Studies of inhibitor binding to Escherichia coli purine nucleoside phosphorylase using the transferred nuclear Overhauser effect and rotating-frame nuclear Overhauser enhancement.

Abstract:

:NMR studies of the adenosine analog tubercidin have been carried out in the presence of Escherichia coli purine nucleoside phosphorylase (PNP) in order to characterize the conformation of the enzyme-complexed nucleoside. Although analysis of transferred NOE data at various enzyme/inhibitor ratios indicated a predominantly syn nucleoside conformation in the enzyme-complexed state, the results, particularly the 8(1') and 8(3') NOE interactions, were not quantitatively consistent with any single bound conformation. Dissociation rate constants for the tubercidin-PNP complex were determined based on analysis of chemical shift and line width data as a function of enzyme/inhibitor ratio, Carr-Purcell-Meiboom-Gill measurements of the transverse relaxation rate as a function of pulse rate, and T1 rho experiments as a function of the spin-lock field strength. Dissociation rate constants of 2100 s-1 at 20 degrees C and 1400 s-1 at 10 degrees C were determined using the latter two methods. These rates are sufficiently high to justify the validity of the transferred NOE method for an enzyme as large as PNP. The possible significance of spin diffusion was investigated by the use of the deuterated analog [2'-2H]tubercidin, for which many of the intraligand spin diffusion pathways are eliminated, and by performing a series of transferred ROE experiments. A comparison of data obtained using transferred NOE and ROE measurements provides a basis for separating direct and indirect relaxation pathways. Both approaches indicated that the relatively significant 8(3') NOE interaction was not dominated by spin diffusion. Furthermore, analysis of chemical shift and transverse relaxation data for the tubercidin H-2 resonance gave inconsistent results for the chemical shift of the bound species and was inconsistent with the assumption of a single, bound conformation. These results were interpreted in terms of a 2:1 ratio of a syn, 3'-exo:anti, 3'-endo geometry for bound tubercidin. Ligand competition experiments using 9-deazainosine show that all of the tubercidin TRNOE effects are reversed by addition of the second nucleoside, suggesting that the TRNOE data for tubercidin arise due to interactions at the active sites of PNP rather than as a consequence of nonspecific binding to the enzyme.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Perlman ME,Davis DG,Koszalka GW,Tuttle JV,London RE

doi

10.1021/bi00190a007

subject

Has Abstract

pub_date

1994-06-21 00:00:00

pages

7547-59

issue

24

eissn

0006-2960

issn

1520-4995

journal_volume

33

pub_type

杂志文章
  • Purification, characterization, and fibrinogen cleavage sites of three fibrinolytic enzymes from the venom of Crotalus basiliscus basiliscus.

    abstract::Three distinct fibrinolytic enzymes have been purified from the venom of Crotalus basiliscus basiliscus (the Mexican west coast rattlesnake). The high-performance liquid chromatography-based purification comprised the following steps: (a) hydrophobic interaction chromatography; (b) hydroxylapatite chromatography; (c) ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00134a003

    authors: Retzios AD,Markland FS Jr

    更新日期:1992-05-19 00:00:00

  • Spin labeling analysis of structure and dynamics of the Na(+)/proline transporter of Escherichia coli.

    abstract::With respect to the functional importance attributed to the N-terminal part of the Na(+)/proline transporter of Escherichia coli (PutP), we report here on the structural arrangement and functional dynamics of transmembrane domains (TMs) II and III and the adjoining loop regions. Information on membrane topography was ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi992442x

    authors: Wegener C,Tebbe S,Steinhoff HJ,Jung H

    更新日期:2000-04-25 00:00:00

  • Crystal structure of arginase from Plasmodium falciparum and implications for L-arginine depletion in malarial infection .

    abstract::The 2.15 A resolution crystal structure of arginase from Plasmodium falciparum, the parasite that causes cerebral malaria, is reported in complex with the boronic acid inhibitor 2(S)-amino-6-boronohexanoic acid (ABH) (K(d) = 11 microM). This is the first crystal structure of a parasitic arginase. Various protein const...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100390z

    authors: Dowling DP,Ilies M,Olszewski KL,Portugal S,Mota MM,Llinás M,Christianson DW

    更新日期:2010-07-06 00:00:00

  • Steady-state kinetics and isotope effects on the mutant catalytic trimer of aspartate transcarbamoylase containing the replacement of histidine 134 by alanine.

