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1.
Biochemistry ; 44(15): 5931-9, 2005 Apr 19.
Article in English | MEDLINE | ID: mdl-15823053

ABSTRACT

To gain new insights into the function of photosystem II (PSII) herbicides DCMU (a urea herbicide) and bromoxynil (a phenolic herbicide), we have studied their effects in a better understood system, the bacterial photosynthetic reaction center of the terbutryn-resistant mutant T4 of Blastochloris (Bl.) viridis. This mutant is uniquely sensitive to these herbicides. We have used redox potentiometry and time-resolved absorption spectroscopy in the nanosecond and microsecond time scale. At room temperature the P(+)(*)Q(A)(-)(*) charge recombination in the presence of bromoxynil was faster than in the presence of DCMU. Two phases of P(+)(*)Q(A)(-)(*) recombination were observed. In accordance with the literature, the two phases were attributed to two different populations of reaction centers. Although the herbicides did induce small differences in the activation barriers of the charge recombination reactions, these did not explain the large herbicide-induced differences in the kinetics at ambient temperature. Instead, these were attributed to a change in the relative amplitude of the phases, with the fast:slow ratio being approximately 3:1 with bromoxynil and approximately 1:2 with DCMU at 300 K. Redox titrations of Q(A) were performed with and without herbicides at pH 6.5. The E(m) was shifted by approximately -75 mV by bromoxynil and by approximately +55 mV by DCMU. As the titrations were done over a time range that is assumed to be much longer than that for the transition between the two different populations, the potentials measured are considered to be a weighted average of two potentials for Q(A). The influence of the herbicides can thus be considered to be on the equilibrium of the two reaction center forms. This may also be the case in photosystem II.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/drug effects , Herbicides/pharmacology , Hyphomicrobiaceae/chemistry , Hyphomicrobiaceae/drug effects , Photosystem II Protein Complex/chemistry , Photosystem II Protein Complex/drug effects , Bacterial Proteins/genetics , Diuron/pharmacology , Drug Resistance, Bacterial/genetics , Electrochemistry , Hyphomicrobiaceae/genetics , Kinetics , Mutation , Nitriles/pharmacology , Oxidation-Reduction , Photosystem II Protein Complex/genetics , Potentiometry , Spectrophotometry , Temperature , Triazines/pharmacology
2.
FEBS Lett ; 504(3): 133-41, 2001 Aug 31.
Article in English | MEDLINE | ID: mdl-11532445

ABSTRACT

The structure of Wolinella succinogenes quinol:fumarate reductase by X-ray crystallography has been determined at 2.2-A resolution [Lancaster et al. (1999), Nature 402, 377-385]. Based on the structure of the three protein subunits A, B, and C and the arrangement of the six prosthetic groups (a covalently bound FAD, three iron-sulphur clusters, and two haem b groups) a pathway of electron transfer from the quinol-oxidising dihaem cytochrome b in the membrane to the site of fumarate reduction in the hydrophilic subunit A has been proposed. By combining the results from site-directed mutagenesis, functional and electrochemical characterisation, and X-ray crystallography, a residue was identified which is essential for menaquinol oxidation. [Lancaster et al. (2000), Proc. Natl. Acad. Sci. USA 97, 13051-13056]. The location of this residue in the structure suggests that the coupling of the oxidation of menaquinol to the reduction of fumarate in dihaem-containing succinate:quinone oxidoreductases could be associated with the generation of a transmembrane electrochemical potential. Based on crystallographic analysis of three different crystal forms of the enzyme and the results from site-directed mutagenesis, we have derived a mechanism of fumarate reduction and succinate oxidation [Lancaster et al. (2001) Eur. J. Biochem. 268, 1820-1827], which should be generally relevant throughout the superfamily of succinate:quinone oxidoreductases.


