Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene.

Abstract:

:The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determine the mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarily cis-syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotational and translational settings of 5S rDNA on the histone octamer surface after induction of up to 0.8 CPD/nucleosome core (2.5 kJ/m(2) UV dose). DNase I and hydroxyl radical footprints indicate that UV damage at these levels does not affect the average rotational setting of the 5S rDNA molecules. Moreover, a combination of nuclease trimming and restriction enzyme digestion indicates the preferred translational positions of the histone octamer are not affected by this level of UV damage. We also did not observe differences in the UV damage patterns of irradiated 5S rDNA before or after nucleosome formation, indicating there is little difference in the inhibition of nucleosome folding by specific CPD sites in the 5S rRNA gene. Conversely, nucleosome folding significantly restricts CPD formation at all sites in the three helical turns of the nontranscribed strand located in the dyad axis region of the nucleosome, where DNA is bound exclusively by the histone H3-H4 tetramer. Finally, modulation of the CPD distribution in a 14 nt long pyrimidine tract correlates with its rotational setting on the histone surface, when the strong sequence bias for CPD formation in this tract is minimized by normalization. These results help establish the mutual roles of histone binding and UV photoproducts on their formation in chromatin.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Liu X,Mann DB,Suquet C,Springer DL,Smerdon MJ

doi

10.1021/bi991771m

subject

Has Abstract

pub_date

2000-01-25 00:00:00

pages

557-66

issue

3

eissn

0006-2960

issn

1520-4995

pii

bi991771m

journal_volume

39

pub_type

杂志文章
  • Relaxation kinetics of glutamate dehydrogenase self-association by pressure perturbation.

    abstract::The kinetics of self-association for beef liver glutamate dehydrogenase (EC 1.4.1.3) have been measured by using pressure perturbation in both the time domain and the frequency domain by monitoring scattered light intensity. The kinetic behavior is entirely consistent with the random self-association model proposed by...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00579a007

    authors: Halvorson HR

    更新日期:1979-06-12 00:00:00

  • The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps.

    abstract::Deazapurine-containing secondary metabolites comprise a broad range of structurally diverse nucleoside analogues found throughout biology, including various antibiotics produced by species of Streptomyces bacteria and the hypermodified tRNA bases queuosine and archaeosine. Despite early interest in deazapurines as ant...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi900400e

    authors: McCarty RM,Somogyi A,Lin G,Jacobsen NE,Bandarian V

    更新日期:2009-05-12 00:00:00

  • Attenuated total reflection Fourier transform infrared studies of redox changes in bovine cytochrome c oxidase: resolution of the redox Fourier transform infrared difference spectrum of heme a(3).

    abstract::Attenuated total reflection Fourier transform infrared (ATR-FTIR) difference spectroscopy has been performed on samples of bovine cytochrome c oxidase that have been deposited as a thin film on the surface of a silicon microprism. The technique has several advantages over transmission methods in terms of amount of mat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0109717

    authors: Rich PR,Breton J

    更新日期:2002-01-22 00:00:00

  • Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.

    abstract::Known crystal structures of class II aminoacyl-tRNA synthetases complexed to their cognate tRNAs reveal that critical acceptor stem contacts are made by the variable loop connecting the beta-strands of motif 2 located within the catalytic core of class II synthetases. To identify potential acceptor stem contacts made ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi001835p

    authors: Burke B,Yang F,Chen F,Stehlin C,Chan B,Musier-Forsyth K

    更新日期:2000-12-19 00:00:00

  • Three-dimensional structure of toxin OSK1 from Orthochirus scrobiculosus scorpion venom.

    abstract::A 600 MHz 1H NMR study of toxin OSK1, blocker of small-conductance Ca2+-activated K+ channels, is presented. The unambiguous sequential assignment of all the protons of the toxin was obtained using TOCSY, DQF-COSY, and NOESY experiments at pH 3.0 (10, 30, and 45 degrees C) in aqueous solution. 3J(N alpha), 3J(alphabet...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9614390

    authors: Jaravine VA,Nolde DE,Reibarkh MJ,Korolkova YV,Kozlov SA,Pluzhnikov KA,Grishin EV,Arseniev AS