    abstract::A detailed kinetic analysis of the catalytic trimer of aspartate transcarbamoylase containing the active site substitution H134A was performed to investigate the role of His 134 in the catalytic mechanism. Replacement of histidine by alanine resulted in decreases in the affinities for the two substrates, carbamoyl pho...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00143a031

    authors: Waldrop GL,Turnbull JL,Parmentier LE,O'Leary MH,Cleland WW,Schachman HK

    更新日期:1992-07-21 00:00:00

  • Chemical modification of mitochondrial transhydrogenase: evidence for two classes of sulfhydryl groups.

    abstract::Chemical-modification studies on submitochondrial particle pyridine dinucleotide transhydrogenase (EC 1.6.1.1) demonstrate the presence of one class of sulfhydryl group in the nicotinamide adenine dinucleotide phosphate (NADP) site and another peripheral to the active site. Reaction of the peripheral sulfhydryl group ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00615a015

    authors: Earle SR,O'Neal SG,Fisher RR

    更新日期:1978-10-31 00:00:00

  • Evidence by site-directed mutagenesis supports long-range electron transfer in mouse ribonucleotide reductase.

    abstract::Mammalian ribonucleotide reductase consists of two nonidentical subunits, proteins R1 and R2, each inactive alone. The R1 protein binds the ribonucleotide substrates while the R2 protein contains a binuclear iron center and a tyrosyl free radical, essential for activity. The crystal structures of the corresponding Esc...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00013a016

    authors: Rova U,Goodtzova K,Ingemarson R,Behravan G,Gräslund A,Thelander L

    更新日期:1995-04-04 00:00:00

  • Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site.

    abstract::We have used nucleobase substitution and kinetic analysis to test the hypothesis that hammerhead catalysis occurs by a general acid-base mechanism, in which nucleobases are directly involved in deprotonation of the attacking 2'-hydroxyl group and protonation of the 5'-oxygen that serves as the leaving group in the cle...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047941z

    authors: Han J,Burke JM

    更新日期:2005-05-31 00:00:00

  • Benzothiazepine binding domain of purified L-type calcium channels: direct labeling using a novel fluorescent diltiazem analogue.

    abstract::We have synthesized a series of N-propylamino-substituted benzazepinones (NPSBs) as specific probes for the benzothiazepinone (BTZ) binding domain of muscle L-type calcium channels (LTCCs). NPSBs were identified which possess high affinity for the channel after purification. We synthesized a fluorescent NPSB, DMBODIPY...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00010a039

    authors: Brauns T,Cai ZW,Kimball SD,Kang KC,Haugland RP,Berger W,Berjukov S,Hering S,Glossmann H,Striessnig J

    更新日期:1995-03-14 00:00:00

  • Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1.

    abstract::The l-lyxonate dehydratase (LyxD) in vitro enzymatic activity and in vivo metabolic function were assigned to members of an isofunctional family within the mandelate racemase (MR) subgroup of the enolase superfamily. This study combined in vitro and in vivo data to confirm that the dehydration of l-lyxonate is the bio...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi5004298

    authors: Ghasempur S,Eswaramoorthy S,Hillerich BS,Seidel RD,Swaminathan S,Almo SC,Gerlt JA

    更新日期:2014-05-27 00:00:00

  • Crystal structure of guanosine-free ribonuclease T1, complexed with vanadate (V), suggests conformational change upon substrate binding.

    abstract::Ribonuclease T1 was crystallized in the presence of vanadate(V). The crystal structure was solved by molecular replacement and refined by least-squares methods using stereochemical restraints. The refinement was based on data between 10 and 1.8 A and converged at a crystallographic R factor of 0.137. Except for the su...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00445a014

    authors: Kostrewa D,Choe HW,Heinemann U,Saenger W

    更新日期:1989-09-19 00:00:00

  • Structural Diversity of Amyloid Fibrils and Advances in Their Structure Determination.

    abstract::Protein amyloid fibrils are originally identified as pathological entities in a variety of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. Recent studies have revealed that amyloid fibrils also serve as functional protein assemblies to fulfill a wide range of biological functions. Decip...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/acs.biochem.9b01069

    authors: Li D,Liu C

    更新日期:2020-02-11 00:00:00

  • Binding kinetics of glucose and allosteric activators to human glucokinase reveal multiple conformational states.

    abstract::Slow conformational changes have been proposed to be responsible for the kinetic positive cooperativity of glucokinase (GK) with glucose. Induced-fit and preexisting equilibrium kinetic models have been previously suggested. In the present study, equilibrium and pre-steady-state fluorescence spectroscopy has been used...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi900374c

    authors: Antoine M,Boutin JA,Ferry G

    更新日期:2009-06-16 00:00:00

  • Kinetic studies of site-directed mutational isomalto-dextranase-catalyzed hydrolytic reactions on a 27 MHz quartz-crystal microbalance.

