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https://www.readbyqxmd.com/read/19518050/on-the-contributions-of-diffusion-and-thermal-activation-to-electron-transfer-between-phormidium-laminosum-plastocyanin-and-cytochrome-f-brownian-dynamics-simulations-with-explicit-modeling-of-nonpolar-desolvation-interactions-and-electron-transfer-events
#1
Razif R Gabdoulline, Rebecca C Wade
The factors that determine the extent to which diffusion and thermal activation processes govern electron transfer (ET) between proteins are debated. The process of ET between plastocyanin (PC) and cytochrome f (CytF) from the cyanobacterium Phormidium laminosum was initially thought to be diffusion-controlled but later was found to be under activation control (Schlarb-Ridley, B. G.; et al. Biochemistry 2005, 44, 6232). Here we describe Brownian dynamics simulations of the diffusional association of PC and CytF, from which ET rates were computed using a detailed model of ET events that was applied to all of the generated protein configurations...
July 8, 2009: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/18824464/docking-of-cytochrome-c6-and-plastocyanin-to-the-aa3-type-cytochrome-c-oxidase-in-the-cyanobacterium-phormidium-laminosum
#2
Sarah E Hart, Christopher J Howe, Kenji Mizuguchi, Juan Fernandez-Recio
The interactions between redox proteins are transient in nature. Therefore, very few crystal structures are available for the complexes formed between these proteins. Computational docking simulations thus provide a useful alternative method for studying the interactions between electron transfer proteins. In this paper, we have studied the interactions between the aa(3)-type cytochrome c oxidase of the cyanobacterium Phormidium laminosum and its redox partners plastocyanin and cytochrome c(6) using a combination of comparative modelling techniques and docking simulations...
December 2008: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/16979296/purification-and-properties-of-nrtc-and-nrtd-the-atp-binding-subunits-of-the-abc-nitrate-nitrite-transporter-of-phormidium-laminosum
#3
Marta Llarena, María J Llama, Juan L Serra
A genomic region from the thermophilic, filamentous, nondiazotrophic cyanobacterium Phormidium laminosum including nrtC and nrtD was cloned and sequenced. These genes encode NrtC and NrtD, the ATP-binding subunits of the ABC bispecific transporter of nitrate/nitrite NRT. We report a different nrtC sequence from the one previously reported (Merchán et al., Plant Mol. Biol. 28:759-766, 1995) and we identified the presence of nrtD gene downstream nrtC in the nirA operon. Each gene was expressed in E. coli cells as a hexahistidine-tagged fusion protein...
December 2006: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/16214856/a-brownian-dynamics-study-of-the-interaction-of-phormidium-cytochrome-f-with-various-cyanobacterial-plastocyanins
#4
Elizabeth L Gross, Irving Rosenberg
Brownian dynamics simulations were used to study the role of electrostatic forces in the interactions of cytochrome f from the cyanobacterium Phormidium laminosum with various cyanobacterial plastocyanins. Both the net charge on the plastocyanin molecule and the charge configuration around H92 (H87 in higher plants) are important in determining the interactions. Those plastocyanins (PCs) with a net charge more negative than -2.0, including those from Synechococcus sp. PCC7942, Synechocystis sp. 6803, and P...
January 1, 2006: Biophysical Journal
https://www.readbyqxmd.com/read/15345580/a-brownian-dynamics-study-of-the-interaction-of-phormidium-laminosum-plastocyanin-with-phormidium-laminosum-cytochrome-f
#5
Elizabeth L Gross
The interaction of Phormidium laminosum plastocyanin (PC) with P. laminosum cytochrome f (cyt f) was studied using Brownian dynamics (BD) simulations. Few complexes and a low rate of electron transfer were observed for wild-type PC. Increasing the positive electrostatic field on PC by the addition of a Zn(2+) ion in the neighborhood of D44 and D45 on PC (as found in crystal structure of plastocyanin) increased the number of complexes formed and the calculated rates of electron transfer as did PC mutations D44A, D45A, E54A, and E57A...
