当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.

Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip.

Abstract：

:p50 protein is a member of the Y-box binding transcription factor family and is a counterpart of YB-1 protein. The generic microchip was used to analyze the sequence specificity of p50 binding to single (ss) and double-stranded (ds) oligodeoxyribonucleotides. The generic microchip contained 4,096 single-stranded octadeoxyribonucleotides in which all possible core 6-mers (4(6)=4,096) were flanked at their 3' and 5'-ends with degenerated nucleotides. The oligonucleotides were chemically immobilized within polyacrylamide gel pads fixed on a glass slide. The binding of p50 to the generic microchip was shown to be the most specific to ss GGGG motif and then to ss CACC and CATC motifs. GC-rich ds oligonucleotides of the generic microchip, and particularly those containing GGTG/CACC, GATG/CATC, and GTGG/CCAC heterogeneous motifs, were most efficiently destabilized due to interaction with p50. Gel-shift electrophoresis has shown that the protein exhibits much higher binding specificity to 24-mer oligoA-TGGGGG-oligoA containing G-rich 6-mer, in comparison with 24-mer oligoA-AAATAT-oligoA carrying A,T-rich 6-mer in full correspondence with the data obtained with the microchip. Studies of DNA-binding proteins using gel-immobilized ss and ds DNA fragments provide a unique possibility to detect low-affinity complexes of these proteins with short sequence motifs and assess the role of these motifs in sequence-specific interactions with long recognition sites.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Zasedateleva OA,Krylov AS,Prokopenko DV,Skabkin MA,Ovchinnikov LP,Kolchinsky A,Mirzabekov AD

doi

10.1016/s0022-2836(02)00937-3

keywords:

subject

Has Abstract

pub_date

2002-11-15 00:00:00

pages

73-87

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022283602009373

journal_volume

324

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex.

    abstract：:Binding of the TATA-binding protein (TBP) to the "TATA" sequences present in the promoters of eukaryotic class II genes is the first step in the sequential assembly of transcription pre-initiation complexes. Myriad structural changes, including severe bending of the DNA, accompany TBP-TATA complex formation. A detaile...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2835

    authors： Parkhurst KM,Richards RM,Brenowitz M,Parkhurst LJ

    更新日期：1999-06-25 00:00:00

  • First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution.

    abstract：:This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(02)00473-4

    authors： Chandra V,Jasti J,Kaur P,Betzel Ch,Srinivasan A,Singh TP

    更新日期：2002-07-05 00:00:00

  • Analysis and prediction of functional sub-types from protein sequence alignments.

    abstract：:The increasing number and diversity of protein sequence families requires new methods to define and predict details regarding function. Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4036

    authors： Hannenhalli SS,Russell RB

    更新日期：2000-10-13 00:00:00

  • Modelling transcriptional interference and DNA looping in gene regulation.

    abstract：:We describe a hybrid statistical mechanical and dynamical approach for modelling the formation of closed, open and elongating complexes of RNA polymerase, the interactions of these polymerases to produce transcriptional interference, and the regulation of these processes by a DNA-binding and DNA-looping regulatory pro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.04.041

    authors： Dodd IB,Shearwin KE,Sneppen K

    更新日期：2007-06-22 00:00:00

  • Trypanosoma brucei variant-specific glycoprotein gene chromatin is sensitive to single-strand-specific endonuclease digestion.

    abstract：:Active variant surface glycoprotein (VSG) gene chromatin is preferentially digested by the restriction enzyme HinfI in nuclei of bloodstream variants of Trypanosoma brucei. HinfI sensitivity of VSG gene chromatin is not observed in nuclei of relapse variants in which the VSG gene has been inactivated in situ. Active V...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90559-6

    authors： Greaves DR,Borst P

    更新日期：1987-10-05 00:00:00

  • Thermodynamics of RNA unfolding: stabilization of a ribosomal RNA tertiary structure by thiostrepton and ammonium ion.

    abstract：:RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0291

    authors： Draper DE,Xing Y,Laing LG

    更新日期：1995-06-02 00:00:00

  • pK values of histidine residues in ribonuclease Sa: effect of salt and net charge.

    abstract：:The primary goal of this study was to gain a better understanding of the effect of environment and ionic strength on the pK values of histidine residues in proteins. The salt-dependence of pK values for two histidine residues in ribonuclease Sa (RNase Sa) (pI=3.5) and a variant in which five acidic amino acids have be...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01274-3

    authors： Huyghues-Despointes BM,Thurlkill RL,Daily MD,Schell D,Briggs JM,Antosiewicz JM,Pace CN,Scholtz JM

    更新日期：2003-01-31 00:00:00

  • Characterization of the interaction of GABARAPL-1 with the LIR motif of NBR1.