    abstract::A quartz-crystal microbalance (QCM) technique was applied to analyze effects of site-directed mutagenesis of a glycosidase (isomalto-dextranase) on the hydrolysis mechanism of the substrate binding (k(on), k(off), and K(d)) and the catalytic process (k(cat)), separately, by using a dextran-immobilized QCM in buffer so...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi050079q

    authors: Nihira T,Mizuno M,Tonozuka T,Sakano Y,Mori T,Okahata Y

    更新日期:2005-07-12 00:00:00

  • Thermotropic and mixing behavior of mixed-chain phosphatidylcholines with molecular weights identical with that of L-alpha-dipalmitoylphosphatidylcholine.

    abstract::The thermotropic phase behavior of 10 mixed-chain phosphatidylcholines, in excess water, has been examined and compared with that of identical-chain C(16):C(16)PC by using high-resolution differential scanning calorimetry (DSC). The molecular weights (MW) of these 11 molecular species are the same, but their delta C/C...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00243a022

    authors: Bultmann T,Lin HN,Wang ZQ,Huang CH

    更新日期:1991-07-23 00:00:00

  • Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine.

    abstract::Purine riboswitches are RNA regulatory elements that control purine metabolism in response to intracellular concentrations of the purine ligands. Conformational changes of the guanine riboswitch aptamer domain induced by guanine binding lead to transcriptional regulation of genes involved in guanine biosynthesis. The ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9019912

    authors: Brenner MD,Scanlan MS,Nahas MK,Ha T,Silverman SK

    更新日期:2010-03-02 00:00:00

  • Metamorphic response of the CLIC1 chloride intracellular ion channel protein upon membrane interaction.

    abstract::A striking feature of the CLIC (chloride intracellular channel) protein family is the ability of its members to convert between a soluble state and an integral membrane channel form. Direct evidence of the structural transition required for the CLIC protein to autonomously insert into the membrane is lacking, largely ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100111c

    authors: Goodchild SC,Howell MW,Littler DR,Mandyam RA,Sale KL,Mazzanti M,Breit SN,Curmi PM,Brown LJ

    更新日期:2010-06-29 00:00:00

  • The activating transcription factor region within the E2A promoter exists in a novel conformation.

    abstract::The ATF (activating transcription factor) binding site within the E2A promoter region of adenovirus is shown to exist in a novel conformation in vitro via nuclear magnetic resonance methods. This novel conformation may be important to the protein DNA recognition process. This conformation has characteristics of both A...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00077a003

    authors: Borden KL

    更新日期:1993-07-06 00:00:00

  • Temperature-sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein.

    abstract::Twenty-five different temperature-sensitive point mutations at 20 sites in the lysozyme gene of bacteriophage T4 have been identified. All of the mutations alter amino acid side chains that have lower than average crystallographic thermal factors and reduced solvent accessibility in the folded protein. This suggests t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00387a002

    authors: Alber T,Sun DP,Nye JA,Muchmore DC,Matthews BW

    更新日期:1987-06-30 00:00:00

  • Isolation and characterization of an organic solvent soluble polypeptide component from photoreceptor complexes of Rhodospirillum rubrum.

    abstract::An organic solvent soluble polypeptide has been isolated from photoreceptor complexes and chromatophores of Rhodospirillum rubrum. After extraction of the protein from lyophilized samples with 1:1 chloroform-methanol, it was purified by column chromatography. Its isoelectric point determined by isoelectric focusing wa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00624a011

    authors: Tonn SJ,Gogel GE,Loach PA

    更新日期:1977-03-08 00:00:00

  • Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

    abstract::Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00380

    authors: Ng DP,Deber CM

    更新日期:2016-08-09 00:00:00

  • NMR backbone dynamics of the human type I interferon binding subunit, a representative cytokine receptor.

    abstract::The antiviral and antiproliferative activities of type I interferons (IFNs) are mediated by a common receptor, and its second subunit (IFNAR2) exhibits nanomolar affinity to both IFNalpha and IFNbeta subtypes. We have previously determined the structure of the IFN-binding extracellular domain of IFNAR2 (IFNAR2-EC) usi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049606g

    authors: Chill JH,Quadt SR,Anglister J

    更新日期:2004-08-10 00:00:00

  • Picosecond absorption studies on rhodopsin and isorhodopsin in detergent and native membrane.

