Electron transfer mechanism of the Rieske protein from Thermus thermophilus from solution nuclear magnetic resonance investigations.

Abstract:

:We report nuclear magnetic resonance (NMR) data indicating that the Rieske protein from the cytochrome bc complex of Thermus thermophilus (TtRp) undergoes modest redox-state-dependent and ligand-dependent conformational changes. To test models concerning the mechanism by which TtRp transfers between different sites on the complex, we monitored (1)H, (15)N, and (13)C NMR signals as a function of the redox state and molar ratio of added ligand. Our studies of full-length TtRp were conducted in the presence of dodecyl phosphocholine micelles to solvate the membrane anchor of the protein and the hydrophobic tail of the ligand (hydroubiquinone). NMR data indicated that hydroubiquinone binds to TtRp and stabilizes an altered protein conformation. We utilized a truncated form of the Rieske protein lacking the membrane anchor (trunc-TtRp) to investigate redox-state-dependent conformational changes. Local chemical shift perturbations suggested possible conformational changes at prolyl residues. Detailed investigations showed that all observable prolyl residues of oxidized trunc-TtRp have trans peptide bond configurations but that two of these peptide bonds (Cys151-Pro152 and Gly169-Pro170 located near the iron-sulfur cluster) become cis in the reduced protein. Changes in the chemical shifts of backbone signals provided evidence of redox-state- and ligand-dependent conformational changes localized near the iron-sulfur cluster. These structural changes may alter interactions between the Rieske protein and the cytochrome b and c sites and provide part of the driving force for movement of the Rieske protein between these two sites.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Hsueh KL,Tonelli M,Cai K,Westler WM,Markley JL

doi

10.1021/bi400296c

subject

Has Abstract

pub_date

2013-04-30 00:00:00

pages

2862-73

issue

17

eissn

0006-2960

issn

1520-4995

journal_volume

52

pub_type

杂志文章
  • Characterization of the N-terminal and C-terminal domains of human apolipoprotein(a): relevance to fibrin binding.

    abstract::The structural domains of human apolipoprotein(a) (apo(a)) in the lipoprotein(a) (Lp(a)) particle have been recently investigated by limited proteolysis [Huby, T., Doucet, C., Dieplinger, H., Chapman, J., & Thillet, J. (1994) Biochemistry 33, 3335-3341]. We have shown that apo(a) can be cleaved into two structural dom...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00022a011

    authors: Huby T,Schröder W,Doucet C,Chapman J,Thillet J

    更新日期:1995-06-06 00:00:00

  • The murine urokinase-type plasminogen activator gene.

    abstract::The murine urokinase-type plasminogen activator (uPA) gene has been isolated from a BALB/c liver DNA cosmid library and its nucleotide sequence established. The gene is organized into 11 exons comprising 34.7% of the 6710 base pair (bp) region spanning the interval between the presumed transcription initiation and pol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00399a038

    authors: Degen SJ,Heckel JL,Reich E,Degen JL

    更新日期:1987-12-15 00:00:00

  • Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli.

    abstract::Homoserine kinase, an enzyme in the aspartate pathway of amino acid biosynthesis in Escherichia coli, catalyzes the conversion of L-homoserine to L-homoserine phosphate. This enzyme has been found to have broad substrate specificity, including the phosphorylation of L-homoserine analogs where the carboxyl functional g...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962203z

    authors: Huo X,Viola RE

    更新日期:1996-12-17 00:00:00

  • Calvarial cells synthesize 1 alpha,25-dihydroxyvitamin D3 from 25-hydroxyvitamin D3.

    abstract::A metabolite of vitamin D has been isolated in pure form from incubation of 25-hydroxyvitamin D3 with embryonic chick calvarial cells that had been grown on Cytodex 1 microcarrier beads. The isolation involved dichloromethane extraction of the cells and incubation medium, followed by Sephadex LH-20 column chromatograp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00274a012

    authors: Turner RT,Howard GA,Puzas JE,Baylink DJ,Knapp DR

    更新日期:1983-03-01 00:00:00

  • Multiple replacements of glutamine 143 in human manganese superoxide dismutase: effects on structure, stability, and catalysis.

    abstract::Glutamine 143 in human manganese superoxide dismutase (MnSOD) forms a hydrogen bond with the manganese-bound solvent molecule and is investigated by replacement using site-specific mutagenesis. Crystal structures showed that the replacement of Gln 143 with Ala made no significant change in the overall structure of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9929958

    authors: Lévêque VJ,Stroupe ME,Lepock JR,Cabelli DE,Tainer JA,Nick HS,Silverman DN

