Solution studies on the structure of bent DNA in the cAMP receptor protein-lac DNA complex.

Abstract:

:Cyclic AMP receptor protein is involved in the regulation of more than 20 genes. A step in the mechanism of activation of transcription is to induce a significant bending of the DNA upon complex formation between specific DNA and the protein. The induced DNA bending and a structure of the protein-DNA complex were studied by fluorescence energy transfer in 50 mM Tris, 1 mM EDTA, and 50 mM KCl at pH 7.8 and 20 degrees C. The symmetry of the DNA bend was estimated by measuring the efficiency of transfer between the protein and a label on either the upstream or the downstream end of a lac DNA fragment. The results show that the bend, despite the asymmetry in the DNA sequence, is symmetrical, for the fragments which length ranges from 26 to 40 bp. Using fluorescence energy transfer, the extent of DNA bending was estimated by measuring the end-to-end distance of the DNA fragment which was labeled with a donor-acceptor pair on two opposite ends. Both steady-state and time-resolved measurements showed that in a 26 bp lac DNA fragment complexed with cyclic AMP receptor protein, the end-to-end distance is about 77 A which corresponds to a bending angle of 80 degrees or 100 degrees, depending on the actual contour length between the fluorophores in the free DNA fragment. The results using longer DNA fragments show no measurable amount of energy transfer; thus, it is very unlikely that the DNA completely wraps around the CRP molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

journal_name

Biochemistry

journal_title

Biochemistry

authors

Heyduk T,Lee JC

doi

10.1021/bi00137a011

subject

Has Abstract

pub_date

1992-06-09 00:00:00

pages

5165-71

issue

22

eissn

0006-2960

issn

1520-4995

journal_volume

31

pub_type

杂志文章
  • Purification and characterization of a human platelet cyclic nucleotide phosphodiesterase.

    abstract::A cyclic nucleotide phosphodiesterase was extensively purified from the 100000g supernatant fraction of human platelets. The purification was 2500-3000-fold with 30% recovery of activity. The enzyme was isolated by DEAE-cellulose chromatography followed by adsorption to blue dextran-Sepharose and elution with cAMP. Th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00303a034

    authors: Grant PG,Colman RW

    更新日期:1984-04-10 00:00:00

  • Monovalent cation transport: lack of structural deformation upon cation binding.

    abstract::Cations often deform the structure of regulatory proteins to affect a functional response, but for other protein functions a more passive effect is desired. For instance, it is shown here that in the conductance of Na+ by the gramicidin channel there appears to be no significant structural deformation of either the si...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961170k

    authors: Tian F,Lee KC,Hu W,Cross TA

    更新日期:1996-09-17 00:00:00

  • The Interaction between the Third Type III Domain from Fibronectin and Anastellin Involves β-Strand Exchange.

    abstract::Anastellin is a small recombinant fragment derived from the extracellular matrix protein fibronectin; it comprises the first type III (FN3) domain without the two N-terminal β-strands. It inhibits angiogenesis, tumor growth, and metastasis in mouse models and requires endogenous fibronectin for its in vivo anti-angiog...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00633

    authors: Stine JM,Ahl GJH,Schlenker C,Rusnac DV,Briknarová K

    更新日期:2017-09-05 00:00:00

  • Reconstitution and further characterization of the cholesterol transport activity of the small-intestinal brush border membrane.

    abstract::The sterol (free and esterified cholesterol) transport activity of the small-intestinal brush border membrane was solubilized with the short-chain detergent diheptanoylphosphatidylcholine and reconstituted to an artificial membrane system (proteoliposomes). The resulting proteoliposomes were identified as unilamellar ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970625i

    authors: Boffelli D,Weber FE,Compassi S,Werder M,Schulthess G,Hauser H

    更新日期:1997-09-02 00:00:00

  • Genetic regulation of testosterone 15 alpha-hydroxylase (cytochrome P-450(15)alpha) in renal microsomes of female mice.

    abstract::P-450(15)alpha is a form of cytochrome P-450 purified from liver microsomes of female 129/J mice that is specific for oxidation of testosterone to its 15 alpha-hydroxylated product. Testosterone 15 alpha-hydroxylase activity that was inhibited by anti-P-450(15)alpha antibody was approximately 50 times higher in renal ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00365a028

    authors: Squires EJ,Negishi M

    更新日期:1986-08-26 00:00:00

  • Interactions of myelin basic protein with mixed dodecylphosphocholine/palmitoyllysophosphatidic acid micelles.