September 2004: Biophysical Journal
https://www.readbyqxmd.com/read/12783525/detection-of-short-lived-transient-protein-protein-interactions-by-intermolecular-nuclear-paramagnetic-relaxation-plastocyanin-from-anabaena-variabilis
#6
D Flemming Hansen, Mathias A S Hass, Hans M Christensen, Jens Ulstrup, Jens J Led
An NMR approach is presented that provides detailed information about short-lived, transient interactions between protein molecules in solution. The approach is based on the longitudinal paramagnetic relaxation rates of the protein nuclei and requires that at least one of the interacting molecules is paramagnetic. The specific interactions are monitored by the intermolecular paramagnetic contribution to the relaxation of protons at or close to the interaction surface. By applying the approach to plastocyanin from Anabaena variabilis, specific regions of interaction that may be involved in the electron self-exchange process of this plastocyanin were identified...
June 11, 2003: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/12718523/role-of-charges-on-cytochrome-f-from-the-cyanobacterium-phormidium-laminosum-in-its-interaction-with-plastocyanin
#7
Sarah E Hart, Beatrix G Schlarb-Ridley, Christine Delon, Derek S Bendall, Christopher J Howe
The role of charge on the surface of cytochrome f from the cyanobacterium Phormidium laminosum in the reaction with plastocyanin was investigated in vitro using site-directed mutagenesis. Charge was neutralized at five acidic residues individually and introduced at a residue close to the interface between the two proteins. The effects on the kinetics of the reaction were measured using stopped-flow spectrophotometry, and the midpoint potentials of the mutant proteins were determined. The dependence of the bimolecular rate constant of reaction, k(2), on ionic strength was determined for the reactions of the cytochrome f mutants with wild-type and mutant forms of plastocyanin...
May 6, 2003: Biochemistry
https://www.readbyqxmd.com/read/12680759/relation-between-interface-properties-and-kinetics-of-electron-transfer-in-the-interaction-of-cytochrome-f-and-plastocyanin-from-plants-and-the-cyanobacterium-phormidium-laminosum
#8
Beatrix G Schlarb-Ridley, Derek S Bendall, Christopher J Howe
Cytochrome f and plastocyanin from the cyanobacterium Phormidium laminosum react an order of magnitude faster than their counterparts from chloroplasts when long-range electrostatic interactions have been screened out by high salt concentration [Schlarb-Ridley, B. G., et al. (2002) Biochemistry 41, 3279-3285]. To investigate the relative contributions of the reaction partners to these differences, the reactions of turnip cytochrome f with P. laminosum plastocyanin and P. laminosum cytochrome f with pea plastocyanin were examined...
April 15, 2003: Biochemistry
https://www.readbyqxmd.com/read/12444978/role-of-electrostatics-in-the-interaction-between-plastocyanin-and-photosystem-i-of-the-cyanobacterium-phormidium-laminosum
#9
COMPARATIVE STUDY
Beatrix G Schlarb-Ridley, José A Navarro, Matthew Spencer, Derek S Bendall, Manuel Hervás, Christopher J Howe, Miguel A De La Rosa
The interactions between photosystem I and five charge mutants of plastocyanin from the cyanobacterium Phormidium laminosum were investigated in vitro. The dependence of the overall rate constant of reaction, k2, on ionic strength was investigated using laser flash photolysis. The rate constant of the wild-type reaction increased with ionic strength, indicating repulsion between the reaction partners. Removing a negative charge on plastocyanin (D44A) accelerated the reaction and made it independent of ionic strength; removing a positive charge adjacent to D44 (K53A) had little effect...
December 2002: European Journal of Biochemistry
https://www.readbyqxmd.com/read/11876635/role-of-electrostatics-in-the-interaction-between-cytochrome-f-and-plastocyanin-of-the-cyanobacterium-phormidium-laminosum
#10
Beatrix G Schlarb-Ridley, Derek S Bendall, Christopher J Howe
The role of charged residues on the surface of plastocyanin from the cyanobacterium Phormidium laminosum in the reaction with soluble cytochrome f in vitro was studied using site-directed mutagenesis. The charge on each of five residues on the eastern face of plastocyanin was neutralized and/or inverted, and the effect of the mutation on midpoint potentials was determined. The dependence of the overall rate constant of reaction, k(2), on ionic strength was investigated using stopped-flow spectrophotometry. Removing negative charges (D44A or D45A) accelerated the reaction and increased the dependence on ionic strength, whereas removing positive charges slowed it down...