    更新日期:2000-06-20 00:00:00

  • Examination of the solvent perturbation technique as a method to identify enzyme catalytic groups.

    abstract::The present study was undertaken for the purpose of evaluating the solvent perturbation technique as a method to identify enzyme catalytic residues. For establishment of expected directions and sizes of pKa perturbations for different types of acids in different classes of solvents, a study of the pKa of a series of a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00287a013

    authors: Grace S,Dunaway-Mariano D

    更新日期:1983-08-30 00:00:00

  • The C-terminus is critical for the functional expression of the human serotonin transporter.

    abstract::The plasma membrane serotonin transporter (SERT) has an important role in terminating serotonergic neurotransmission by re-uptake of 5-HT from the synaptic cleft. The expression of SERT on the cell surface is therefore a critical factor. In this study, we examined the role of the carboxyl terminus of SERT in trafficki...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0508688

    authors: Larsen MB,Fjorback AW,Wiborg O

    更新日期:2006-01-31 00:00:00

  • Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

    abstract::The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00679a018

    authors: Wolf B,Hanlon S

    更新日期:1975-04-22 00:00:00

  • Kinetic mechanism of orotate phosphoribosyltransferase from Salmonella typhimurium.

    abstract::The chemical mechanism of the phosphoribosyltransferases (PRTases), although largely unknown, may proceed either via a concerted direct-transfer mechanism or with a two-step mechanism involving a carboxonium-like intermediate. To study this question, we have cloned the Salmonella typhimurium pyrE gene, coding for the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00498a009

    authors: Bhatia MB,Vinitsky A,Grubmeyer C

    更新日期:1990-11-20 00:00:00

  • Interaction of ribosomal protein S1 and initiation factor IF3 with the 3' major domain and the decoding site of the 30S subunit of Escherichia coli.

    abstract::We have studied the effect of the binding of ribosomal protein S1 and initiation factor IF3 on the accessibility of nucleotide residues 584-1506 in the small subunit of the Escherichia coli ribosome. Protein S1 strongly decreases RNase V1 attack at G1164, in hairpin 40 of the 3' major domain, and weakly decreases DMS ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00112a007

    authors: Laughrea M,Tam J

    更新日期:1991-12-03 00:00:00

  • Donor-acceptor distance distributions in a double-labeled fluorescent oligonucleotide both as a single strand and in duplexes.

    abstract::A 16-mer deoxyribonucleotide was labeled at the 5'-end with x-rhodamine and at the 3'-end with fluorescein. Förster resonance energy transfer was used to determine the distribution, P(R), of donor-acceptor distances for the oligomer in three duplex structures (hybridized to complementary strands having 10, 16, and 24 ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00001a036

    authors: Parkhurst KM,Parkhurst LJ

    更新日期:1995-01-10 00:00:00

  • A proton nuclear magnetic resonance study of the quaternary structure of human homoglobins in water.

    abstract::Proton nuclear magnetic resonance spectra of human hemoglobins in water reveal several exchangeable protons which are indicators of the quaternary structures of both the liganded and unliganded molecules. A comparison of the spectra of normal human adult hemoglobin with those of mutant hemoglobins Chesapeake (FG4alpha...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00682a036

    authors: Fung LW,Ho C

    更新日期:1975-06-03 00:00:00

  • Substrate-Induced Facilitated Dissociation of the Competitive Inhibitor from the Active Site of O-Acetyl Serine Sulfhydrylase Reveals a Competitive-Allostery Mechanism.

    abstract::By classical competitive antagonism, a substrate and competitive inhibitor must bind mutually exclusively to the active site. The competitive inhibition of O-acetyl serine sulfhydrylase (OASS) by the C-terminus of serine acetyltransferase (SAT) presents a paradox, because the C-terminus of SAT binds to the active site...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00500

    authors: Singh AK,Ekka MK,Kaushik A,Pandya V,Singh RP,Banerjee S,Mittal M,Singh V,Kumaran S

    更新日期:2017-09-19 00:00:00

  • Heme synthase (ferrochelatase) catalyzes the removal of iron from heme and demetalation of metalloporphyrins.

    abstract::The red pigments in meat products, including cooked cured ham, arise from the reaction of myoglobin with nitric oxide generated from exogenous nitrite. Since carcinogenic nitrosoamines may be generated by the treatment of meats with nitrite, the production of nitrite-free meat products is an attractive alternative. Ra...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi701460x

    authors: Taketani S,Ishigaki M,Mizutani A,Uebayashi M,Numata M,Ohgari Y,Kitajima S

