Using saturation-recovery EPR to measure distances in proteins: applications to photosystem II.

Abstract:

:The stable tyrosine radical YD. (tyrosine 160 in the D2 polypeptide) in photosystem II (PSII) exhibits nonexponential electron spin-lattice relaxation transients at low temperature. As previously reported, the tetranuclear Mn complex in PSII significantly enhances the spin-lattice relaxation of YD.. However, in Mn-depleted PSII membranes, the spin-lattice relaxation transients of YD. are also nonexponential, and progressive power saturation (P 1/2) experiments show that it does not behave like an isolated tyrosine radical. A model is developed to treat the interaction of two paramagnets in a rigid lattice at a fixed distance apart but with a random orientation in a magnetic field. This model describes the spin-lattice relaxation of a radical in proximity to another paramagnetic site in terms of three relaxation rate constants: the "intrinsic" relaxation rate, the relaxation rate due to scalar exchange, and the relaxation rate due to dipole-dipole interactions. The intrinsic and the scalar exchange relaxation rates are isotropic and together contribute a single rate constant to the spin-lattice relaxation transients. However, the dipolar relaxation rate is orientation dependent. Each orientation contributes a different dipolar relaxation rate constant to the net spin-lattice relaxation rate constant. The result is a superposition of single-exponential recoveries, each with a different net rate constant, causing the observed saturation-recovery transients to be non-(single)-exponential. Saturation-recovery relaxation transients of YD. are compared with those of a model tyrosine radical, generated by UV photolysis of L-tyrosine in a borate glass. From this comparison, we conclude that scalar exchange does not make a significant contribution to the spin-lattice relaxation of YD. in Mn-depleted PSII. We account for the nonexponential relaxation transients obtained from YD. in Mn-depleted PSII membranes in terms of dipolar-induced relaxation enhancement from the non-heme Fe(II). From simulations of the spin-lattice relaxation transients, we obtain the magnitude of the magnetic dipolar interaction between YD. and the non-heme Fe(II), which can be used to calculate the distance between them. Using data on the non-heme Fe(II) in the reaction center of Rhodobacter sphaeroides to model the non-heme Fe(II) in PSII, we calculate a YD.-Fe(II) distance of greater than or equal to 38 A in PSII. This agrees well with the distance predicted from the structure of the bacterial reaction center.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Hirsh DJ,Beck WF,Innes JB,Brudvig GW

doi

10.1021/bi00117a033

subject

Has Abstract

pub_date

1992-01-21 00:00:00

pages

532-41

issue

2

eissn

0006-2960

issn

1520-4995

journal_volume

31

pub_type

杂志文章
  • The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic acid dehalogenase: a kinetic, NMR, and mutational analysis.

    abstract::trans-3-Chloroacrylic acid dehalogenase (CaaD) converts trans-3-chloroacrylic acid to malonate semialdehyde by the addition of H(2)O to the C-2, C-3 double bond, followed by the loss of HCl from the C-3 position. Sequence similarity between CaaD, an (alphabeta)(3) heterohexamer (molecular weight 47,547), and 4-oxalocr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi030241u

    authors: Azurmendi HF,Wang SC,Massiah MA,Poelarends GJ,Whitman CP,Mildvan AS

    更新日期:2004-04-13 00:00:00

  • Characterization of human calcitonin fibrillation in aqueous urea solution by 1H NMR spectroscopy.

    abstract::The inhibitory effects of urea on the normally rapid fibrillation of human calcitonin (hCT) were investigated by 1H NMR. From subtle differences in the chemical shift of hCT in the presence and absence of urea, the occurrence of weak interactions between urea and hCT was confirmed. The chemical shifts on the NH and C ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961013l

    authors: Kanaori K,Nosaka AY

    更新日期:1996-10-01 00:00:00

  • Selective labeling of the erythrocyte hexose carrier with a maleimide derivative of glucosamine: relationship of an exofacial sulfhydryl to carrier conformation and structure.

    abstract::Sulfhydryl-reactive derivatives of glucosamine were synthesized as potentially transportable affinity labels of the human erythrocyte hexose carrier. N-Maleoylglycyl derivatives of either 6- or 2-amino-2-deoxy-D-glucopyranose were the most potent inhibitors of 3-O-methylglucose uptake, with concentrations of half-maxi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00430a044

    authors: May JM

    更新日期:1989-02-21 00:00:00

  • Soluble phosphatidylserine binds to a single identified site in the C2 domain of human factor Va.