Subject(s)
Multienzyme Complexes/chemistry , Multienzyme Complexes/physiology , Oxidoreductases/chemistry , Oxidoreductases/physiology , Succinate Dehydrogenase/chemistry , Succinate Dehydrogenase/physiology , Wolinella/enzymology , Cell Membrane/enzymology , Crystallography, X-Ray , Electron Transport , Electron Transport Complex II , Models, Biological , Models, Chemical , Models, Molecular , Mutagenesis, Site-Directed , Oxygen/metabolism , Protein Conformation , Protons
3.
J Biol Chem ; 276(38): 35231-4, 2001 Sep 21.
Article in English | MEDLINE | ID: mdl-11481318

ABSTRACT

Bifurcated electron flow to high potential "Rieske" iron-sulfur cluster and low potential heme b(L) is crucial for respiratory energy conservation by the cytochrome bc(1) complex. The chemistry of ubiquinol oxidation has to ensure the thermodynamically unfavorable electron transfer to heme b(L). To resolve a central controversy about the number of ubiquinol molecules involved in this reaction, we used high resolution magic-angle-spinning nuclear magnetic resonance experiments to show that two out of three n-decyl-ubiquinones bind at the ubiquinol oxidation center of the complex. This substantiates a proposed mechanism in which a charge transfer between a ubiquinol/ubiquinone pair explains the bifurcation of electron flow.


Subject(s)
Electron Transport Complex III/metabolism , Mitochondria/enzymology , Ubiquinone/metabolism , Animals , Cattle , Protein Binding , Substrate Specificity
4.
Biochim Biophys Acta ; 1505(2-3): 280-90, 2001 Jun 01.
Article in English | MEDLINE | ID: mdl-11334792

ABSTRACT

Previously, two binding sites for the secondary quinone Q(B) in the photosynthetic reaction center (RC) from Rhodopseudomonas viridis were identified by X-ray crystallography, a 'proximal' binding site close to the non-heme iron, and a 'distal' site, displaced by 4.2 A along the path of the isoprenoid tail [C.R.D. Lancaster and H. Michel, Structure 5 (1997) 1339-1359]. The quinone ring planes in the two sites differ by roughly a 180 degrees rotation around the isoprenoid tail. Here we present molecular dynamics simulations, which support the theory of a spontaneous transfer of Q(B) between the distal site and the proximal site. In contrast to earlier computational studies on RCs, the molecular dynamics simulations of Q(B) migration resulted in a proximal Q(B) binding pattern identical to that of the crystallographic findings. Also, we demonstrate that the preference towards the proximal Q(B) location is not necessarily attributed to reduction of Q(B) to the semiquinone, but already to the preceding reduction of the primary quinone Q(A) and resulting protonation changes in the protein. Energy mapping of the Q(B) binding pocket indicates that the quinone ring rotation required for completion of the transfer between the two sites is improbable at the distal or proximal binding sites due to high potential barriers, but may be possible at a newly identified position near the distal binding site.


Subject(s)
Photosynthetic Reaction Center Complex Proteins/chemistry , Protons , Quinones/chemistry , Rhodopseudomonas/chemistry , Binding Sites , Computer Simulation , Electron Transport , Models, Molecular , Molecular Structure , Oxidation-Reduction , Photosynthesis , Static Electricity
5.
Eur J Biochem ; 268(6): 1820-7, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11248702

ABSTRACT

Quinol:fumarate reductase (QFR) is a membrane protein complex that couples the reduction of fumarate to succinate to the oxidation of quinol to quinone. Previously, the crystal structure of QFR from Wolinella succinogenes was determined based on two different crystal forms, and the site of fumarate binding in the flavoprotein subunit A of the enzyme was located between the FAD-binding domain and the capping domain [Lancaster, C.R.D., Kröger, A., Auer, M., & Michel, H. (1999) Nature 402, 377--385]. Here we describe the structure of W. succinogenes QFR based on a third crystal form and refined at 3.1 A resolution. Compared with the previous crystal forms, the capping domain is rotated in this structure by approximately 14 degrees relative to the FAD-binding domain. As a consequence, the topology of the dicarboxylate binding site is much more similar to those of membrane-bound and soluble fumarate reductase enzymes from other organisms than to that found in the previous crystal forms of W. succinogenes QFR. This and the effects of the replacement of Arg A301 by Glu or Lys by site-directed mutagenesis strongly support a common mechanism for fumarate reduction in this superfamily of enzymes.


