For information regarding the update status of previously released profiles, contact ATSDR at: Agency for Toxic Substances and Disease Registry Division of Toxicology/Toxicology Information Branch 1600 Clifton Road NE, Mailstop F-32 Atlanta, Georgia 30333 COPPER vii QUICK REFERENCE FOR HEALTH CARE PROVIDERS Toxicological Profiles are a unique compilation of toxicological information on a given hazardous substance. Each profile reflects a comprehensive and extensive evaluation, summary, and interpretation of available toxicologic and epidemiologic information on a substance. Health care providers treating patients potentially exposed to hazardous substances will find the following information helpful for fast answers to often-asked questions. Primary Chapters/Sections of Interest Chapter 1: Public Health Statement: The Public Health Statement can be a useful tool for educating patients about possible exposure to a hazardous substance. It explains a substance’s relevant toxicologic properties in a nontechnical, question-and-answer format, and it includes a review of the general health effects observed following exposure. Chapter 2: Relevance to Public Health: The Relevance to Public Health Section evaluates, interprets, and assesses the significance of toxicity data to human health.
    [Show full text]
  • Nitrosocyanin, a Red Cupredoxin-Like Protein from Nitrosomonas Europaea† David M
    © Copyright 2002 by the American Chemical Society Volume 41, Number 6 February 12, 2002 Accelerated Publications Nitrosocyanin, a Red Cupredoxin-like Protein from Nitrosomonas europaea† David M. Arciero,‡ Brad S. Pierce,§ Michael P. Hendrich,§ and Alan B. Hooper*,‡ Department of Biochemistry, Molecular Biology and Biophysics, UniVersity of Minnesota, St. Paul, Minnesota 55108, and Department of Chemistry, Carnegie Mellon UniVersity, Pittsburgh, PennsylVania 15213 ReceiVed NoVember 1, 2001; ReVised Manuscript ReceiVed December 20, 2001 ABSTRACT: Nitrosocyanin (NC), a soluble, red Cu protein isolated from the ammonia-oxidizing autotrophic bacterium Nitrosomonas europaea, is shown to be a homo-oligomer of 12 kDa Cu-containing monomers. Oligonucleotides based on the amino acid sequence of the N-terminus and of the C-terminal tryptic peptide were used to sequence the gene by PCR. The translated protein sequence was significantly homologous with the mononuclear cupredoxins such as plastocyanin, azurin, or rusticyanin, the type 1 copper-binding region of nitrite reductase, and the binuclear CuA binding region of N2O reductase or cytochrome oxidase. The gene for NC contains a leader sequence indicating a periplasmic location. Optical bands for the red Cu center at 280, 390, 500, and 720 nm have extinction coefficients of 13.9, 7.0, 2.2, and 0.9 mM-1, respectively. The reduction potential of NC (85 mV vs SHE) is much lower than those for known cupredoxins. Sequence alignments with homologous blue copper proteins suggested copper ligation by Cys95, His98, His103, and Glu60. Ligation by these residues (and a water), a trimeric protein structure, and a cupredoxin â-barrel fold have been established by X-ray crystallography of the protein [Lieberman, R.
    [Show full text]
  • Single-Molecule Study of Redox Control Involved in Establishing the Spinach Plastocyanin-Cytochrome B6f Electron Transfer Complex
    This is a repository copy of Single-molecule study of redox control involved in establishing the spinach plastocyanin-cytochrome b6f electron transfer complex. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/151341/ Version: Accepted Version Article: Mayneord, G.E., Vasilev, C. orcid.org/0000-0002-0536-882X, Malone, L.A. orcid.org/0000-0002-7625-7545 et al. (3 more authors) (2019) Single-molecule study of redox control involved in establishing the spinach plastocyanin-cytochrome b6f electron transfer complex. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1860 (7). pp. 591-599. ISSN 0005-2728 https://doi.org/10.1016/j.bbabio.2019.06.013 Article available under the terms of the CC-BY-NC-ND licence (https://creativecommons.org/licenses/by-nc-nd/4.0/). Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) licence. This licence only allows you to download this work and share it with others as long as you credit the authors, but you can’t change the article in any way or use it commercially. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 Single-molecule study of redox control involved in establishing the 2 spinach plastocyanin-cytochrome b6f electron transfer complex 3 Guy E.