March 12, 2002: Biochemistry
https://www.readbyqxmd.com/read/11673974/hydrophobic-interactions-in-a-cyanobacterial-plastocyanin-cytochrome-f-complex
#11
P B Crowley, G Otting, B G Schlarb-Ridley, G W Canters, M Ubbink
The complex of the photosynthetic redox partners plastocyanin and cytochrome f from the thermophilic cyanobacterium, Phormidium laminosum, was investigated by nuclear magnetic resonance (NMR). Chemical-shift perturbation analysis of amide proton and nitrogen nuclei implicates the hydrophobic patch and, to a lesser extent, the "eastern face" of plastocyanin in the complex interface. Intermolecular pseudocontact shifts observed in the complex of cadmium-substituted plastocyanin and ferric cytochrome f specifically define the site of interaction to be between the hydrophobic patch of plastocyanin and the heme region of cytochrome f...
October 31, 2001: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/10821668/tryptophan-heme-pi-electrostatic-interactions-in-cytochrome-f-of-oxygenic-photosynthesis
#12
M V Ponamarev, B G Schlarb, C J Howe, C J Carrell, J L Smith, D S Bendall, W A Cramer
Cytochrome f of oxygenic photosynthesis has an unprecedented structure, including the N-terminus being a heme ligand. The adjacent N-terminal heme-shielding domain is enriched in aromatic amino acids. The atomic structures of the chloroplast and cyanobacterial cytochromes f were compared to explain spectral and redox differences between them. The conserved aromatic side chain in the N-terminal heme-shielding peptide at position 4, Phe and Tyr in plants and algae, respectively, and Trp in cyanobacteria, is in contact with the heme...
May 23, 2000: Biochemistry
https://www.readbyqxmd.com/read/10423236/structure-of-the-soluble-domain-of-cytochrome-f-from-the-cyanobacterium-phormidium-laminosum
#13
COMPARATIVE STUDY
C J Carrell, B G Schlarb, D S Bendall, C J Howe, W A Cramer, J L Smith
Cytochrome f from the photosynthetic cytochrome b(6)f complex is unique among c-type cytochromes in its fold and heme ligation. The 1. 9-A crystal structure of the functional, extrinsic portion of cytochrome f from the thermophilic cyanobacterium Phormidium laminosum demonstrates that an unusual buried chain of five water molecules is remarkably conserved throughout the biological range of cytochrome f from cyanobacteria to plants [Martinez et al. (1994) Structure 2, 95-105]. Structure and sequence conservation of the cytochrome f extrinsic portion is concentrated at the heme, in the buried water chain, and in the vicinity of the transmembrane helix anchor...
July 27, 1999: Biochemistry
https://www.readbyqxmd.com/read/10395900/expression-of-plastocyanin-and-cytochrome-f-of-the-cyanobacterium-phormidium-laminosum-in-escherichia-coli-and-paracoccus-denitrificans-and-the-role-of-leader-peptides
#14
B G Schlarb, M J Wagner, E Vijgenboom, M Ubbink, D S Bendall, C J Howe
The gene for plastocyanin from the cyanobacterium Phormidium laminosum was successfully expressed in Escherichia coli. Expression of the gene for cytochrome f resulted in the production of holocytochrome f in the periplasmic space of E. coli, but the yield was low. Expression in Paracoccus denitrificans yielded no holoprotein. When the region encoding the cytochrome f leader sequence was replaced with more typical bacterial leader sequences (those from the P. laminosum plastocyanin gene and the Paracoccus versutus cytochrome c-550 gene), much higher yields were consistently obtained in both species...
July 8, 1999: Gene
https://www.readbyqxmd.com/read/10089349/the-structure-of-plastocyanin-from-the-cyanobacterium-phormidium-laminosum
#15
C S Bond, D S Bendall, H C Freeman, J M Guss, C J Howe, M J Wagner, M C Wilce
The crystal structure of the 'blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 A X--ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 A and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity)...