Subject(s)
Oxidoreductases/chemistry , Wolinella/enzymology , Amino Acid Substitution , Base Sequence , Crystallography, X-Ray , DNA Primers , Protein Conformation , Wolinella/growth & development
6.
J Biol Chem ; 275(50): 39364-8, 2000 Dec 15.
Article in English | MEDLINE | ID: mdl-11005826

ABSTRACT

It has previously been shown that replacement of the residue His L168 with Phe (HL168F) in the Rhodopseudomonas viridis reaction center (RC) leads to an unprecedented drastic acceleration of the initial electron transfer rate. Here we describe the determination of the x-ray crystal structure at 2.00-A resolution of the HL168F RC. The electron density maps confirm that a hydrogen bond from the protein to the special pair is removed by this mutation. Compared with the wild-type RC, the acceptor of this hydrogen bond, the ring I acetyl group of the "special pair" bacteriochlorophyll, D(L), is rotated, and its acetyl oxygen is found 1.1 A closer to the bacteriochlorophyll-Mg(2+) of the other special pair bacteriochlorophyll, D(M). The rotation of this acetyl group and the increased interaction between the D(L) ring I acetyl oxygen and the D(M)-Mg(2+) provide the structural basis for the previously observed 80-mV decrease in the D(+)/D redox potential and the drastically increased rate of initial electron transfer to the accessory bacteriochlorophyll, B(A). The high quality of the electron density maps also allowed a reliable discussion of the mode of binding of the triazine herbicide terbutryn at the binding site of the secondary quinone, Q(B).


Subject(s)
Mutation , Photosynthetic Reaction Center Complex Proteins/chemistry , Rhodopseudomonas/chemistry , Rhodopseudomonas/genetics , Bacteriochlorophylls/chemistry , Binding Sites , Crystallography, X-Ray , Electron Transport , Herbicides/chemistry , Hydrogen Bonding , Light-Harvesting Protein Complexes , Magnesium/chemistry , Models, Chemical , Models, Molecular , Oxidation-Reduction , Oxygen/chemistry , Protein Binding , Triazines/chemistry
7.
Biochim Biophys Acta ; 1459(2-3): 422-31, 2000 Aug 15.
Article in English | MEDLINE | ID: mdl-11004459

ABSTRACT

Membrane-bound succinate dehydrogenases (succinate:quinone reductases, SQR) and fumarate reductases (quinol:fumarate reductases, QFR) couple the oxidation of succinate to fumarate to the reduction of quinone to quinol and also catalyse the reverse reaction. SQR (respiratory complex II) is involved in aerobic metabolism as part of the citric acid cycle and of the aerobic respiratory chain. QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor, and is part of an electron transport chain catalysing the oxidation of various donor substrates by fumarate. QFR and SQR complexes are collectively referred to as succinate:quinone oxidoreductases (EC 1.3.5.1), have very similar compositions and are predicted to share similar structures. The complexes consist of two hydrophilic and one or two hydrophobic, membrane-integrated subunits. The larger hydrophilic subunit A carries covalently bound flavin adenine dinucleotide and subunit B contains three iron-sulphur centres. QFR of Wolinella succinogenes and SQR of Bacillus subtilis contain only one hydrophobic subunit (C) with two haem b groups. In contrast, SQR and QFR of Escherichia coli contain two hydrophobic subunits (C and D) which bind either one (SQR) or no haem b group (QFR). The structure of W. succinogenes QFR has been determined at 2.2 A resolution by X-ray crystallography (C.R.D. Lancaster, A. Kröger, M. Auer, H. Michel, Nature 402 (1999) 377-385). Based on this structure of the three protein subunits and the arrangement of the six prosthetic groups, a pathway of electron transfer from the quinol-oxidising dihaem cytochrome b to the site of fumarate reduction and a mechanism of fumarate reduction was proposed. The W. succinogenes QFR structure is different from that of the haem-less QFR of E. coli, described at 3.3 A resolution (T.M. Iverson, C. Luna-Chavez, G. Cecchini, D.C. Rees, Science 284 (1999) 1961-1966), mainly with respect to the structure of the membrane-embedded subunits and the relative orientations of soluble and membrane-embedded subunits. Also, similarities and differences between QFR transmembrane helix IV and transmembrane helix F of bacteriorhodopsin and their implications are discussed.