    更新日期:1997-02-11 00:00:00

  • Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants.

    abstract::Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of bili...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100728q

    authors: Kohler AC,Gae DD,Richley MA,Stoll S,Gunn A,Lim S,Martin SS,Doukov TI,Britt RD,Ames JB,Lagarias JC,Fisher AJ

    更新日期:2010-07-27 00:00:00

  • One-electron reduction of D-amino acid oxidase. Kinetics of conversion from the red semiquinone to the blue semiquinone.

    abstract::The reduction of D-amino acid oxidase (DAAO) by hydrated electrons (eaq-) has been studied in the absence and presence of benzoate by pulse radiolysis. The eaq-did not reduce the flavin moiety in DAAO and reacted with the amino acid residues in the protein. In the presence of benzoate, eaq- first reacted with benzoate...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00278a028

    authors: Kobayashi K,Hirota K,Ohara H,Hayashi K,Miura R,Yamano T

    更新日期:1983-04-26 00:00:00

  • Membrane topology of the di- and tripeptide transport protein of Lactococcus lactis.

    abstract::Transport of hydrophilic di- and tripeptides into Lactococcus lactis is mediated by a proton motive force-driven peptide transport protein (DtpT) that shares similarity with eukaryotic peptide transporters, e.g., from kidney and small intestine of rabbit, man, and rat. Hydropathy profiling in combination with the "pos...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi963068t

    authors: Hagting A,vd Velde J,Poolman B,Konings WN

    更新日期:1997-06-03 00:00:00

  • Redox reactions associated with iron release from mammalian ferritin.

    abstract::The early redox events involved in iron reduction and mobilization in mammalian ferritin have been investigated by several techniques. Sedimentation velocity measurements of ferritin samples with altered core sizes, prepared by partial reduction and Fe2+ chelation, suggest two different events occur during iron loss f...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00430a033

    authors: Jacobs DL,Watt GD,Frankel RB,Papaefthymiou GC

    更新日期:1989-02-21 00:00:00

  • Endonuclease II of Escherichia coli: DNA reacted with 7-bromomethyl-12-methylbenz[alpha]anthracene as a substrate.

    abstract::An endonuclease II preparation from Escherichia coli makes single strand breaks in DNA which has been treated with the carcinogen 7-bromomethyl-12-methylbenz[alpha]anthracene. In addition, the enzyme preparation excises N6-(12-methylbenz[alpha]anthracenyl-7-methyl)adenine and N2-(12-methylbenz[alpha]anthracenyl-7-met...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00697a002

    authors: Kirtikar DM,Dipple A,Goldthwait DA

    更新日期:1975-12-30 00:00:00

  • Reaction of nitric oxide with the turnover intermediates of cytochrome c oxidase: reaction pathway and functional effects.

    abstract::The reactions of nitric oxide (NO) with the turnover intermediates of cytochrome c oxidase were investigated by combining amperometric and spectroscopic techniques. We show that the complex of nitrite with the oxidized enzyme (O) is obtained by reaction of both the "peroxy" (P) and "ferryl" (F) intermediates with stoi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000447k

    authors: Giuffrè A,Barone MC,Mastronicola D,D'Itri E,Sarti P,Brunori M

    更新日期:2000-12-19 00:00:00

  • NMR structure determination of a novel conotoxin, [Pro 7,13] alpha A-conotoxin PIVA.

    abstract::A high-resolution solution conformation of a novel conotoxin, [Pro 7,13] alpha A-conotoxin PIVA, GCCGSYPNAACHPCSCKDROSYCGQ-NH2, has been determined by two-dimensional 1H NMR methods and distance geometry calculations. The total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962301k

    authors: Han KH,Hwang KJ,Kim SM,Kim SK,Gray WR,Olivera BM,Rivier J,Shon KJ

    更新日期:1997-02-18 00:00:00

  • Disulfide bond rearrangement during formation of the chorionic gonadotropin beta-subunit cystine knot in vivo.

    abstract::The intracellular kinetic folding pathway of the human chorionic gonadotropin beta-subunit (hCG-beta) reveals the presence of a disulfide between Cys residues 38-57 that is not detected by X-ray analysis of secreted hCG-beta. This led us to propose that disulfide rearrangement is an essential feature of cystine knot f...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049856x

    authors: Wilken JA,Bedows E

    更新日期:2004-05-04 00:00:00

  • Probing the heme iron coordination structure of alkaline chloroperoxidase.