    abstract::The interactions of myelin basic protein and peptides derived from it with detergent micelles of lysophosphatidylglycerol, lysophosphatidylserine, palmitoyllysophosphatidic acid, and sodium lauryl sulfate, and with mixed micelles of the neutral detergent dodecylphosphocholine and the negatively charged detergent palmi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00461a014

    authors: Mendz GL,Brown LR,Martenson RE

    更新日期:1990-03-06 00:00:00

  • Refined 1.8-A structure reveals the mode of binding of beta-cyclodextrin to the maltodextrin binding protein.

    abstract::The maltodextrin binding protein from Escherichia coli serves as the initial receptor for both the active transport of and chemotaxis toward a range of linear maltose sugars. The X-ray structures of both the maltose-bound and sugar-free forms of the protein have been previously described [Spurlino, J. C., Lu, G.-Y., &...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00091a004

    authors: Sharff AJ,Rodseth LE,Quiocho FA

    更新日期:1993-10-12 00:00:00

  • Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase.

    abstract::Several mutant Escherichia coli aspartate aminotransferases (eAATases) have been characterized in the attempt to evolve or rationally redesign the substrate specificity of eAATase into that of E. coli tyrosine aminotransferase (eTATase). These include HEX (designed), HEX + A293D (design followed by directed evolution)...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0487544

    authors: Chow MA,McElroy KE,Corbett KD,Berger JM,Kirsch JF

    更新日期:2004-10-12 00:00:00

  • Effect and cellular site of action of cysteine protease inhibitors on the cholesterol esterification pathway in macrophages and Chinese hamster ovary cells.

    abstract::Stimulation of intracellular cholesterol esterification, which is catalyzed by the enzyme acyl-CoA:cholesterol O-acyltransferase (ACAT), by atherogenic lipoproteins in macrophages is a key step in the development of atheroma foam cells. Since other aspects of intracellular cholesterol metabolism involve proteolytic re...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00033a019

    authors: Schissel SL,Beatini N,Zha X,Maxfield FR,Tabas I

    更新日期:1995-08-22 00:00:00

  • Kinetics and equilibria in ligand binding by nitrophorins 1-4: evidence for stabilization of a nitric oxide-ferriheme complex through a ligand-induced conformational trap.

    abstract::Nitrophorins 1-4 (NP1-4) are ferriheme proteins from the blood-sucking insect Rhodnius prolixus that transport nitric oxide (NO) to the victim, sequester histamine, and inhibit blood coagulation. Here, we report kinetic and thermodynamic analyses for ligand binding by all four proteins and their reduction potentials. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000766b

    authors: Andersen JF,Ding XD,Balfour C,Shokhireva TK,Champagne DE,Walker FA,Montfort WR

    更新日期:2000-08-22 00:00:00

  • Structural studies of the contractile tail sheath protein of bacteriophage T4. 2. Structural analyses of the tail sheath protein, Gp18, by limited proteolysis, immunoblotting, and immunoelectron microscopy.

    abstract::The molecular structure of the T4 phage tail sheath protein, gp18, was studied by limited proteolysis, immunoblotting, and immunoelectron microscopy. Gp18 is extremely resistant to proteolysis in the assembled form of either extended or contracted sheaths, but it is readily cleaved by proteases in the monomeric form, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00473a009

    authors: Arisaka F,Takeda S,Funane K,Nishijima N,Ishii S

    更新日期:1990-05-29 00:00:00

  • Resonance Raman interrogation of the consequences of heme rotational disorder in myoglobin and its ligated derivatives.

    abstract::Resonance Raman spectroscopy is employed to characterize heme site structural changes arising from conformational heterogeneity in deoxyMb and ligated derivatives, i.e., the ferrous CO (MbCO) and ferric cyanide (MbCN) complexes. The spectra for the reversed forms of these derivatives have been extracted from the spect...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801779d

    authors: Rwere F,Mak PJ,Kincaid JR

    更新日期:2008-12-02 00:00:00

  • Purification and characterization of a transmembrane domain-deleted form of lecithin retinol acyltransferase.

    abstract::Lecithin retinol acyltransferase (LRAT) catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester, an essential reaction in the vertebrate visual cycle. Since all-trans-retinyl esters are the substrates for the isomerization reaction that generates 11-cis-retinoids, this esterification reaction is...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0342416

    authors: Bok D,Ruiz A,Yaron O,Jahng WJ,Ray A,Xue L,Rando RR

    更新日期:2003-05-27 00:00:00

  • Composite organization of the cobalamin binding and cubilin recognition sites of intrinsic factor.