Subject(s)
Multienzyme Complexes/chemistry , Oxidoreductases/chemistry , Succinate Dehydrogenase/chemistry , Animals , Binding Sites , Crystallography, X-Ray , Electron Transport , Electron Transport Complex II , Escherichia coli , Flavoproteins/chemistry , Humans , Iron-Sulfur Proteins/chemistry , Membrane Potentials , Membrane Proteins/chemistry , Models, Chemical , Models, Molecular , Molecular Structure , Multienzyme Complexes/deficiency , Multienzyme Complexes/metabolism , Oxidoreductases/deficiency , Oxidoreductases/metabolism , Succinate Dehydrogenase/deficiency , Succinate Dehydrogenase/metabolism , Wolinella
8.
Proc Natl Acad Sci U S A ; 97(24): 13051-6, 2000 Nov 21.
Article in English | MEDLINE | ID: mdl-11186225

ABSTRACT

Quinol:fumarate reductase (QFR) is a membrane protein complex that couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalyzed by the related enzyme succinate:quinone reductase (succinate dehydrogenase). In the previously determined structure of QFR from Wolinella succinogenes, the site of fumarate reduction in the flavoprotein subunit A of the enzyme was identified, but the site of menaquinol oxidation was not. In the crystal structure, the acidic residue Glu-66 of the membrane spanning, diheme-containing subunit C lines a cavity that could be occupied by the substrate menaquinol. Here we describe that, after replacement of Glu-C66 with Gln by site-directed mutagenesis, the resulting mutant is unable to grow on fumarate and the purified enzyme lacks quinol oxidation activity. X-ray crystal structure analysis of the Glu-C66-->Gln variant enzyme at 3.1-A resolution rules out any major structural changes compared with the wild-type enzyme. The oxidation-reduction potentials of the heme groups are not significantly affected. We conclude that Glu-C66 is an essential constituent of the menaquinol oxidation site. Because Glu-C66 is oriented toward a cavity leading to the periplasm, the release of two protons on menaquinol oxidation is expected to occur to the periplasm, whereas the uptake of two protons on fumarate reduction occurs from the cytoplasm. Thus our results indicate that the reaction catalyzed by W. succinogenes QFR generates a transmembrane electrochemical potential.


Subject(s)
Glutamic Acid , Naphthols/metabolism , Succinate Dehydrogenase/chemistry , Succinate Dehydrogenase/metabolism , Terpenes/metabolism , Wolinella/enzymology , Amino Acid Sequence , Amino Acid Substitution , Crystallography, X-Ray , Electrochemistry , Glutamine , Models, Molecular , Mutagenesis, Site-Directed , Oxidation-Reduction , Protein Conformation , Protein Subunits , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Wolinella/growth & development
9.
Nature ; 402(6760): 377-85, 1999 Nov 25.
Article in English | MEDLINE | ID: mdl-10586875

ABSTRACT

Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase). Here we describe the crystal structure at 2.2 A resolution of the three protein subunits containing fumarate reductase from the anaerobic bacterium Wolinella succinogenes. Subunit A contains the site of fumarate reduction and a covalently bound flavin adenine dinucleotide prosthetic group. Subunit B contains three iron-sulphur centres. The menaquinol-oxidizing subunit C consists of five membrane-spanning, primarily helical segments and binds two haem b molecules. On the basis of the structure, we propose a pathway of electron transfer from the dihaem cytochrome b to the site of fumarate reduction and a mechanism of fumarate reduction. The relative orientations of the soluble and membrane-embedded subunits of succinate:quinone oxidoreductases appear to be unique.