    abstract::The mechanism by which the heme-containing peroxidase, chloroperoxidase, is able to chlorinate substrates is poorly understood. One approach to advance our understanding of the mechanism of the enzyme is to determine those factors which contribute to its stability. In particular, under alkaline conditions, chloroperox...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961512m

    authors: Blanke SR,Martinis SA,Sligar SG,Hager LP,Rux JJ,Dawson JH

    更新日期:1996-11-19 00:00:00

  • Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex.

    abstract::Minor adducts, derived from the covalent binding of anti-benzo[a]pyrene-7,8-dihydroxy-9,10-epoxide to cellular DNA, may play an important role in generating mutations and initiating cancer. We have applied a combined NMR-computational approach including intensity based refinement to determine the solution structure of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991212f

    authors: Mao B,Gu Z,Gorin A,Chen J,Hingerty BE,Amin S,Broyde S,Geacintov NE,Patel DJ

    更新日期:1999-08-17 00:00:00

  • N-terminal disordered domain of Saccharomyces cerevisiae Hop1 protein is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is necessary for spore formation.

    abstract::The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi4005528

    authors: Khan K,Madhavan TP,Kshirsagar R,Boosi KN,Sadhale P,Muniyappa K

    更新日期:2013-08-06 00:00:00

  • Effect of flap modifications on human FEN1 cleavage.

    abstract::The flap endonuclease, FEN1, plays a critical role in DNA replication and repair. Human FEN1 exhibits both a 5' to 3' exonucleolytic and a structure-specific endonucleolytic activity. On primer-template substrates containing an unannealed 5'-tail, or flap structure, FEN1 employs a unique mechanism to cleave at the poi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991321u

    authors: Bornarth CJ,Ranalli TA,Henricksen LA,Wahl AF,Bambara RA

    更新日期:1999-10-05 00:00:00

  • Ciliary dynein conformational changes as evidenced by the extrinsic fluorescent probe 8-anilino-1-naphthalenesulfonate.

    abstract::The binding of 8-anilino-1-naphthalenesulfonate (ANS) to ciliary dynein ATPase leads to a marked increase in the dye's fluorescence intensity, accompanied by a blue shift in the observed fluorescence emission maximum. We found that dynein has 37 +/- 3 ANS binding sites and that experimentally applied ANS concentration...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00347a012

    authors: Saucier AC,Mariotti S,Anderson SA,Purich DL

    更新日期:1985-12-17 00:00:00

  • Rhodamine 123 binds to multiple sites in the multidrug resistance protein (MRP1).

    abstract::The mechanisms of MRP1-drug binding and transport are not clear. In this study, we have characterized the interaction between MRP1 and rhodamine 123 (Rh123) using the photoreactive-iodinated analogue, [(125)I]iodoaryl azido-rhodamine 123 (or IAARh123). Photoaffinity labeling of plasma membranes from HeLa cells transfe...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0020574

    authors: Daoud R,Kast C,Gros P,Georges E

    更新日期:2000-12-19 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

  • X-ray crystal structure of human acidic fibroblast growth factor.

    abstract::Fibroblast growth factors (FGFs) are mitogenic and chemotactic agents for a wide variety of cell types and play a primary role in the regulation of angiogenesis. Angiogenesis is involved in a variety of critical physiological events including organogenesis, wound healing, ischemic collateral circulation, and solid tum...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9521755

    authors: Blaber M,DiSalvo J,Thomas KA

    更新日期:1996-02-20 00:00:00

  • Structure of the interhelical loops and carboxyl terminus of bacteriorhodopsin by X-ray diffraction using site-directed heavy-atom labeling.

    abstract::The positions of single amino acids in the interhelical loop regions and the C-terminal tail of bacteriorhodopsin (bR) were investigated by X-ray diffraction using site-directed heavy-atom labeling. Since wild-type bR does not contain any cysteines, appropriate cysteine mutants were produced with a unique sulfhydryl g...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971735s

    authors: Behrens W,Alexiev U,Mollaaghababa R,Khorana HG,Heyn MP

    更新日期:1998-07-21 00:00:00

  • Biochemical and structural analysis of an Eis family aminoglycoside acetyltransferase from bacillus anthracis.