    abstract::Intrinsic factor (IF(50)) is a cobalamin (Cbl)-transporting protein of 50 kDa, which can be cleaved into two fragments: the 30 kDa N-terminal peptide IF(30) and the 20 kDa C-terminal glycopeptide IF(20). Experiments on binding of Cbl to IF(30), IF(20), and IF(50) revealed comparable association rate constants (k(+)(Cb...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047936v

    authors: Fedosov SN,Fedosova NU,Berglund L,Moestrup SK,Nexø E,Petersen TE

    更新日期:2005-03-08 00:00:00

  • Effect of β,γ-CHF- and β,γ-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase β.

    abstract::Recently, we synthesized the first individual β,γ-CHX-dGTP diastereomers [(R)- or (S)-CHX, where X is F or Cl] and determined their structures in ternary complexes with DNA polymerase β (pol β). We now report stereospecificity by pol β on the mixed β,γ-CHX diastereomer pairs using nuclear magnetic resonance and on the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi3010335

    authors: Oertell K,Wu Y,Zakharova VM,Kashemirov BA,Shock DD,Beard WA,Wilson SH,McKenna CE,Goodman MF

    更新日期:2012-10-30 00:00:00

  • Recognition of G-U mismatches by tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III).

    abstract::The coordination complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III) [Rh(DIP)3(3+)], which promotes RNA cleavage upon photoactivation, has been shown to target specifically guanine-uracil (G-U) mismatches in double-helical regions of folded RNAs. Photoactivated cleavage by Rh(DIP)3(3+) has been examined on a se...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00139a001

    authors: Chow CS,Barton JK

    更新日期:1992-06-23 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

  • p21rac does not participate in the early interaction between p47-phox and cytochrome b558 that leads to phagocyte NADPH oxidase activation in vitro.

    abstract::The phagocyte superoxide-generating NADPH oxidase, a multicomponent, membrane-bound electron transport chain, consists of cytochrome b558, p47-phox, p67-phox, and p21rac1 or p21rac2. The mechanisms of oxidase assembly are poorly understood. In previous studies using a cell-free NADPH oxidase system, we showed that pre...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00175a018

    authors: Kleinberg ME,Malech HL,Mital DA,Leto TL

    更新日期:1994-03-08 00:00:00

  • Thermal unfolding and aggregation of human complement protein C9: a differential scanning calorimetry study.

    abstract::The thermotropic behavior of purified human complement protein C9 was investigated by high-sensitivity differential scanning calorimetry. When dissolved in physiological buffers (pH 7.2, 150 mM NaCl), C9 underwent three endothermic transitions with transition temperatures (Tm) centered at about 32, 48, and 53 degrees ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00240a035

    authors: Lohner K,Esser AF

    更新日期:1991-07-02 00:00:00

  • Folding of the SARS coronavirus spike glycoprotein immunological fragment (SARS_S1b): thermodynamic and kinetic investigation correlating with three-dimensional structural modeling.

    abstract::Spike glycoprotein of SARS coronavirus (S protein) plays a pivotal role in SARS coronavirus (SARS_CoV) infection. The immunological fragment of the S protein (Ala251-His641, SARS_S1b) is believed to be essential for SARS_CoV entering the host cell through S protein-ACE-2 interaction. We have quantitatively characteriz...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0482396

    authors: Yu C,Gui C,Luo H,Chen L,Zhang L,Yu H,Yang S,Jiang W,Shen J,Shen X,Jiang H

    更新日期:2005-02-08 00:00:00

  • Phosphorylation-dependent sumoylation of estrogen-related receptor alpha1.

    abstract::We previously showed that estrogen-related receptor alpha1 (ERRalpha1) can compete with estrogen receptor alpha (ERalpha) for binding to estrogen response elements (EREs), repressing transcription in the mammary carcinoma cell line MCF-7. Given that ERRalpha1 can function in the absence of ligands and exists as a phos...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700316g

    authors: Vu EH,Kraus RJ,Mertz JE

    更新日期:2007-08-28 00:00:00

  • New insights into the activation of Escherichia coli tyrosine kinase revealed by molecular dynamics simulation and biochemical analysis.

    abstract::Escherichia coli tyrosine kinase (Etk) regulates the export of pathogenic capsular polysaccharide (CPS) by intermolecularly autophosphorylating its C-terminal tyrosine cluster. The kinase Etk, however, needs to be first activated by the intramolecular phosphorylation of a tyrosine residue, Y574, next to the active sit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi900811p

    authors: Lu T,Tan H,Lee D,Chen G,Jia Z

    更新日期:2009-08-25 00:00:00

  • High-resolution crystal structure of manganese peroxidase: substrate and inhibitor complexes.