    abstract::Factor V(a) (FV(a)) is a cofactor for the serine protease factor X(a) that activates prothrombin to thrombin in the presence of Ca(2+) and a membrane surface. FV(a) is a heterodimer composed of one heavy chain (A1 and A2 domains) and one light chain (A3, C1, and C2 domains). We use fluorescence, circular dichroism, an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010449k

    authors: Srivastava A,Quinn-Allen MA,Kim SW,Kane WH,Lentz BR

    更新日期:2001-07-27 00:00:00

  • Modified nucleosides in the first positions of the anticodons of tRNA(Leu)4 and tRNA(Leu)5 from Escherichia coli.

    abstract::Minor leucine tRNA species, tRNA(Leu)4 and tRNA(Leu)5, from Escherichia coli B have been reported to recognize leucine codons UUA and UUG [Goldman, E., Holmes, W. M., and Hatfield, G. W. (1979) J. Mol. Biol. 129, 567-585]. In the present study, these two tRNA(Leu) species were purified from E. coli A19, and the nucleo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981865g

    authors: Horie N,Yamaizumi Z,Kuchino Y,Takai K,Goldman E,Miyazawa T,Nishimura S,Yokoyama S

    更新日期:1999-01-05 00:00:00

  • Expression of cDNAs encoding wild-type and mutant neuromodulins in Escherichia coli: comparison with the native protein from bovine brain.

    abstract::Murine cDNA that encodes neuromodulin, a neurospecific calmodulin binding protein, was inserted into the plasmid pKK223-3 for expression in Escherichia coli. After being transformed into E. coli strain SG20252 (lon-), the expression vector directed the synthesis of a protein that was recognized by polyclonal antibodie...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00446a027

    authors: Au DC,Apel ED,Chapman ER,Estep RP,Nicolson TA,Storm DR

    更新日期:1989-10-03 00:00:00

  • Characterization of autocatalytic conversion of precursor BACE1 by heteronuclear NMR spectroscopy.

    abstract::Accumulation of the cytotoxic 40- to 42-residue beta-amyloid peptide represents the primary pathological process in Alzheimer's disease (AD). BACE1 (beta-site APP cleaving enzyme 1) is responsible for the initial required step in the neuronal amyloidogenic processing of beta-amyloid precursor protein and is a major dr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051040o

    authors: Wang YS,Beyer BM,Senior MM,Wyss DF

    更新日期:2005-12-20 00:00:00

  • Directed hydroxyl radical probing of 16S ribosomal RNA in 70S ribosomes from internal positions of the RNA.

    abstract::Directed hydroxyl radical probing of 16S ribosomal RNA from Fe(II) tethered to specific sites within the RNA was used to determine RNA-RNA proximities in 70S ribosomes. We have transcribed 16S ribosomal RNA in vitro as two separate fragments, covalently attached an Fe(II) probe to a 5'-guanosine-alpha-phosphorothioate...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981644a

    authors: Newcomb LF,Noller HF

    更新日期:1999-01-19 00:00:00

  • Seipin is a discrete homooligomer.

    abstract::Seipin is a transmembrane protein that resides in the endoplasmic reticulum and concentrates at junctions between the ER and cytosolic lipid droplets. Mutations in the human seipin gene, including the missense mutation A212P, lead to congenital generalized lipodystrophy (CGL), characterized by the lack of normal adipo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi1013003

    authors: Binns D,Lee S,Hilton CL,Jiang QX,Goodman JM

    更新日期:2010-12-21 00:00:00

  • Substrates induce conformational changes in human anion exchanger 1 (hAE1) as observed by fluorescence resonance energy transfer.

    abstract::The one-for-one exchange of Cl(-) and HCO(3)(-) ions is catalyzed by human erythrocyte anion exchanger 1 (hAE1) through a ping-pong mechanism whereby the protein exists in two main conformations, with the single anion-binding site exposed at either the cytoplasmic (inner) side (E(i)) or the extracellular side (E(o)), ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051916r

    authors: Pal P,Lebedev D,Salim S,Knauf PA

    更新日期:2006-05-23 00:00:00

  • Thermodynamics of glycophorin in phospholipid bilayer membranes.

    abstract::We have developed a model of glycophorin in a phospholipid bilayer membrane in order to study the thermodynamics of this system and to understand the detailed behavior of recent calorimetric data. We assume that the larger glycophorin polar group can be considered as either adopting a pancakelike conformation at the b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00381a019

    authors: MacDonald AL,Pink DA

    更新日期:1987-04-07 00:00:00

  • An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites.

    abstract::Fourier transform infrared (FTIR) spectroscopy and a library of FTIR marker bands have been used to examine the structure and relative flexibilities conferred by different flanking sequences on the EcoRI binding site. This approach allowed us to examine unique peaks and subtle changes in the spectra of d(AAAGAATTCTTT)...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi8015235

    authors: Kahn TR,Fong KK,Jordan B,Lek JC,Levitan R,Mitchell PS,Wood C,Hatcher ME

    更新日期:2009-02-17 00:00:00

  • Bioluminescence of beetle luciferases with 6'-amino-D-luciferin analogues reveals excited keto-oxyluciferin as the emitter and phenolate/luciferin binding site interactions modulate bioluminescence colors.