Subject(s)
Succinate Dehydrogenase/chemistry , Wolinella/enzymology , Cell Membrane/enzymology , Crystallography, X-Ray , Dicarboxylic Acids/metabolism , Electron Transport , Escherichia coli/enzymology , Flavin-Adenine Dinucleotide/metabolism , Heme/metabolism , Iron-Sulfur Proteins/metabolism , Metals/metabolism , Models, Molecular , Oxidation-Reduction , Protein Binding , Protein Conformation , Quinones/metabolism , Solubility
10.
J Mol Biol ; 286(3): 883-98, 1999 Feb 26.
Article in English | MEDLINE | ID: mdl-10024457

ABSTRACT

In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled with the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). It has been established by X-ray crystallography that the triazine herbicide terbutryn binds to the QB site. However, the exact description of protein-triazine interactions has had to await the refinement of higher-resolution structures. In addition, there is also interest in the role of chirality in the activity of herbicides. Here, we report the structural characterisation of triazine binding by crystallographic refinement of complexes of the RC either with the triazine inhibitor atrazine (Protein Data Bank (PDB) entry 5PRC) or with the chiral atrazine derivatives, DG-420314 (S(-) enantiomer, PDB entry 6PRC) or DG-420315 (R(+) enantiomer, PDB entry 7PRC). Due to the high quality of the data collected, it has been possible to describe the exact nature of triazine binding and its effect on the structure of the protein at high-resolution limits of 2.35 A (5PRC), 2.30 A (6PRC), and 2.65 A (7PRC), respectively. In addition to two previously implied hydrogen bonds, a third hydrogen bond, binding the distal side of the inhibitors to the protein, and four additional hydrogen bonds mediated by two tightly bound water molecules on the proximal side of the inhibitors, are apparent. Based on the high quality data collected on the RC complexes of the two chiral atrazine derivatives, unequivocal assignment of the structure at the chiral centres was possible, even though the differences in structures of the substituents are small. The structures provide explanations for the relative binding affinities of the two chiral compounds. Although it was not an explicit goal of this work, the new data were of sufficient quality to improve the original model also regarding the structure of the bound carotenoid 1,2-dihydroneurosporene. A carotenoid model with a cis double bond at the 15,15' position fits the electron density better than the original model with a 13,14-cis double bond.


Subject(s)
Atrazine/chemistry , Carotenoids/chemistry , Photosynthetic Reaction Center Complex Proteins/chemistry , Rhodopseudomonas/chemistry , Atrazine/analogs & derivatives , Binding Sites , Carotenoids/metabolism , Crystallography, X-Ray , Hydrogen Bonding , Models, Molecular , Molecular Conformation , Molecular Sequence Data , Photophosphorylation , Protein Binding , Quinones/chemistry , Water/metabolism
12.
Mol Microbiol ; 30(3): 639-46, 1998 Nov.
Article in English | MEDLINE | ID: mdl-9822828

ABSTRACT

The cytochrome b subunit (HydC) of Wolinella succinogenes hydrogenase binds two haem B groups. This is concluded from the haem B content of the isolated hydrogenase and is confirmed by the response of its cytochrome b to redox titration. In addition, three of the four haem B ligands were identified by characterizing mutants with the corresponding histidine residues replaced by alanine or methionine. Substitution in HydC of His-25, His-67 or His-186, which are, in addition to His-200, predicted to be haem B ligands, caused the loss of quinone reactivity of the hydrogenase, while the activity of benzylviologen reduction was retained. The corresponding mutants did not grow with H2 as electron donor and either fumarate or polysulphide as terminal electron acceptor. The mutants grown with formate and fumarate did not catalyse electron transport from H2 to fumarate or to polysulphide, or quinone reduction by H2, in contrast to the wild-type strain. Cytochrome b was not reduced by H2 in the Triton X-100 extract of the mutant membranes, which contained wild-type amounts of the mutated HydC protein. Substitution in HydC of His-122, His-158 or His-187, which are predicted not to be haem B ligands, yielded mutants with wild-type properties. Substitution in HydA of His-188 or of His-305 resulted in mutants with the same properties as those lacking one of the haem B ligands of HydC. His-305 is located in the membrane-integrated C-terminal helix of HydA. His-188 of HydA is predicted to be a ligand of the distal iron-sulphur centre that may serve as the direct electron donor to the haem B groups of HydC. The results suggest that each of the three predicted haem B ligands of HydC tested (out of four) is required for electron transport from H2 to either fumarate or polysulphide, and for quinone reactivity. This also holds true for the two conserved histidine residues of HydA.


