当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Quantitative agarose gel electrophoresis of chromatin: nucleosome-dependent changes in charge, sharp, and deformability at low ionic strength.

Quantitative agarose gel electrophoresis of chromatin: nucleosome-dependent changes in charge, sharp, and deformability at low ionic strength.

Abstract：

:The surface electrical charge density and the deformability of nucleosomal arrays have been characterized by quantitative agarose gel electrophoresis. Monodisperse linear DNA (2.5-3.3 kbp) was reconstituted with histone octamers into either saturated (approximately 1 nucleosome/200-bp DNA) or subsaturated (< 1 nucleosome/200-bp DNA) nucleosomal arrays. The electrophoretic mobility (mu) of both nucleosome-free DNA and nucleosomal arrays was determined at low ionic strength in 0.2-3.0% agarose gels. A semilogarithmic plot of mu vs gel concentration was linear for DNA and convex for saturated nucleosomal arrays. By extrapolating the mu to 0% agarose, the magnitude of the gel-free mu of saturated nucleosomal arrays was found to be approximately 20% lower than that of nucleosome-free DNA molecules. This difference is explained by the net neutralization of approximately 85 DNA negative charges by each histone octamer. By using an internal standard to measure the effective pore size (Pe) of the agarose gel, the effective radius (R) of DNA and nucleosomal arrays was determined at each agarose concentration. In the more dilute gels (Pe > or = 400 nm), the differences between the effective R values of DNA, subsaturated nucleosomal arrays, and saturated nucleosomal arrays are consistent with the differences in their hydrodynamic shapes as measured by analytical velocity centrifugation. However, as Pe decreases, the effective R of both nucleosome-free DNA and subsaturated nucleosomal arrays decreases significantly. This is in contrast to the effective R of saturated nucleosomal arrays, which remains constant at all Pe.(ABSTRACT TRUNCATED AT 250 WORDS)

journal_name

Biochemistry

journal_title

Biochemistry

authors

Fletcher TM,Krishnan U,Serwer P,Hansen JC

doi

10.1021/bi00174a032

subject

Has Abstract

pub_date

1994-03-01 00:00:00

pages

2226-33

issue

8

eissn

0006-2960

issn

1520-4995

journal_volume

33

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Transcription inhibition of oncogenic KRAS by a mutation-selective peptide nucleic acid conjugated to the PKKKRKV nuclear localization signal peptide.

    abstract：:Mutations in the Kirsten ras (KRAS) gene are present in almost all pancreatic adenocarcinomas, and one common mutation is at codon 12: GGT (Gly) is transformed into GAT (Asp). In this work we have targeted the KRAS coding sequence embracing the GAT mutation with a sense PNA molecule (P14), with the aim of downregulati...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0505215

    authors： Cogoi S,Codognotto A,Rapozzi V,Meeuwenoord N,van der Marel G,Xodo LE

    更新日期：2005-08-09 00:00:00

  • Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions.

    abstract：:To characterize the role of water in protein-DNA interactions, we have studied the specificity of the EcoRI restriction endonuclease as a function of osmotic and hydrostatic pressure. The extent of cleavage by the enzyme at noncanonical ("star") sites is shown to depend uniquely upon the osmotic pressure in the reacti...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00179a001

    authors： Robinson CR,Sligar SG

    更新日期：1994-04-05 00:00:00

  • Influence of the photosystem I-light harvesting complex I antenna domains on fluorescence decay.

    abstract：:The time-resolved fluorescence decay of plant PSI-LHCI has been analyzed and compared with its component parts, the PSI core and the peripheral antenna LHCI, in an attempt to (i) define the physical domains associated with the multicomponent decay-associated spectra (DAS) and determine the origin of the kinetically sl...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi060243p

    authors： Engelmann E,Zucchelli G,Casazza AP,Brogioli D,Garlaschi FM,Jennings RC

    更新日期：2006-06-06 00:00:00

  • Pressure-induced effects on cytochrome oxidase: the aerobic steady state.

    abstract：:If cytochrome c oxidase is subjected to pressure during the aerobic steady state, large spectral changes are apparent. These seem to be associated with the inhibition of electron transport within the oxidase. The volume change for the transition is about 80 mL/mol. When the oxidase in the aerobic steady state, with po...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00414a026

    authors： Kornblatt JA,Hui Bon Hoa G,Heremans K

    更新日期：1988-07-12 00:00:00

  • A novel delta(3),delta(2)-enoyl-CoA isomerase involved in the biosynthesis of the cyclohexanecarboxylic acid-derived moiety of the polyketide ansatrienin A.