    abstract::Picosecond transient absorption spectra of rhodopsin and isorhodopsin were measured at room temperature with a double-beam laser spectrophotometer after excitation at 355 nm. Photolysis studies were performed on rhodopsin solubilized in two different detergents (digitonin and 3-[(3-cholamidopropyl)dimethylammonio]-1-p...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00312a008

    authors: Rudzki JE,Peters KS

    更新日期:1984-08-14 00:00:00

  • Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P.

    abstract::Several enzymatic and chemical reagents were used to probe the secondary structure of Saccharomyces cerevisiae nuclear RNase P RNA in the presence and absence of its protein components. Double-stranded regions were detected with RNase V1 and single-stranded regions with RNase ONE (Escherichia coli RNase I). Nucleotide...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00173a022

    authors: Tranguch AJ,Kindelberger DW,Rohlman CE,Lee JY,Engelke DR

    更新日期:1994-02-22 00:00:00

  • Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.

    abstract::The solution of a primary 16S rRNA-binding ribosomal protein, S17, was investigated by two- and three-dimensional homonuclear and heteronuclear magnetic resonance spectroscopy. Almost complete chemical shift assignments for the 1H, 15N, and 13C resonances have been obtained. The NMR data have been rigorously analyzed ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi951062i

    authors: Jaishree TN,Ramakrishnan V,White SW

    更新日期:1996-03-05 00:00:00

  • Deep-UV resonance Raman analysis of the Rhodobacter capsulatus cytochrome bc₁complex reveals a potential marker for the transmembrane peptide backbone.

    abstract::Classical strategies for structure analysis of proteins interacting with a lipid phase typically correlate ensemble secondary structure content measurements with changes in the spectroscopic responses of localized aromatic residues or reporter molecules to map regional solvent environments. Deep-UV resonance Raman (DU...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200596w

    authors: Halsey CM,Oshokoya OO,Jiji RD,Cooley JW

    更新日期:2011-08-02 00:00:00

  • Mechanistic studies on the bovine liver mitochondrial dihydroorotate dehydrogenase using kinetic deuterium isotope effects.

    abstract::Dihydroorotates deuteriated at both C5 and C6 have been prepared and used to probe the mechanism of the bovine liver mitochondrial dihydroorotate dehydrogenase. Primary deuterium isotope effects on kcat are observed with both (6RS)-[5(S)-2H]- and (6RS)-[6-2H] dihydroorotates (3 and 6, respectively); these effects are ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00429a041

    authors: Hines V,Johnston M

    更新日期:1989-02-07 00:00:00

  • Biochemical and kinetic characteristics of the interaction of the antitumor antibiotic sparsomycin with prokaryotic and eukaryotic ribosomes.

    abstract::Using 125I-labeled phenol-alanine sparsomycin, an analogue of sparsomycin having higher biological activity than the unmodified antibiotic, we studied the requirements and the characteristics of its interaction with the ribosome. The drug does not bind to either isolated ribosomal subunits or reconstituted whole ribos...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00104a011

    authors: Lazaro E,van den Broek LA,San Felix A,Ottenheijm HC,Ballesta JP

    更新日期:1991-10-08 00:00:00

  • The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick.

    abstract::Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5'-d-[(A)10TAATTTTAAATATTT]-3' (D1) and 5'-d[(T)10ATTAAAATTTATAAA]-3' (D2) in H2O and D2O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the de...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00226a012

    authors: Otto C,Thomas GA,Rippe K,Jovin TM,Peticolas WL

    更新日期:1991-03-26 00:00:00

  • Determination of proton transfer rates by chemical rescue: application to bacterial reaction centers.

    abstract::The bacterial reaction center (RC) converts light into chemical energy through the reduction of an internal quinone molecule Q(B) to Q(B)H(2). In the native RC, proton transfer is coupled to electron transfer and is not rate-controlling. Consequently, proton transfer is not directly observable, and its rate was unknow...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi020419x

    authors: Paddock ML,Adelroth P,Feher G,Okamura MY,Beatty JT

    更新日期:2002-12-17 00:00:00

  • Scaffold/matrix-attached regions act upon transcription in a context-dependent manner.

    abstract::Scaffold/matrix-attached regions (S/MARs) are cis-acting elements with a function outside transcribed regions and in introns. Although they usually augment transcriptional rates, their action is highly context-dependent. We cloned an 800 bp S/MAR element from the upstream border of the human interferon-beta domain at ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960930o

    authors: Schübeler D,Mielke C,Maass K,Bode J

    更新日期:1996-08-27 00:00:00