Bleaching kinetics of artificial visual pigments with modifications near the ring-polyene chain connection.

Abstract:

:Absorbance difference spectra were recorded at 20 degrees C from 30 ns to milliseconds after photolysis of lauryl maltoside suspensions of artificial visual pigments derived from 9-cis isomers of 5-ethylretinal, 8,16-methanoretinal (a 6-s-trans-bicyclic analogue), or 5-demethyl-8-methylretinal. In all three pigments, the earliest intermediate that was detected had the characteristics of a mixture of bathorhodopsin and a blue-shifted intermediate, BSI, which is the first decay product of bathorhodopsin in bovine rhodopsin. The first decays resolved on the nanosecond time scale were the formation of the lumirhodopsin analogues. Subsequent decays were able to be fit with a mechanistic scheme which has been shown to apply to both membrane and detergent suspensions of rhodopsin. Large increases were seen in the amount of metarhodopsin I which appeared after photolysis of 5-ethylisorhodopsin and the bicyclic isorhodopsin analogue, while 5-demethyl-8-methylisorhodopsin more closely followed native rhodopsin in decaying through meta I380, a 380 nm absorbing precursor to metarhodopsin II. In addition to forming more metarhodopsin I, the bicyclic analogue stabilized the metarhodopsin I-metarhodopsin II equilibrium similarly to what has been previously reported for 9-demethylrhodopsin in detergent, introducing the possibility that the bicyclic analogue could similarly be defective in transducin activation. These observations support the idea that long after initial photolysis, structural details of the retinylidene chromophore continue to play a decisive role in processes leading to the activated form, metarhodopsin II.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Szundi I,de Lera AR,Pazos Y,Alvarez R,Oliana M,Sheves M,Lewis JW,Kliger DS

doi

10.1021/bi011461f

subject

Has Abstract

pub_date

2002-02-12 00:00:00

pages

2028-35

issue

6

eissn

0006-2960

issn

1520-4995

pii

bi011461f

journal_volume

41

pub_type

杂志文章
  • Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus.

    abstract::The crystal structure of a ternary complex of the alcohol dehydrogenase from the archaeon Sulfolobus solfataricus (SsADH) has been determined at 2.3 A. The asymmetric unit contains a dimer with a NADH and a 2-ethoxyethanol molecule bound to each subunit. The comparison with the apo structure of the enzyme reveals that...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi035271b

    authors: Esposito L,Bruno I,Sica F,Raia CA,Giordano A,Rossi M,Mazzarella L,Zagari A

    更新日期:2003-12-16 00:00:00

  • (+/-)-(1S,2R,5S)-5-Amino-2-fluorocyclohex-3-enecarboxylic acid. A potent GABA aminotransferase inactivator that irreversibly inhibits via an elimination-aromatization pathway.

    abstract::Inhibition of gamma-aminobutyric acid aminotransferase (GABA-AT) increases the concentration of GABA, an inhibitory neurotransmitter in human brain, which could have therapeutic applications for a variety of neurological diseases, including epilepsy. On the basis of studies of several previously synthesized conformati...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061592m

    authors: Wang Z,Yuan H,Nikolic D,Van Breemen RB,Silverman RB

    更新日期:2006-12-05 00:00:00

  • Acetylcholine receptor and ionic channel of Torpedo electroplax: binding of perhydrohistrionicotoxin to membrane and solubilized preparations.

    abstract::The electric organ of the ray, Torpedo ocellata, can serve as a source for both the acetylcholine (ACh) receptor and its ionic channel. The two entities were identified by their specific binding of [3H]ACh and [3H]perhydrohistrionicotoxin ([3H]H12-HTX), respectively. Binding of [3H]H12-HTX was inhibited by certain dru...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00618a023

    authors: Eldefrawi ME,Eldefrawi AT,Mansour NA,Daly JW,Witkop B,Albuquerque EX

    更新日期:1978-12-12 00:00:00

  • Characterization of the ligand binding activities of vitronectin: interaction of vitronectin with lipids and identification of the binding domains for various ligands using recombinant domains.

    abstract::Vitronectin is a multifunctional plasma glycoprotein which may regulate the systems related to protease cascades such as the coagulation, fibrinolysis, and complement systems as well as cell adhesion. Solid-phase assays and affinity chromatography on immobilized glycolipids indicated that vitronectin purified under de...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972247n

    authors: Yoneda A,Ogawa H,Kojima K,Matsumoto I

    更新日期:1998-05-05 00:00:00

  • DNA binding of methyl-CpG-binding protein MeCP2 in human MCF7 cells.