    abstract：:The side chain of the antifungal polyketide ansatrienin A produced by Streptomyces collinus contains a cyclohexanecarboxylic acid (CHC) derived moiety. This CHC in the coenzyme A activated form (CHC-CoA) is derived from shikimic acid via a pathway in which the penultimate step is the isomerization of 2-cyclohexenylcar...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0005714

    authors： Patton SM,Cropp TA,Reynolds KA

    更新日期：2000-06-27 00:00:00

  • Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2.

    abstract：:Backbone dynamics in the [5',5"-2H2]2'-deoxythymidine labeled duplex dodecamer [d-(CGCGAAT*T*CGC)]2 have been investigated by solid-state 2H NMR. Quadrupolar echo line shapes, spin-lattice relaxation, and quadrupolar echo decay times were obtained over hydration levels ranging from W = 0.0 to 25.2 (moles of H2O/mole o...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00102a014

    authors： Alam TM,Orban J,Drobny GP

    更新日期：1991-09-24 00:00:00

  • Monoclonal antibodies against distinct determinants of histone H5 bind to chromatin.

    abstract：:A series of monoclonal antibodies specific for distinguishable epitopes in chromosomal protein histone H5 were obtained from mice immunized with either free H5 or H5 . RNA complexes. The antibodies elicited by H5 could be distinguished from those elicited by H5 . RNA by their binding to native or acid-denatured H5, by...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00310a012

    authors： Mendelson E,Bustin M

    更新日期：1984-07-17 00:00:00

  • Energetics of internal GU mismatches in ribooligonucleotide helixes.

    abstract：:Thermodynamic parameters of helix formation were measured spectroscopically for 16 oligoribonucleotides containing either internal GU mismatches or the corresponding AU pairs. Internal GU mismatches stabilize each helix, but not as much as the corresponding AU pairs. The differences in the enthalpy and entropy changes...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00367a061

    authors： Sugimoto N,Kierzek R,Freier SM,Turner DH

    更新日期：1986-09-23 00:00:00

  • Role of protein-water interactions and electrostatics in alpha-synuclein fibril formation.

    abstract：:Deposition of misfolded alpha-synuclein is a critical factor in several neurodegenerative disorders. Filamentous alpha-synuclein is the major component of Lewy bodies and Lewy neurites, the intracellular inclusions in the dopaminergic neurons of the substantia nigra, which are considered the pathological hallmark of P...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi034938r

    authors： Munishkina LA,Henriques J,Uversky VN,Fink AL

    更新日期：2004-03-23 00:00:00

  • Proton involvement in the transition from the "peroxy" to the ferryl intermediate of cytochrome c oxidase.

    abstract：:In the absence of any external electron donor, the "peroxy" intermediate of cytochrome c oxidase (CcO-607) is converted to the ferryl form (CcO-580) and subsequently to oxidized enzyme. The rate of conversion of CcO-607 to the CcO-580 form is pH dependent between pH 3.0 and pH 7.6. A plot of the logarithm of the rate ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi002373i

    authors： Fabian M,Palmer G

    更新日期：2001-02-13 00:00:00

  • Cyclobutane-type pyrimidine photodimer formation and excision in human skin fibroblasts after irradiation with 313-nm ultraviolet light.

    abstract：:The formation and excision of 313-nm light-induced cyclobutane-type pyrimidine photodimers were determined in confluent cultures of human fibroblasts. A new method was developed for the resolution and determination of cytosine-thymine (CT) and thymine-thymine dimers (TT) by using sodium borohydride reduction and high-...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00275a011

    authors： Niggli HJ,Cerutti PA

    更新日期：1983-03-15 00:00:00

  • Subtle Dynamic Changes Accompany Hck Activation by HIV-1 Nef and are Reversed by an Antiretroviral Kinase Inhibitor.

    abstract：:The HIV-1 virulence factor Nef interacts with the macrophage Src-family kinase Hck, resulting in constitutive kinase activation that contributes to viral replication and immune escape. Previous chemical library screens identified the diphenylfuranopyrimdine kinase inhibitor DFP-4AB, which selectively inhibits Nef-depe...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00875

    authors： Wales TE,Hochrein JM,Morgan CR,Emert-Sedlak LA,Smithgall TE,Engen JR

    更新日期：2015-10-20 00:00:00

  • Identification and synthesis of a naturally occurring selenonucleoside in bacterial tRNAs: 5-[(methylamino)methyl]-2-selenouridine.