    abstract::Beetle luciferases produce different bioluminescence colors from green to red using the same d-luciferin substrate. Despite many studies of the mechanisms and structural determinants of bioluminescence colors with firefly luciferases, the identity of the emitters and the specific active site interactions responsible f...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500160m

    authors: Viviani VR,Neves DR,Amaral DT,Prado RA,Matsuhashi T,Hirano T

    更新日期:2014-08-19 00:00:00

  • Calcium regulation of calmodulin binding to and dissociation from the myo1c regulatory domain.

    abstract::Myo1c is an unconventional myosin involved in cell signaling and membrane dynamics. Calcium binding to the regulatory-domain-associated calmodulin affects myo1c motor properties, but the kinetic details of this regulation are not fully understood. We performed actin gliding assays, ATPase measurements, fluorescence sp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700894h

    authors: Manceva S,Lin T,Pham H,Lewis JH,Goldman YE,Ostap EM

    更新日期:2007-10-23 00:00:00

  • Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS.

    abstract::SufS is a type II cysteine desulfurase and acts as the initial step in the Suf Fe-S cluster assembly pathway. In Escherichia coli, this pathway is utilized under conditions of oxidative stress and is resistant to reactive oxygen species. Mechanistically, this means SufS must shift between protecting a covalent persulf...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b01122

    authors: Dunkle JA,Bruno MR,Outten FW,Frantom PA

    更新日期:2019-02-12 00:00:00

  • Movement of the iron-sulfur head domain of cytochrome bc(1) transiently opens the catalytic Q(o) site for reaction with oxygen.

    abstract::Cytochrome bc(1), a key enzyme of biological energy conversion, generates or uses a proton motive force through the Q cycle that operates within the two chains of cofactors that embed two catalytic quinone oxidation/reduction sites, the Q(o) site and the Q(i) site. The Q(o) site relies on the joint action of two cofac...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801207f

    authors: Borek A,Sarewicz M,Osyczka A

    更新日期:2008-11-25 00:00:00

  • Time-dependent inhibition of Bacillus stearothermophilus alanine racemase by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate complexes.

    abstract::An alanine racemase encoded by a gene from the thermophilic Gram-positive bacterium Bacillus stearothermophilus is overproduced to 0.3% of the soluble protein when carried on plasmid pICR4 in Escherichia coli [Inagaki, K., Tanizawa, K., Badet, B., Walsh, C. T., Tanaka, H., & Soda, K. (1986) Biochemistry (third paper o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00359a029

    authors: Badet B,Inagaki K,Soda K,Walsh CT

    更新日期:1986-06-03 00:00:00

  • Functional roles of the invariant aspartic acid 55, tyrosine 306, and aspartic acid 309 in glucoamylase from Aspergillus awamori studied by mutagenesis.

    abstract::Three mutants, Asp55-Gly, Tyr306-->Phe, and Asp309-->Asn, of Aspergillus awamori glucoamylase (identical to Aspergillus niger glucoamylase) were constructed to elucidate the roles of two conserved regions within fungal glucoamylases. Kinetic studies indicate that both of these regions are closely associated with activ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00055a017

    authors: Sierks MR,Svensson B

    更新日期:1993-02-02 00:00:00

  • Novel insights into the INK4-CDK4/6-Rb pathway: counter action of gankyrin against INK4 proteins regulates the CDK4-mediated phosphorylation of Rb.

    abstract::The newly discovered oncogenic protein gankyrin, which contains six ankyrin repeats, has been reported to be involved in the phosphorylation and degradation of the retinoblastoma gene product, Rb. Using in vitro systems, we have identified a peptide fragment of gankyrin, 176LHLACDEERN185, which is responsible for bind...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011550s

    authors: Li J,Tsai MD

    更新日期:2002-03-26 00:00:00

  • Thermal behavior of synthetic sphingomyelin-cholesterol dispersions.

    abstract::The thermotropic behavior of aqueous dispersions of palmitoylsphingomyelin-cholesterol and lignoceryl-sphingomyelin-cholesterol mixtures has been examined by high-sensitivity differential scanning calorimetry. When less than 25 mol % cholesterol is mixed with either sphingomyelin, the calorimetric endotherm is compose...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00577a042

    authors: Estep TN,Mountcastle DB,Barenholz Y,Biltonen RL,Thompson TE

    更新日期:1979-05-15 00:00:00

  • Characterization of alanine-rich peptides, Ac-(AAKAA)n-GY-NH2 (n = 1-4), using vibrational circular dichroism and Fourier transform infrared. Conformational determination and thermal unfolding.