    更新日期:2007-12-25 00:00:00

  • Characterization of Caenorhabditis elegans Nucleosome Assembly Protein 1 Uncovers the Role of Acidic Tails in Histone Binding.

    abstract::Nucleosome assembly proteins (Naps) influence chromatin dynamics by directly binding to histones. Here we provide a comprehensive structural and biochemical analysis of a Nap protein from Caenorhabditis elegans (CeNap1). CeNap1 naturally lacks the acidic N-terminal tail and has a short C-terminal tail compared to many...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b01033

    authors: Sarkar P,Zhang N,Bhattacharyya S,Salvador K,D'Arcy S

    更新日期:2019-01-15 00:00:00

  • Effects of 5' leader and 3' trailer structures on pre-tRNA processing by nuclear RNase P.

    abstract::Eukaryotic transfer RNA precursors (pre-tRNAs) contain a 5' leader preceding the aminoacyl acceptor stem and a 3' trailer extending beyond this stem. An early step in pre-tRNA maturation is removal of the 5' leader by the endoribonuclease, RNase P. Extensive pairing between leader and trailer sequences has previously ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000603n

    authors: Ziehler WA,Day JJ,Fierke CA,Engelke DR

    更新日期:2000-08-15 00:00:00

  • Complex of human apolipoprotein C-1 with phospholipid: thermodynamic or kinetic stability?

    abstract::Thermal unfolding of discoidal complexes of apolipoprotein (apo) C-1 with dimyristoyl phosphatidylcholine (DMPC) reveals a novel mechanism of lipoprotein stabilization that is based on kinetics rather than thermodynamics. Far-UV CD melting curves recorded at several heating/cooling rates from 0.047 to 1.34 K/min show ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi025588w

    authors: Gursky O,Ranjana,Gantz DL

    更新日期:2002-06-11 00:00:00

  • ENDOR structural characterization of a catalytically competent acylenzyme reaction intermediate of wild-type TEM-1 beta-lactamase confirms glutamate-166 as the base catalyst.

    abstract::The catalytically competent active-site structure of a true acylenzyme reaction intermediate of TEM-1 beta-lactamase formed with the kinetically specific spin-labeled substrate 6-N-(2,2,5,5-tetramethyl-1-oxypyrrolinyl-3-carboxyl)-penicillanic acid isolated under cryoenzymologic conditions has been determined by angle-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0021075

    authors: Mustafi D,Sosa-Peinado A,Makinen MW

    更新日期:2001-02-27 00:00:00

  • Kinetic studies of Thermobifida fusca Cel9A active site mutant enzymes.

    abstract::Thermobifida fusca Cel9A-90, an unusual family 9 enzyme, is a processive endoglucanase containing a catalytic domain closely linked to a family 3c cellulose binding domain (Cel9A-68) followed by a fibronectin III-like domain and a family 2 cellulose binding domain. To study its catalytic mechanism, 12 mutant genes wit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049394n

    authors: Zhou W,Irwin DC,Escovar-Kousen J,Wilson DB

    更新日期:2004-08-03 00:00:00

  • Probing conformational changes within LC2 domains of cardiac myosin.

    abstract::Nine monoclonal antibodies were used to test calcium and EDTA effects on the molecular conformation of ventricular VLC2 within myosin. Antibody epitopes were located in six domains of VLC2 using recombinant proteins. The apparent association constants of these antibodies were measured in solution in the presence of ca...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00208a005

    authors: Eldin P,Cathiard AM,Anoal M,Léger J,Mornet D,Léger JJ,Cornillon B

    更新日期:1994-10-25 00:00:00

  • Calmodulin-dependent protein phosphatase: a developmental study.

    abstract::Calmodulin-dependent protein phosphatase, one of the major calmodulin-binding proteins in bovine brain, dephosphorylates casein with a specific activity of 15 nmol mg-1 min-1 at 30 degrees C. The stimulation of phosphatase activity by calmodulin is reversed by ethylene glycol bis (beta-aminoethyl ether)-N,N,N',N'-tetr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00284a014

    authors: Tallant EA,Cheung WY

    更新日期:1983-07-19 00:00:00

  • Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant.

    abstract::Gemcitabine 5'-diphosphate (F(2)CDP) is a potent inhibitor of ribonucleotide reductases (RNRs), enzymes that convert nucleotides (NDPs) to deoxynucleotides and are essential for DNA replication and repair. The Escherichia coli RNR, an alpha2beta2 complex, when incubated with 1 equiv of F(2)CDP catalyzes the release of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901590q

    authors: Artin E,Wang J,Lohman GJ,Yokoyama K,Yu G,Griffin RG,Bar G,Stubbe J

    更新日期:2009-12-15 00:00:00

  • Water catalysis of peptide hydrogen isotope exchange.