Subject(s)
Hydrogen/metabolism , Hydrogenase/chemistry , Vitamin K/metabolism , Wolinella/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cell Division/genetics , Cytochrome b Group/chemistry , Cytochrome b Group/genetics , Electron Transport/genetics , Genes, Bacterial/genetics , Heme/chemistry , Hydrogenase/genetics , Oxidation-Reduction , Protein Conformation , Spectrophotometry
13.
J Bioenerg Biomembr ; 30(1): 81-7, 1998 Feb.
Article in English | MEDLINE | ID: mdl-9623809

ABSTRACT

In recent years, the enormous increase in high-resolution three-dimensional structures of proteins together with the development of powerful theoretical techniques have provided the basis for a more detailed examination of the role of electrostatics in determining the midpoint potentials of redox-active metal centers and in influencing the protonation behavior of titratable groups in proteins. Based on the coordinates of the Paracoccus denitrificans cytochrome c oxidase, we have determined the electrostatic potential in and around the protein, calculated the titration curves for all ionizable residues in the protein, and analyzed the response of the protein environment to redox changes at the metal centers. The results of this study provide insight into how charged groups can be stabilized within a low-dielectric environment and how the range of their electrostatic effects can be modulated by the protein. A cluster of 18 titratable groups around the heme a3-CuB binuclear center, including a hydroxide ion bound to the copper, was identified that accounts for most of the proton uptake associated with redox changes at the binuclear site. Predicted changes in net protonation were in reasonable agreement with experimentally determined values. The relevance of these findings in the light of possible mechanisms of redox-coupled proton movement is discussed.


Subject(s)
Electron Transport Complex IV/chemistry , Electron Transport Complex IV/metabolism , Paracoccus denitrificans/enzymology , Electron Transport , Enzyme Activation , Static Electricity
14.
Biophys J ; 74(2 Pt 1): 708-21, 1998 Feb.
Article in English | MEDLINE | ID: mdl-9533684

ABSTRACT

We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed.


Subject(s)
Electron Transport Complex IV/chemistry , Electron Transport Complex IV/metabolism , Paracoccus denitrificans/enzymology , Protein Conformation , Catalysis , Cell Membrane/enzymology , Cell Membrane/ultrastructure , Electron Transport , Heme/chemistry , Heme/metabolism , Macromolecular Substances , Models, Molecular , Oxidation-Reduction , Protein Structure, Secondary , Static Electricity , Thermodynamics
15.
Structure ; 5(10): 1339-59, 1997 Oct 15.
Article in English | MEDLINE | ID: mdl-9351808

ABSTRACT

BACKGROUND: In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In the original structure of the RC from Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined because in the standard RC crystals it was only approximately 30% occupied with ubiquinone-9 (UQ9). We report here the structural characterization of the QB site by crystallographic refinement of UQ9-depleted RCs and of complexes of the RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor stigmatellin in the QB site. RESULTS: The structure of the RC complex with UQ2, refined at 2.45 A resolution, constitutes the first crystallographically reliably defined binding site for quinones from the bioenergetically important quinone pool of biological, energy-transducing membranes. In the UQ9-depleted QB site of the RC structure, refined at 2.4 A resolution, apparently five (and possibly six) water molecules are bound instead of the ubiquinone head group, and a detergent molecule binds in the region of the isoprenoid tail. All of the protein-cofactor interactions implicated in the binding of the ubiquinone head group are also implicated in the binding of the stigmatellin head group. In the structure of the stigmatellin-RC complex, refined at 2.4 A resolution, additional hydrogen bonds stabilize the binding of stigmatellin over that of ubiquinone. The tentative position of UQ9 in the QB site in the original data set (1PRC) was re-examined using the structure of the UQ9-depleted RC as a reference. A modified QB site model, which exhibits greater similarity to the distal ubiquinone-10 (UQ10) positioning in the structure of the RC from Rhodobacter sphaeroides (PDB entry code 1PCR), is suggested as the dominant binding site for native UQ9. CONCLUSIONS: The structures reported here can provide models of quinone reduction cycle intermediates. The binding pattern observed for the stigmatellin complex, where the ligand donates a hydrogen bond to Ser L223 (where 'L' represents the L subunit of the RC), can be viewed as a model for the stabilization of a monoprotonated reduced intermediate (QBH or QBH-). The presence of Ser L223 in the QB site indicates that the QB site is not optimized for QB binding, but for QB reduction to the quinol.