    abstract::Vibrational circular dichroism (VCD) and Fourier transform IR (FTIR) were measured for a series of short alanine-based peptides having the general formula Ac-(AAKAA)n-GY-NH2 (n = 1-4) from 5 to 50 degrees C in D2O and at room temperature in both TFE and H2O. In both of these latter solvents, the dominant structural fo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971460g

    authors: Yoder G,Pancoska P,Keiderling TA

    更新日期:1997-12-09 00:00:00

  • Identity of the axial ligand of the high-spin heme in cytochrome oxidase: spectroscopic characterization of mutants in the bo-type oxidase of Escherichia coli and the aa3-type oxidase of Rhodobacter sphaeroides.

    abstract::Prokaryotic and eukaryotic cytochrome c oxidases and several bacterial ubiquinol oxidases compose a superfamily of heme-copper oxidases. These enzymes are terminal components of aerobic respiratory chains, the principal energy-generating systems of aerobic organisms. Two such heme-copper oxidases are the aa3-type cyto...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00091a046

    authors: Calhoun MW,Thomas JW,Hill JJ,Hosler JP,Shapleigh JP,Tecklenburg MM,Ferguson-Miller S,Babcock GT,Alben JO,Gennis RB

    更新日期:1993-10-12 00:00:00

  • Effect of the 17- and 23-kilodalton polypeptides, calcium, and chloride on electron transfer in photosystem II.

    abstract::Electron paramagnetic resonance (EPR) measurements were performed on photosystem II (PSII) membranes that were treated with 2 M NaCl to release the 17- and 23-kilodalton (kDa) polypeptides. By using 75 microM 3-(3,4-dichlorophenyl)-1,1-dimethylurea to limit the photosystem II samples to one stable charge separation in...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00369a022

    authors: de Paula JC,Li PM,Miller AF,Wu BW,Brudvig GW

    更新日期:1986-10-21 00:00:00

  • Purification and characterization of a plasminogen activator secreted by cultured human pancreatic carcinoma cells.

    abstract::A plasminogen activator secreted by cultured human pancreatic carcinoma (Mia PaCa-2) cells has been purified to apparent homogeneity by procedures including Sepharose-L-arginine methyl ester affinity chromatography, Sephadex G-200 gel filtration, isoelectric focusing, and sodium dodecyl sulfate gel electrophoresis. Th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00628a023

    authors: Wu M,Arimura GK,Yunis AA

    更新日期:1977-05-03 00:00:00

  • 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...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi400296c

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

    更新日期:2013-04-30 00:00:00

  • Thioredoxin reductase-thioredoxin fusion enzyme from Mycobacterium leprae: comparison with the separately expressed thioredoxin reductase.

    abstract::Thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin (Trx) by NADPH. A unique gene organization of TrxR and Trx has been found in Mycobacterium leprae, where TrxR and Trx are encoded by a single gene and, therefore, are expressed as a fusion protein (MlTrxR-Trx). This fusion enzyme is able to catalyze t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980754e

    authors: Wang PF,Marcinkeviciene J,Williams CH Jr,Blanchard JS

    更新日期:1998-11-17 00:00:00

  • P-Bodies: Composition, Properties, and Functions.

    abstract::Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/acs.biochem.7b01162

    authors: Luo Y,Na Z,Slavoff SA

    更新日期:2018-05-01 00:00:00

  • A kinetic and allosteric model for the acetylcholine transporter-vesamicol receptor in synaptic vesicles.

    abstract::The ligand binding relationship between the acetylcholine transporter (AcChT) and the vesamicol receptor (VR) and the kinetics of active transport were studied in synaptic vesicles purified from the Torpedo electric organ using analogues of AcCh and vesamicol. Methoxyvesamicol, which should exhibit better equilibratio...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00140a010

    authors: Bahr BA,Clarkson ED,Rogers GA,Noremberg K,Parsons SM

    更新日期:1992-06-30 00:00:00

  • Structural homology discloses a bifunctional structural motif at the N-termini of G alpha proteins.

    abstract::In a family of proteins, often the three-dimensional structure has been experimentally determined only for one member or a few members of the family. Homology modeling can be used to model the structures of all other members of the family and thus allow comparison of these structures. This approach was applied to hete...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi026729x

    authors: Kosloff M,Elia N,Selinger Z

    更新日期:2002-12-10 00:00:00

  • A putative Fe2+-bound persulfenate intermediate in cysteine dioxygenase.

    abstract::The common reactions of dioxygen, superoxide, and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 A resolution crystal structure of the Fe(2+)-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801546n

    authors: Simmons CR,Krishnamoorthy K,Granett SL,Schuller DJ,Dominy JE Jr,Begley TP,Stipanuk MH,Karplus PA

    更新日期:2008-11-04 00:00:00