    abstract::The temperature dependence of the hydrogen-tritium and deuterium-hydrogen exchange reactions in poly(DL-alanine) has been reexamined. The results indicate a significant contribution to the observed exchange rates from the water-catalyzed reaction at pD values near pDmin. The activation enthalpy for water-catalyzed deu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00273a031

    authors: Gregory RB,Crabo L,Percy AJ,Rosenberg A

    更新日期:1983-02-15 00:00:00

  • Comparative orientation of the fluorene residue in native DNA modified by N-acetoxy-N-2-acetylaminofluorene and two 7-halogeno derivatives.

    abstract::Native calf thymus DNA was reacted with N-acetoxy-N-2-acetylaminofluorene (N-AcO-AAF) and its 7-fluoro and 7-iodo derivatives. Different ways of purification of the fluorene modified DNA samples were checked in order ot obtain a nucleic acid free from all noncovalently bound fluorene residues. The decrease in melting ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00660a027

    authors: Fuchs RP,Lefevre JF,Pouyet J,Daune MP

    更新日期:1976-07-27 00:00:00

  • Translocation of E. coli RecQ helicase on single-stranded DNA.

    abstract::A member of the SF2 family of helicases, Escherichia coli RecQ, is involved in the recombination and repair of double-stranded DNA breaks and single-stranded DNA (ssDNA) gaps. Although the unwinding activity of this helicase has been studied biochemically, the mechanism of translocation remains unclear. To this end, u...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi3000676

    authors: Rad B,Kowalczykowski SC

    更新日期:2012-04-03 00:00:00

  • Imaging and mapping heparin-binding sites on single fibronectin molecules with atomic force microscopy.

    abstract::Fibronectin is composed of multiple homologous repeats and contains many functional domains. Two major heparin-binding domains have previously been identified: the Hep I site near the amino terminus and the Hep II site near the carboxyl terminus. The Hep II site has been considered the high-affinity heparin-binding si...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991624o

    authors: Lin H,Lal R,Clegg DO

    更新日期:2000-03-28 00:00:00

  • pH dependence and structural interpretation of the reactions of Coprinus cinereus peroxidase with hydrogen peroxide, ferulic acid, and 2,2'-azinobis.

    abstract::Steady-state and transient-state analysis of Coprinus cinereus peroxidase, CIP (identical to Arthromyces ramosus peroxidase), was used to characterize the kinetics of the three fundamental steps in heme peroxidase catalysis: compound I (cpd I) formation, cpd I reduction, and compound II (cpd II) reduction. The rate co...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970387r

    authors: Abelskov AK,Smith AT,Rasmussen CB,Dunford HB,Welinder KG

    更新日期:1997-08-05 00:00:00

  • Human B1 and B2 bradykinin receptors and their agonists target caveolae-related lipid rafts to different degrees in HEK293 cells.

    abstract::To address the targeting of G protein-coupled receptors to caveolae-related lipid rafts (CLR), we studied the human B2 (B2R) and B1 (B1R) bradykinin receptor subtypes in HEK293 cells. CLR were enriched on the basis of their unique buoyant density and composition of cholesterol, caveolin-1, and flotillin-1 but not clat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi020231d

    authors: Lamb ME,Zhang C,Shea T,Kyle DJ,Leeb-Lundberg LM

    更新日期:2002-12-03 00:00:00

  • Structural analysis of integrin recognition and the inhibition of integrin-mediated cell functions by novel nonpeptidic surrogates of the Arg-Gly-Asp sequence.

    abstract::The pivotal role of the Arg-Gly-Asp (RGD) peptide motif in integrin-mediated cell adhesive interactions with extracellular matrix and plasma proteins stimulated the present design of nonpeptidic mimetics of this sequence. To probe the structural requirements for RGD recognition by integrins, we designed various struct...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00055a002

    authors: Greenspoon N,Hershkoviz R,Alon R,Varon D,Shenkman B,Marx G,Federman S,Kapustina G,Lider O

    更新日期:1993-02-02 00:00:00

  • Energetics of coiled coil folding: the nature of the transition states.

    abstract::Coiled coils are simple models for studying the association of two polypeptide chains to form a folded protein. Previous work has shown that the folding of a coiled coil can be described by a two-state transition between two unfolded monomeric peptide chains and a folded coiled coil dimer. Here we report the thermodyn...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002161l

    authors: Bosshard HR,Dürr E,Hitz T,Jelesarov I

    更新日期:2001-03-27 00:00:00