Subject(s)
Photosynthetic Reaction Center Complex Proteins/chemistry , Rhodopseudomonas/metabolism , Ubiquinone/chemistry , Bacteriochlorophylls/chemistry , Binding Sites , Crystallography, X-Ray , Electron Transport , Energy Metabolism/physiology , Hydrogen Bonding , Light , Light-Harvesting Protein Complexes , Membrane Proteins/chemistry , Models, Molecular , Molecular Structure , Photosynthetic Reaction Center Complex Proteins/metabolism , Polyenes/chemistry , Polyenes/metabolism , Protein Binding , Protons , Rhodopseudomonas/chemistry , Ubiquinone/metabolism , Water/chemistry
16.
Biophys J ; 70(6): 2469-92, 1996 Jun.
Article in English | MEDLINE | ID: mdl-8744288

ABSTRACT

Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes.


Subject(s)
Photosynthetic Reaction Center Complex Proteins/metabolism , Rhodopseudomonas/metabolism , Amino Acid Sequence , Amino Acids/chemistry , Binding Sites , Biophysical Phenomena , Biophysics , Electron Transport , Hydrogen-Ion Concentration , Kinetics , Models, Molecular , Molecular Sequence Data , Molecular Structure , Monte Carlo Method , Mutagenesis, Site-Directed , Oxidation-Reduction , Photosynthetic Reaction Center Complex Proteins/chemistry , Photosynthetic Reaction Center Complex Proteins/genetics , Protons , Rhodopseudomonas/chemistry , Rhodopseudomonas/genetics , Static Electricity , Thermodynamics
17.
Photosynth Res ; 48(1-2): 65-74, 1996 May.
Article in English | MEDLINE | ID: mdl-24271287

ABSTRACT

In this article, the three-dimensional structures of photosynthetic reaction centers (RCs) are presented mainly on the basis of the X-ray crystal structures of the RCs from the purple bacteria Rhodopseudomonas (Rp.) viridis and Rhodobacter (Rb.) sphaeroides. In contrast to earlier comparisons and on the basis of the best-defined Rb. sphaeroides structure, a number of the reported differences between the structures cannot be confirmed. However, there are small conformational differences which might provide a basis for the explanation of observed spectral and functional discrepancies between the two species.A particular focus in this review is on the binding site of the secondary quinone (QB), where electron transfer is coupled to the uptake of protons from the cytoplasm. For the discussion of the QB site, a number of newlydetermined coordinate sets of Rp. viridis RCs modified at the QB site have been included. In addition, chains of ordered water molecules are found leading from the cytoplasm to the QB site in the best-defined structures of both Rp. viridis and Rb. sphaeroides RCs.

18.
Biochemistry ; 30(19): 4715-26, 1991 May 14.
Article in English | MEDLINE | ID: mdl-1674217

ABSTRACT

The structural requirements for the binding of dynorphin to the kappa-opioid receptor are of profound clinical interest in the search for a powerful nonaddictive analgesic. These requirements are thought to be met by the membrane-mediated conformation of the opioid peptide dynorphin A-(1-13)-peptide, Tyr1-Gly2-Gly3-Phe4-Leu5-Arg6-Arg7-Ile8-Arg9-Pro10- Lys11-Leu12-Lys13. Schwyzer has proposed an essentially alpha-helical membrane-mediated conformation of the 13 amino acid peptide [Schwyzer, R. (1986) Biochemistry 25, 4281-4286]. In the present study, circular dichroism (CD) studies on dynorphin A-(1-13)-peptide bound to an anionic phospholipid signified negligible helical content of the peptide. CD studies also demonstrated that the aqueous-membraneous interphase may be mimicked by methanol. The 500- and 620-MHz 1H nuclear magnetic resonance (NMR) spectra of dynorphin A-(1-13)-peptide in methanolic solution were sequence-specifically assigned with the aid of correlated spectroscopy (COSY), double-quantum filtered phase-sensitive COSY (DQF-COSY), relayed COSY (RELAY), and nuclear Overhauser enhancement spectroscopy (NOESY). 2-D CAMELSPIN/ROESY experiments indicated that at least the part of the molecule from Arg7 to Arg9 was in an extended or beta-strand conformation, which agreed with deuterium-exchange and temperature-dependence studies of the amide protons and analysis of the vicinal spin-spin coupling constants 3JHN alpha. The results clearly demonstrated the absence of extensive alpha-helix formation. chi 1 rotamer analysis of the 3J alpha beta demonstrated no preferred side-chain conformations.