    abstract：:Escherichia coli, Clostridium sticklandii, and Methanococcus vannielii synthesize 75Se-labeled amino acid transfer ribonucleic acids [( 75Se]tRNAs) when grown with low levels (approximately equal to 1 microM) of 75SeO32-. When E. coli [75Se]tRNA was digested to nucleosides and analyzed by reversed-phase high-performan...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00315a021

    authors： Wittwer AJ,Tsai L,Ching WM,Stadtman TC

    更新日期：1984-09-25 00:00:00

  • Contribution of structural peculiarities of onconase to its high stability and folding kinetics.

    abstract：:Onconase (ONC) from Rana pipiens is the smallest member of the ribonuclease A (RNase A) superfamily. Despite a tertiary structure similar to RNase A, ONC is distinguished by an extremely high thermodynamic stability. In the present paper we have probed the significance of three structural regions, which exhibit struct...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0525223

    authors： Arnold U,Schulenburg C,Schmidt D,Ulbrich-Hofmann R

    更新日期：2006-03-21 00:00:00

  • Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein.

    abstract：:The dimeric two-component system transmitter protein NRII (NtrB) of Escherichia coli, product of glnL (ntrB), controls transcription of nitrogen-regulated genes by catalyzing the phosphorylation and dephosphorylation of the transcription factor NRI (NtrC). Previous studies showed that the PII signal transduction prote...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi000794u

    authors： Jiang P,Atkinson MR,Srisawat C,Sun Q,Ninfa AJ

    更新日期：2000-11-07 00:00:00

  • The C2 catalytic domain of adenylyl cyclase contains the second metal ion (Mn2+) binding site.

    abstract：:Membrane-bound mammalian adenylyl cyclase isoforms contain two internally homologous cytoplasmic domains (C1 and C2). When expressed separately, C1 and C2 are catalytically inactive, but conversion of ATP to cAMP is observed if C1 and C2 are combined. By analogy with DNA polymerases, adenylyl cyclases are thought to r...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi981441m

    authors： Mitterauer T,Hohenegger M,Tang WJ,Nanoff C,Freissmuth M

    更新日期：1998-11-17 00:00:00

  • Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal.

    abstract：:A series of peptide fragments of sperm whale myoglobin, corresponding to segments of the region between the G- and H-helices of the protein, have been synthesized and their conformational preferences investigated using circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution and in solvent mi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00076a007

    authors： Shin HC,Merutka G,Waltho JP,Wright PE,Dyson HJ

    更新日期：1993-06-29 00:00:00

  • Probing the specificity determinants of amino acid recognition by arginase.

    abstract：:Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi801911v

    authors： Shishova EY,Di Costanzo L,Emig FA,Ash DE,Christianson DW

    更新日期：2009-01-13 00:00:00

  • Structural evidence that the methionyl aminopeptidase from Escherichia coli is a mononuclear metalloprotease.

    abstract：:The Co and Fe K-edge extended X-ray absorption fine structure (EXAFS) spectra of the methionyl aminopeptidase from Escherichia coli (EcMetAP) have been recorded in the presence of 1 and 2 equiv of either Co(II) or Fe(II) (i.e., [Co(II)_(EcMetAP)], [Co(II)Co(II)(EcMetAP)], [Fe(II)_(EcMetAP)], and [Fe(II)Fe(II)(EcMetAP)...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi010837m

    authors： Cosper NJ,D'souza VM,Scott RA,Holz RC

    更新日期：2001-11-06 00:00:00

  • Identification of the ATP binding sites of the carbamyl phosphate synthetase domain of the Syrian hamster multifunctional protein CAD by affinity labeling with 5'-[p-(fluorosulfonyl)benzoyl]adenosine.

    abstract：:The ATP analogue 5'-[p-(fluorosulfonyl)benzoyl]adenosine (FSBA) was used to chemically modify the ATP binding sites of the carbamyl phosphate synthetase domain of CAD, the multifunctional protein that catalyzes the first steps in mammalian pyrimidine biosynthesis. Reaction of CAD with FSBA resulted in the inactivation...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00106a033

    authors： Kim HS,Lee L,Evans DR

    更新日期：1991-10-22 00:00:00

  • Inactivation of soybean lipoxygenase 1 by 12-iodo-cis-9-octadecenoic acid.

    abstract：:12-Iodo-cis-9-octadecenoic acid (12-IODE) is a time-dependent, irreversible inactivator of soybean lipoxygenase 1. The rate of inactivation is independent of 12-IODE concentration above 20 microM and is half-maximal at about 4 microM. Inactivation by 12-IODE requires lipid hydroperoxide, which must be present even aft...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00424a019

    authors： Rotenberg SA,Grandizio AM,Selzer AT,Clapp CH

    更新日期：1988-11-29 00:00:00

  • Conformational states of N-acylalanine dithio esters: correlation of resonance Raman spectra with structures.