    abstract::MeCP2 has been identified as a chromatin-associated protein that recognizes MAR elements as well as methyl-CpGs. To characterize target sequences of MeCP2 in human cells, we employed two complementary methods. First, by use of a preparative chromatin immunoprecipitation protocol, we created from MCF7 cells a library e...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0359271

    authors: Koch C,Strätling WH

    更新日期:2004-05-04 00:00:00

  • Two-site binding of beta-cyclodextrin to the Alzheimer Abeta(1-40) peptide measured with combined PFG-NMR diffusion and induced chemical shifts.

    abstract::The interactions of Alzheimer's amyloid beta-peptide with cyclodextrins were studied by (1)H NMR: the translational diffusion coefficient of the peptide and chemical shift changes were studied by the presence of variable concentrations of cyclodextrins. For the full-length peptide, Abeta(1-40), the combined results of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi036254p

    authors: Danielsson J,Jarvet J,Damberg P,Gräslund A

    更新日期:2004-05-25 00:00:00

  • Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.

    abstract::To better elucidate RNA structure-function relationships and to improve the design of pharmaceutical agents that target specific RNA motifs, an understanding of RNA primary, secondary, and tertiary structure is necessary. The prediction of RNA secondary structure from sequence is an intermediate step in predicting RNA...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi3001227

    authors: Hausmann NZ,Znosko BM

    更新日期:2012-07-03 00:00:00

  • The synthetic/editing active site of an aminoacyl-tRNA synthetase: evidence for binding of thiols in the editing subsite.

    abstract::The active site of methionyl-tRNA synthetase (MetRS) possesses two functions: synthetic, which provides Met-tRNA for protein synthesis, and editing, which rejects inadvertently misactivated homocysteine. During editing, the side chain -SH group of homocysteine reacts with its activated carboxyl group forming a cyclic ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960344v

    authors: Jakubowski H

    更新日期:1996-06-25 00:00:00

  • Structural basis of DNA recognition and mechanism of quadruplex formation by the beta subunit of the Oxytricha telomere binding protein.

    abstract::Interactions of the beta subunit of the Oxytricha nova telomere binding protein with the telomeric DNA sequences, d(T4G4)2 and dT6(T4G4)2, have been investigated in vitro using Raman and fluorescence spectroscopies. Raman difference spectra show that the beta subunit binds to both d(T4G4)2 and dT6(T4G4)2 but promotes ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972400d

    authors: Laporte L,Thomas GJ Jr

    更新日期:1998-02-03 00:00:00

  • Enantiomeric free radicals and enzymatic control of stereochemistry in a radical mechanism: the case of lysine 2,3-aminomutases.

    abstract::The product of yjeK in Escherichia coli is a homologue of lysine 2,3-aminomutase (LAM) from Clostridium subterminale SB4, and both enzymes catalyze the isomerization of (S)- but not (R)-alpha-lysine by radical mechanisms. The turnover number for LAM from E. coli is 5.0 min(-1), 0.1% of the value for clostridial LAM. T...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061328t

    authors: Behshad E,Ruzicka FJ,Mansoorabadi SO,Chen D,Reed GH,Frey PA

    更新日期:2006-10-24 00:00:00

  • Is aspartate 52 essential for catalysis by chicken egg white lysozyme? The role of natural substrate-assisted hydrolysis.

    abstract::The chicken and goose egg white lysozymes (ChEWL and GoEWL) are homologues, but differ in substrate specificity. ChEWL catalyzes the hydrolysis of the glycosidic bonds of bacterial peptidoglycans and chitin-derived substrates, while GoEWL is specific for bacterial peptidoglycans. The active-site aspartate 52 residue o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi951671q

    authors: Matsumura I,Kirsch JF

    更新日期:1996-02-13 00:00:00

  • Effect of 2,3-butanedione monoxime on myosin and myofibrillar ATPases. An example of an uncompetitive inhibitor.

    abstract::2,3-Butanedione monoxime (BDM) reversibly inhibits force production in muscle. At least part of its action appears to be directly on the contractile apparatus. To understand better its mechanism of action, we studied the effect of BDM on the steps of myosin subfragment 1 Mg(2+)-ATPase in 0.1 M potassium acetate, pH 7....