    abstract::Proteins from the enhanced intracellular survival (Eis) family are versatile acetyltransferases that acetylate amines at multiple positions of several aminoglycosides (AGs). Their upregulation confers drug resistance. Homologues of Eis are present in diverse bacteria, including many pathogens. Eis from Mycobacterium t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00244

    authors: Green KD,Biswas T,Chang C,Wu R,Chen W,Janes BK,Chalupska D,Gornicki P,Hanna PC,Tsodikov OV,Joachimiak A,Garneau-Tsodikova S

    更新日期:2015-05-26 00:00:00

  • Irreversible inhibition of serine proteases by peptide derivatives of (alpha-aminoalkyl)phosphonate diphenyl esters.

    abstract::Peptidyl derivatives of diphenyl (alpha-aminoalkyl)phosphonates have been synthesized and are effective and specific inhibitors of serine proteases at low concentrations. Z-PheP(OPh)2 irreversibly reacts with chymotrypsin (kobsd/[I] = 1200 M-1 s-1) and does not react with two elastases. The best inhibitor for most chy...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00216a026

    authors: Oleksyszyn J,Powers JC

    更新日期:1991-01-15 00:00:00

  • Essential histidyl residues of ferredoxin-NADP+ oxidoreductase revealed by diethyl pyrocarbonate inactivation.

    abstract::Diethyl pyrocarbonate inhibited diaphorase activity of ferredoxin-NADP+ oxidoreductase with a second-order rate constant of 2 mM-1 X min-1 at pH 7.0 and 20 degrees C, showing a concomitant increase in absorbance at 242 nm due to formation of carbethoxyhistidyl derivatives. Activity could be restored by hydroxylamine, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00294a031

    authors: Carrillo N,Vallejos RH

    更新日期:1983-12-06 00:00:00

  • Kinetics of peptide binding to the class II MHC protein I-Ek.

    abstract::Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an extended type II polyproline-like conformation and present them for immune recognition. Because empty MHC is unstable, measurement of the rate of the second-order reaction between peptide and MHC is challenging. In this report, we use dissociation ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9921337

    authors: Kasson PM,Rabinowitz JD,Schmitt L,Davis MM,McConnell HM

    更新日期:2000-02-08 00:00:00

  • Steric constraints in the retinal binding pocket of sensory rhodopsin I.

    abstract::Steric constraints in the retinal binding pocket of sensory rhodopsin I (SR-I) are analyzed by studying effects of sample temperature and retinal analogs. The flash-induced yield of the earliest detected intermediate S610, which corresponds to the K intermediate in the bacteriorhodopsin (BR) photocycle, decreases belo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00089a044

    authors: Yan B,Xie A,Nienhaus GU,Katsuta Y,Spudich JL

    更新日期:1993-09-28 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

  • Hemorrhagic toxins from Western diamondback rattlesnake (Crotalus atrox) venom: isolation and characterization of five toxins and the role of zinc in hemorrhagic toxin e.

    abstract::Five previously unknown hemorrhagic proteins, designated hemorrhagic toxins a,b,c,d, and e, were isolated from the venom of the western diamondback rattlesnake (Crotalus atrox). Molecular weights of hemorrhagic toxins a-e were determined to be 68 000, 24 000, 24 000, 24 000, and 25 700, respectively, by sodium dodecyl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00609a033

    authors: Bjarnason JB,Tu AT

    更新日期:1978-08-08 00:00:00

  • Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences.

    abstract::The generation of multiprotein complexes at receptors and adapter proteins is crucial for the activation of intracellular signaling pathways. In this study, we used multiple biochemical and biophysical methods to examine the binding properties of several SH2 and SH3 domain-containing signaling proteins as they interac...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0357311

    authors: Houtman JC,Higashimoto Y,Dimasi N,Cho S,Yamaguchi H,Bowden B,Regan C,Malchiodi EL,Mariuzza R,Schuck P,Appella E,Samelson LE

    更新日期:2004-04-13 00:00:00