Subject(s)
Dynorphins/chemistry , Cell Membrane , Circular Dichroism , Dynorphins/metabolism , Magnetic Resonance Spectroscopy , Methanol , Protein Conformation , Receptors, Opioid/metabolism , Receptors, Opioid, kappa , Solutions
19.
Biochem Cell Biol ; 67(11-12): 759-62, 1989.
Article in English | MEDLINE | ID: mdl-2619990

ABSTRACT

Lipoprotein fractions from some individuals have inhibitory effects on rat liver adenylate cyclase. Precipitation of the lipoprotein fractions with acetone released an inhibitory factor, which was soluble in acetone-H2O (3:1, v/v). The inhibition was greater against glucagon-stimulated activity than against basal activity. Acetone extraction increased the potency of inhibition. All three lipoprotein fractions, i.e., very low, low, and high density lipoproteins, released some inhibitory component after acetone extraction. The inhibitor was concentrated in the lipoprotein fractions, since acetone extraction of plasma did not release an inhibitor. The acetone extract from the very low density lipoprotein was the most inhibitory. This material was further purified and partially characterized. The inhibitor had a molecular mass of about 500. It was inhibitory at micromolar concentrations. The material was sufficiently hydrophobic to migrate in normal-phase thin-layer chromatography (TLC). Nuclear magnetic resonance results indicated that it was not a polar lipid. There were several different inhibitory factors that were separable by TLC. The sequestration of these inhibitors into lipoproteins reduced their effectiveness in inhibiting the action of counter-regulatory hormones, such as glucagon.


Subject(s)
Adenylyl Cyclase Inhibitors , Lipoproteins, VLDL/blood , Adenylyl Cyclases/isolation & purification , Adenylyl Cyclases/metabolism , Animals , Chromatography, Gel , Chromatography, Thin Layer , Glucagon/physiology , Humans , Liver/enzymology , Male , Rats , Rats, Inbred Strains
20.
Biochim Biophys Acta ; 945(2): 161-6, 1988 Nov 22.
Article in English | MEDLINE | ID: mdl-3191119

ABSTRACT

The effect of mono-, di- and triacylglycerols on the bilayer to hexagonal phase (HII) transition was studied by differential scanning calorimetry and 31P-NMR spectroscopy. The acylglycerols were mixed with either dielaidoylphosphatidylethanoline or with 1-palmitoyl-2-oleoylphosphatidylethanolamine. Acylglycerols of lauric, oleic and stearic acids were utilized. All of the acylglycerols lowered the bilayer to HII phase transition temperature. Diacylglycerols were much better HII phase promoters than monoacylglycerols while triacylglycerols were the most potent bilayer phase destabilizers. Fatty acid composition generally had less of an effect except for the monoacylglycerols where bilayer destabilization increased from monolaurin to monostearin to monoolein. The most marked difference in behaviour resulting from changes in the fatty acid composition of the acylglycerol occurred with tristearin. This was the only acylglycerol which decreased the bilayer to HII phase transition temperature only below a mol fraction of 0.005. Above this mol fraction, further addition of tristearin had no effect on the bilayer to HII phase transition. These results suggest that the tristearin has limited solubility in phosphatidylethanolamine.


Subject(s)
Glycerides , Lipid Bilayers , Phosphatidylethanolamines , Magnetic Resonance Spectroscopy , Thermodynamics
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