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00163a036

    authors: Herrmann C,Wray J,Travers F,Barman T

    更新日期:1992-12-08 00:00:00

  • Ultrafast water dynamics at the interface of the polymerase-DNA binding complex.

    abstract::DNA polymerases slide on DNA during replication, and the interface must be mobile for various conformational changes. The role of lubricant interfacial water is not understood. In this report, we systematically characterize the water dynamics at the interface and in the active site of a tight binding polymerase (pol β...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500810a

    authors: Yang Y,Qin Y,Ding Q,Bakhtina M,Wang L,Tsai MD,Zhong D

    更新日期:2014-08-26 00:00:00

  • Zinc is associated with the beta subunit of DNA-dependent RNA polymerase of Bacillus subtilis.

    abstract::The Bacillus subtilis DNA-dependent RNA polymerase holoenzyme and core enzyme each contain approximately two atoms of zinc per molecule. When the dissociated subunits of the enzyme are passed through a blue dextran-Sepharose affinity column, only the beta subunit binds to the column. The total zinc content of the enzy...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00632a012

    authors: Halling SM,Sanchez-Anzaldo FJ,Fukuda R,Doi RH,Meares CF

    更新日期:1977-06-28 00:00:00

  • Specific RNA binding by Q beta coat protein.

    abstract::The interaction between the bacteriophage Q beta coat protein and its specific binding site on Q beta genomic RNA was characterized by using a nitrocellulose filter binding assay. Q beta coat protein bound to a synthetic 29-nucleotide RNA hairpin with an association constant of 400 microM-1 at 4 degrees C, 0.2 M ionic...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00427a011

    authors: Witherell GW,Uhlenbeck OC

    更新日期:1989-01-10 00:00:00

  • Comparison of N-glycosides of fetuins from different species and human alpha 2-HS-glycoprotein.

    abstract::Complex type N-glycosides of commercial bovine fetuin preparations from pooled fetal calf serum have been shown to contain comparable amounts of Gal4,4,4TRI (see structure A below) and Gal4,4,3TRI (structure B) as major asialo-structures. To investigate whether there is a clear genetic specificity for synthesis of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00135a024

    authors: Hayase T,Rice KG,Dziegielewska KM,Kuhlenschmidt M,Reilly T,Lee YC

    更新日期:1992-05-26 00:00:00

  • Purification, characterization, and inhibition of peptide deformylase from Escherichia coli.

    abstract::Peptide deformylase (EC 3.5.1.31) catalyzes the removal of a formyl group from the N-termini of nascent ribosome-synthesized polypeptides, an obligatory step during protein maturation in eubacteria. Since its discovery in crude Escherichia coli extracts 3 decades ago, the deformylase has resisted all attempts of purif...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971155v

    authors: Rajagopalan PT,Datta A,Pei D

    更新日期:1997-11-11 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

  • Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis.

    abstract::The existence of temperature optima in enzyme catalysis that occur before protein melting sets in can be described by different types of kinetic models. Such optima cause distinctly curved Arrhenius plots and have, for example, been observed in several cold-adapted enzymes from psychrophilic species. The two main expl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.0c00705

    authors: Åqvist J,Sočan J,Purg M

    更新日期:2020-10-13 00:00:00

  • Design of a selective insulin receptor tyrosine kinase inhibitor and its effect on glucose uptake and metabolism in intact cells.

    abstract::An inhibitor of the insulin receptor tyrosine kinase (IRTK), (hydroxy-2-naphthalenyl-methyl) phosphonic acid, was designed and synthesized and was shown to be an inhibitor of the biological effects of insulin in vitro. With a wheat germ purified human placental insulin receptor preparation, this compound inhibited the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00439a053

    authors: Saperstein R,Vicario PP,Strout HV,Brady E,Slater EE,Greenlee WJ,Ondeyka DL,Patchett AA,Hangauer DG

    更新日期:1989-06-27 00:00:00

  • Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding.

    abstract::Applications of sensitive new technologies, in particular, two-dimensional NMR spectroscopy, have allowed detection of folded structures in short peptide fragments of proteins in aqueous solution under conditions where native proteins fold. These structures are in rapid dynamic exchange with unfolded states. These obs...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi00419a001

    authors: Wright PE,Dyson HJ,Lerner RA

    更新日期:1988-09-20 00:00:00

  • A single amino acid substitution in the human and a bacterial hypoxanthine phosphoribosyltransferase modulates specificity for the binding of guanine.

    abstract::Early studies involving purine salvage in Salmonella typhimurium resulted in the isolation and identification of a mutant strain possessing a genetically modified hypoxanthine phosphoribosyl-transferase (HPRT) with enhanced substrate specificity for guanine [Benson, C. E., and Gots, J. S. (1975) J. Bacteriol. 121, 77-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9720179

    authors: Lee CC,Craig SP 3rd,Eakin AE

    更新日期:1998-03-10 00:00:00

  • Phosphorus-31 nuclear magnetic resonance studies of wild-type and glycolytic pathway mutants of Saccharomyces cerevisiae.