    [Show full text]
  • Regulation of Photosynthetic Electron Transport☆
    Biochimica et Biophysica Acta 1807 (2011) 375–383 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Review Regulation of photosynthetic electron transport☆ Jean-David Rochaix ⁎ Department of Molecular Biology, University of Geneva, Geneva, Switzerland Department of Plant Biology, University of Geneva, Geneva, Switzerland article info abstract Article history: The photosynthetic electron transport chain consists of photosystem II, the cytochrome b6 f complex, Received 14 September 2010 photosystem I, and the free electron carriers plastoquinone and plastocyanin. Light-driven charge separation Received in revised form 11 November 2010 events occur at the level of photosystem II and photosystem I, which are associated at one end of the chain Accepted 13 November 2010 with the oxidation of water followed by electron flow along the electron transport chain and concomitant Available online 29 November 2010 pumping of protons into the thylakoid lumen, which is used by the ATP synthase to generate ATP. At the other end of the chain reducing power is generated, which together with ATP is used for CO assimilation. A Keywords: 2 Electron transport remarkable feature of the photosynthetic apparatus is its ability to adapt to changes in environmental Linear electron flow conditions by sensing light quality and quantity, CO2 levels, temperature, and nutrient availability. These Cyclic electron flow acclimation responses involve a complex signaling network in the chloroplasts comprising the thylakoid Photosystem II protein kinases Stt7/STN7 and Stl1/STN7 and the phosphatase PPH1/TAP38, which play important roles in Photosystem I state transitions and in the regulation of electron flow as well as in thylakoid membrane folding.
    [Show full text]
  • Are Plastocyanin and Ferredoxin Specific Electron Carriers Or Generic Redox Capacitors?
    1 Are plastocyanin and ferredoxin specific electron carriers or generic redox 2 capacitors? Classical and murburn perspectives on two chloroplast proteins 3 Daniel Andrew Gideon1,2*, Vijay Nirusimhan2 & Kelath Murali Manoj1* 4 *Corresponding authors 5 Email: [email protected]; [email protected] 6 7 1Satyamjayatu: The Science & Ethics Foundation 8 Kulappully, Shoranur-2 (PO), Palakkad District, Kerala State, India-679122. 9 10 2 Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), 11 Vayalur Road, Tiruchirappalli, Tamil Nadu, India-620017. 12 13 ABSTRACT: Within the context of light reaction of photosynthesis, the structure-function 14 correlations of the chloroplast proteins of plastocyanin and ferredoxins (Fd) are analyzed via 15 two perspectives: 1) The Z-scheme, which considers PC/Fd as specific affinity binding-based 16 electron-relay agents, thereby deterministically linking the functions of Cytochrome b6f (Cyt. + 17 b6f) and Photosystem I (PS I) to NADP reduction by Fd:NADPH oxidoreductase (FNR) via 18 protein-protein contacts and 2) The murburn explanation for oxygenic photophosphorylation, 19 which deems PC/Fd as generic ‘redox capacitors’, temporally accepting and releasing one- 20 electron equivalents in reaction milieu. Amino acid residues located on the surface loci of key 21 patches of PC/Fd vary in electrostatic/contour (topography) signatures. Crystal structures of 22 four different complexes each of cyt.f-PC and Fd-FNR show little conservation in the 23 contact-surfaces, thereby discrediting ‘affinity binding-based electron transfers (ET)’ as an 24 evolutionary logic. Further, thermodynamic and kinetic data on wildtype and mutant proteins 25 interactions do not align well with model 1.
    [Show full text]