    abstract::Manganese peroxidase (MnP) is an extracellular heme enzyme that catalyzes the peroxide-dependent oxidation of Mn(II) to Mn(III). The Mn(III) is released from the enzyme in complex with oxalate. One heme propionate and the side chains of Glu35, Glu39, and Asp179 were identified as Mn(II) ligands in the 2.0 A resolution...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047318e

    authors: Sundaramoorthy M,Youngs HL,Gold MH,Poulos TL

    更新日期:2005-05-03 00:00:00

  • High-pressure 31P NMR study of dipalmitoylphosphatidylcholine bilayers.

    abstract::High-pressure 31P NMR was used for the first time to investigate the effects of pressure on the structure and dynamics of the phosphocholine headgroup in pure 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) multilamellar aqueous dispersions and in DPPC bilayers containing the positively charged form of the local an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00143a004

    authors: Peng X,Jonas J

    更新日期:1992-07-21 00:00:00

  • A multifunctional protein possessing glycinamide ribonucleotide synthetase, glycinamide ribonucleotide transformylase, and aminoimidazole ribonucleotide synthetase activities in de novo purine biosynthesis.

    abstract::Three activities on the pathway of purine biosynthesis de novo in chicken liver, namely, glycinamide ribonucleotide synthetase, glycinamide ribonucleotide transformylase, and aminoimidazole ribonucleotide synthetase, have been found to reside on the same polypeptide chain. Three diverse purification schemes, utilizing...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00346a006

    authors: Daubner SC,Schrimsher JL,Schendel FJ,Young M,Henikoff S,Patterson D,Stubbe J,Benkovic SJ

    更新日期:1985-12-03 00:00:00

  • Thermal behavior of stearoylsphingomyelin-cholesterol dispersions.

    abstract::The thermotropic behavior of aqueous dispersions of stearoylsphingomyelin-cholesterol mixtures was examined by high-sensitivity differential scanning calorimetry. When less than 20 mol % cholesterol was mixed with the sphingomyelin and the samples were held at room temperature for 7-9 days before the initiation of cal...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00528a010

    authors: Estep TN,Freire E,Anthony F,Barenholz Y,Biltonen RL,Thompson TE

    更新日期:1981-12-08 00:00:00

  • Role of metals in the reaction catalyzed by protein farnesyltransferase.

    abstract::Protein farnesyltransferase catalyzes the posttranslational farnesylation of several proteins involved in signal transduction, including Ras, and is a target enzyme for antitumor therapies. Efficient product formation catalyzed by protein farnesyltransferase requires an enzyme-bound zinc cation and high concentrations...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0011781

    authors: Saderholm MJ,Hightower KE,Fierke CA

    更新日期:2000-10-10 00:00:00

  • DNA sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans.

    abstract::In our previous papers, seven structural genes (NQO1-7) of the energy-transducing NADH-quinone (Q) oxidoreductase of Paracoccus denitrificans were characterized [Xu, X., Matsuno-Yagi, A., & Yagi, T. (1991a) Biochemistry 30, 8678-8684; (1991b) Biochemistry 30, 6422-6428; (1992a) Biochemistry 31, 6925-6932; (1992b) Arch...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00054a030

    authors: Xu X,Matsuno-Yagi A,Yagi T

    更新日期:1993-01-26 00:00:00

  • Influence of lipid composition on physical properties and peg-mediated fusion of curved and uncurved model membrane vesicles: "nature's own" fusogenic lipid bilayer.

    abstract::Poly(ethylene glycol) (PEG)-mediated fusion of phosphatidylcholine model membranes has been shown to mimic the protein-mediated biomembrane process [Lee, J., and Lentz, B. R. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9274-9279]. Unlike the simple model membranes used in this earlier study, the lipid composition of fuso...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002030k

    authors: Haque ME,McIntosh TJ,Lentz BR

    更新日期:2001-04-10 00:00:00

  • Picosecond dynamics of tyrosine side chains in proteins.

    abstract::To probe the details of small amplitude motions in proteins, a dynamical analysis of the orientation fluctuations of two tyrosine side chains in the bovine pancreatic trypsin inhibitor is presented. Detailed results are given for the time history and correlation functions obtained for the ring motion from a molecular ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00573a001

    authors: McCammon JA,Wolynes PG,Karplus M

    更新日期:1979-03-20 00:00:00