    abstract::High-resolution phosphorus-31 nuclear magnetic resonance (31P NMR) spectra of wild-type and mutant strains of Saccharomyces cerevisiae were observed at a frequency of 145.7 MHz. Levels of various phosphorus metabolites were investigated upon addition of glucose under both aerobic and anaerobic conditions. Three mutant...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00588a006

    authors: Navon G,Shulman RG,Yamane T,Eccleshall TR,Lam KB,Baronofsky JJ,Marmur J

    更新日期:1979-10-16 00:00:00

  • 19F NMR studies of the D-galactose chemosensory receptor. 2. Ca(II) binding yields a local structural change.

    abstract::The Escherichia coli D-galactose and D-glucose receptor possesses a Ca(II)-binding site closely related in structure and metal-binding characteristics to the eukaryotic EF-hand sites. Only the structure of the Ca(II)-occupied site is known. To investigate the structural change triggered by Ca(II) and Sr(II) binding, w...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00231a022

    authors: Luck LA,Falke JJ

    更新日期:1991-04-30 00:00:00

  • Phospholipase A2 complexes with gadolinium (III) and interaction of the enzyme-metal ion complex with monomeric and micellar alkylphosphorylcholines. Water proton nuclear magnetic relaxation studies.

    abstract::Gadolinium (III) binds competitively with calcium(II) to porcine pancreatic phospholipase A2 (EC 3.1.1.4) and its zymogen. The enzyme-Gd3+ complex exhibits 4% of the hydrolytic activity of the corresponding Ca2+ complex toward a dispersion of dioctanoyllecithin. Dissociation constants for the Gd3+ complex of enzyme an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00656a004

    authors: Hershberg RD,Reed GH,Slotboom AJ,deHaas GH

    更新日期:1976-06-01 00:00:00

  • Molecular and structural insight into the role of key residues of thrombospondin-1 and calreticulin in thrombospondin-1-calreticulin binding.

    abstract::Thrombospondin-1 (TSP1) binding to calreticulin (CRT) on the cell surface signals focal adhesion disassembly, leading to the intermediate adhesive phenotype, cell migration, anoikis resistance, and collagen stimulation. Residues Lys 24 and 32 in TSP1 and amino acids 24-26 and 32-34 in CRT have been shown through bioch...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101639y

    authors: Yan Q,Murphy-Ullrich JE,Song Y

    更新日期:2011-02-01 00:00:00

  • Subunit disassembly and unfolding kinetics of hemoglobin studied by time-resolved electrospray mass spectrometry.

    abstract::We report the use of electrospray ionization (ESI) mass spectrometry (MS) in conjunction with online rapid mixing to monitor the kinetics of acid-induced ferrihemoglobin denaturation. Under equilibrium conditions, the hemoglobin mass spectrum is dominated by the intact heterotetramer. Dimeric and monomeric species are...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048501a

    authors: Simmons DA,Wilson DJ,Lajoie GA,Doherty-Kirby A,Konermann L

    更新日期:2004-11-23 00:00:00

  • Reduction of cytochrome b in mitochondria from yeast lacking coenzyme Q.

    abstract::Mitochondria isolated from coenzyme Q deficient yeast cells had no detectable NADH:cytochrome c reductase or succinate:cytochrome c reductase but had comparable amounts of cytochromes b and c1 as wild-type mitochondria. Addition of succinate to the mutant mitochondria resulted in a slight reduction of cytochrome b; ho...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00372a029

    authors: Clejan L,Beattie DS

    更新日期:1986-12-02 00:00:00

  • The effect of Mn2+ and Co2+ on the activities of a zinc metallodipeptidase from a mouse ascites tumor.

    abstract::Kinetic studies of the effect of addition of Co2+ or Mn2+ to a highly purified dipeptidase from Ehrlich-Lettré mouse ascites tumor cells show that these metals specifically activate the hydrolyses of certain classes of dipeptides. This enzyme was previously (S. Hayman and E. K. Patterson, 1971, J. Biol. Chem. 246, 660...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00690a018

    authors: Patterson EK,Gatmaitan JS,Hayman S

    更新日期:1975-09-23 00:00:00

  • Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC.

    abstract::RSC (remodel the structure of chromatin) is an essential chromatin remodeler of Saccharomyces cerevisiae that has been shown to have DNA translocase properties. We studied the DNA binding properties of a "trimeric minimal RSC" (RSCt) of the RSC chromatin remodeling complex and the effect of nucleotides on this interac...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200837b

    authors: Malik SS,Rich E,Viswanathan R,Cairns BR,Fischer CJ

    更新日期:2011-09-20 00:00:00