    abstract：:The conformational states of N-acylalanine dithio esters, involving rotational isomers about the RC(=O)NH--CH(CH3) and NHCH(CH3)--C(=S) bonds, are defined and compared to those of N-acylglycine dithio esters. The structure of N-(p-nitrobenzoyl)-DL-alanine ethyl dithio ester has been determined by X-ray crystallographi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00401a038

    authors： Lee H,Angus RH,Storer AC,Varughese KI,Carey PR

    更新日期：1988-01-12 00:00:00

  • Nucleotide specificity of stringent factor and the synthesis of analogs of guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate.

    abstract：:The ribosome-dependent stringent factor reaction was found to be nonspecific with regard to the number of phosphate groups linked to the 5' position of guanosine nucleotides. Both GMP and guanosine 5'-tetraphosphate could accept a pyrophosphoryl group from ATP although at a much lower rate than GDP or GTP. Guanosine 5...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00676a015

    authors： Sy J

    更新日期：1975-03-11 00:00:00

  • Conservative tryptophan mutants of the protein tyrosine phosphatase YopH exhibit impaired WPD-loop function and crystallize with divanadate esters in their active sites.

    abstract：:Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenyla...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00496

    authors： Moise G,Gallup NM,Alexandrova AN,Hengge AC,Johnson SJ

    更新日期：2015-10-27 00:00:00

  • Accumulation of long-chain acylcarnitine and 3-hydroxy acylcarnitine molecular species in diabetic myocardium: identification of alterations in mitochondrial fatty acid processing in diabetic myocardium by shotgun lipidomics.

    abstract：:Diabetic cardiomyopathy is the result of maladaptive changes in energy homeostasis. However, the biochemical mechanisms underlying dysfunctional lipid metabolism in diabetic myocardium are incompletely understood. Herein, we exploit shotgun lipidomics to demonstrate a 4-fold increase in acylcarnitines in diabetic myoc...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi047773a

    authors： Su X,Han X,Mancuso DJ,Abendschein DR,Gross RW

    更新日期：2005-04-05 00:00:00

  • Identification of the protein 4.1 binding site to phosphatidylserine vesicles.

    abstract：:Previous studies have shown that protein 4.1 is a multifunctional protein that binds to spectrin, actin, glycophorins, the anion channel protein, and phosphatidylserine (PS). In this report, we have characterized the binding of protein 4.1 and its major proteolytic fragments to phospholipid vesicles. Pure 125I-labeled...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00402a018

    authors： Cohen AM,Liu SC,Lawler J,Derick L,Palek J

    更新日期：1988-01-26 00:00:00

  • Three-dimensional structure of RK-1: a novel alpha-defensin peptide.

    abstract：:NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of RK-1, an antimicrobial peptide from rabbit kidney recently discovered from homology screening based on the distinctive physicochemical properties of the corticostatins/defensins. RK-1 consists of 32 res...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi000457l

    authors： McManus AM,Dawson NF,Wade JD,Carrington LE,Winzor DJ,Craik DJ

    更新日期：2000-12-26 00:00:00

  • Fragment-based approaches in drug discovery and chemical biology.

    abstract：:Fragment-based approaches to finding novel small molecules that bind to proteins are now firmly established in drug discovery and chemical biology. Initially developed primarily in a few centers in the biotech and pharma industry, this methodology has now been adopted widely in both the pharmaceutical industry and aca...

    journal_title：Biochemistry

    pub_type： 杂志文章,评审

    doi：10.1021/bi3005126

    authors： Scott DE,Coyne AG,Hudson SA,Abell C

    更新日期：2012-06-26 00:00:00

  • Diol lipids of rat liver. Quantitation and structural characteristics of neutral lipids and phospholipids derived from ethanediol, propanediols, and butanediols.

    abstract：:Specific enzymatic and chemical degradation of neutral lipid and phospholipid fractions from rat liver revealed the presence of novel types of lipid metabolites bearing a short-chain diol backbone. Diol-derived lecithin and cephalin analogs were readily cleaved by phospholipase C (EC 3.1.4.3) from Bacillus cereus, alt...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00675a031

    authors： Baumann WJ,Schupp E,Lin JT

    更新日期：1975-02-25 00:00:00

  • Physical properties of myosin from aortic smooth muscle.

    abstract：:Porcine aortic myosin is a smooth muscle contractile protein similar to its striated muscle counterpart. Electrophoresis in sodium dodecyl sulfate indicates that the molecule consists of three classes of subunits with polypeptide chain molecular weights of 192,000, 19,000, and 15,000. At 277 nm the absorption spectrum...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00576a003

    authors： Frederiksen DW

    更新日期：1979-05-01 00:00:00