February 1999: Acta Crystallographica. Section D, Biological Crystallography
https://www.readbyqxmd.com/read/8856106/some-characteristics-of-cytochrome-f-in-the-cyanobacterium-phormidium-laminosum-its-sequence-and-charge-properties-in-the-reaction-with-plastocyanin
#16
COMPARATIVE STUDY
M J Wagner, J C Packer, C J Howe, D S Bendall
Part of the petCA operon was cloned and the sequence of the cytochrome f gene from the moderately thermophilic cyanobacterium Phormidium laminosum determined. A partial sequence of the petC gene encoding the Rieske iron-sulphur protein was also obtained. The cytochrome f gene encodes a mature protein of 385 residues and a leader sequence of 45 residues. The mature protein contains several acidic or neutral residues corresponding to basic residues in the turnip protein. Some of the latter are thought to be important for the interaction with plastocyanin via its "eastern' face...
September 30, 1996: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/7865790/cloning-and-sequence-analysis-of-a-signal-peptidase-i-from-the-thermophilic-cyanobacterium-phormidium-laminosum
#17
COMPARATIVE STUDY
J C Packer, D André, C J Howe
Type I signal peptidases are a widespread family of enzymes which remove the presequences from proteins translocated across cell membranes, including thylakoid and cytoplasmic membranes of cyanobacteria and thylakoid membranes of chloroplasts. We have cloned and sequenced a signal peptidase gene from the thermophilic cyanobacterium Phormidium laminosum which is believed to encode an enzyme common to both membrane systems. The deduced amino acid sequence is 203 residues long and although the overall similarity among signal peptidases is rather low there are a number of identifiable conserved regions present...
January 1995: Plant Molecular Biology
https://www.readbyqxmd.com/read/7766873/isolation-sequence-and-expression-in-escherichia-coli-of-the-nitrite-reductase-gene-from-the-filamentous-thermophilic-cyanobacterium-phormidium-laminosum
#18
COMPARATIVE STUDY
F Merchán, R Prieto, K L Kindle, M J Llama, J L Serra, E Fernández
The nitrite reductase (NiR) gene (nirA) has been isolated and sequenced from the filamentous, thermophilic non-N2-fixing cyanobacterium Phormidium laminosum. Putative promoter-like and Shine-Dalgarno sequences appear at the 5' end of the 1533 bp long nir-coding region. The deduced amino acid sequence of NiR from P. laminosum corresponds to a 56 kDa polypeptide, a size identical to the molecular mass previously determined for the pure enzyme, and shows a high identity with amino acid sequences from ferredoxin-dependent NiR...
March 1995: Plant Molecular Biology
https://www.readbyqxmd.com/read/6772163/photosynthetic-electron-transport-in-a-cell-free-preparation-from-the-thermophilic-blue-green-alga-phormidium-laminosum
#19
A C Stewart, D S Bendall
1. A cell-free preparation of membrane fragments was prepared from the thermophilic blue-green alga Phormidium laminosum by lysozyme treatment of the cells followed by osmotic shock to lyse the spheroplasts. The membrane fragments showed high rates of photosynthetic electron transport and O2 evolution (180-250 mumol of O2/h per mg of chlorophyll a with 2,6-dimethyl-1,4-benzoquinone as electron acceptor). O2-evolution activity was stable provided that cations (e.g. 10mM-Mg2+ or 100mM-Na+) or glycerol (25%, v/v) were present in the suspending medium...
May 15, 1980: Biochemical Journal
https://www.readbyqxmd.com/read/6412632/characterization-of-photosystem-ii-electron-acceptors-in-phormidium-laminosum
#20
J M Bowes, P Horton, D S Bendall
Chlorophyll a fluorescence has been used to monitor the redox state of the primary electron acceptor of photosystem II (PS II) in the blue-green alga Phormidium laminosum during equilibrium titrations. The shape of induction curves measured in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) have been analyzed. The induction curves were very similar in unfractionated thylakoid membranes and PS II particles. In both, the fast (alpha) phase was sigmoidal, and was followed by a slow (beta) exponential tail...
August 1983: Archives of Biochemistry and Biophysics
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