    abstract：:Selective autophagy requires the specific segregation of targeted proteins into autophagosomes. The selectivity is mediated by autophagy receptors, such as p62 and NBR1, which can bind to autophagic effector proteins (Atg8 in yeast, MAP1LC3 protein family in mammals) anchored in the membrane of autophagosomes. Recogni...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.05.003

    authors： Rozenknop A,Rogov VV,Rogova NY,Löhr F,Güntert P,Dikic I,Dötsch V

    更新日期：2011-07-15 00:00:00

  • Modular structure of the trigger factor required for high activity in protein folding.

    abstract：:The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1206

    authors： Zarnt T,Tradler T,Stoller G,Scholz C,Schmid FX,Fischer G

    更新日期：1997-09-05 00:00:00

  • Evolution of specific protein-protein interaction sites following gene duplication.

    abstract：:Gene duplication is a common evolutionary process that leads to the expansion and functional diversification of protein subfamilies. The evolutionary events that cause paralogous proteins to bind different protein ligands (functionally diverged interfaces) are investigated and compared to paralogous proteins that bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.06.039

    authors： Aiello D,Caffrey DR

    更新日期：2012-10-19 00:00:00

  • Specific interaction of the antiapoptotic protein Nr-13 with phospholipid monolayers is prevented by the BH3 domain of Bax.

    abstract：:Members of the Bcl-2 protein family regulate apoptosis by controlling the release of apoptogenic proteins such as cytochrome c from the mitochondrial intermembrane space. Proapoptotic members induce release by increasing outer membrane permeability, while antiapoptotic members prevent this. The activity of Bcl-2 prote...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.10.028

    authors： Girard-Egrot A,Chauvet JP,Gillet G,Moradi-Améli M

    更新日期：2004-01-02 00:00:00

  • Molecular crowding limits the role of fetal hemoglobin in therapy for sickle cell disease.

    abstract：:The dominant assumption central to most treatments for sickle cell anemia has been that replacement of sickle hemoglobin (HbS) by fetal hemoglobin (HbF) would have major clinical benefit. Using laser photolysis, we have measured polymerization kinetics including rates of homogeneous and heterogeneous nucleation on mix...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.02.006

    authors： Rotter M,Aprelev A,Adachi K,Ferrone FA

    更新日期：2005-04-15 00:00:00

  • Identification of a phosphodiesterase I/nucleotide pyrophosphatase-related gene mRNA in rat vascular smooth muscle cells by the differential display approach.

    abstract：:Vascular smooth muscle cell hypertrophy and proliferation may participate in the pathophysiology of cardiovascular disease. The analysis of changes in gene expression in vascular smooth muscle cells is crucial to the understanding of the molecular biology of cardiovascular disease. An effective method for analysis of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1768

    authors： Kettenhofen R,Meyer zu Brickwedde MK,KO Y,Vetter H,Sachinidis A

    更新日期：1998-06-05 00:00:00

  • Functional characterization and modulation of the DNA cleavage efficiency of type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target.

    abstract：:EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely oriented 5'-CAGCAG recognition sites for efficient DNA cleavage. Diverse models have been developed to explain how enzyme complexes bound to both sites move toward each other, DNA translocation, DNA looping and simple diffusion...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.02.047

    authors： Möncke-Buchner E,Rothenberg M,Reich S,Wagenführ K,Matsumura H,Terauchi R,Krüger DH,Reuter M

    更新日期：2009-04-17 00:00:00

  • At least two nodD genes are necessary for efficient nodulation of alfalfa by Rhizobium meliloti.

    abstract：:A Rhizobium meliloti DNA region (nodD1) involved in the regulation of other early nodulation genes has been delimited by directed Tn5 mutagenesis and its nucleotide sequence has been determined. The sequence data indicate a large open reading frame with opposite polarity to nodA, -B and -C, coding for a protein of 308...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90136-1

    authors： Göttfert M,Horvath B,Kondorosi E,Putnoky P,Rodriguez-Quiñones F,Kondorosi A

    更新日期：1986-10-05 00:00:00

  • Phenotypic suppression by incorporation of an alien amino acid.

    abstract：:Azaleucine is a naturally occurring amino acid antibiotic that can be incorporated into proteins by mimicking leucine. In spite of its highly toxic character, the contrast between the hydrophobic side-chain of leucine and the basic side-chain of azaleucine suggested a mechanism for rescuing certain mutants. We constru...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1269

    authors： Lemeignan B,Sonigo P,Marlière P

    更新日期：1993-05-20 00:00:00

  • Isolation and characterization of conditional alleles of the yeast SIR2 gene.

    abstract：:Sir2 is a protein deacetylase that mediates transcriptional silencing at the HM loci, telomeres, and rDNA repeats in yeast. To identify functionally significant regions of the Sir2 protein, we have characterized two types of mutations. First, we used random mutagenesis to create temperature-sensitive alleles of the SI...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.01.044

    authors： Hickman M,McCullough K,Woike A,Raducha-Grace L,Rozario T,Dula ML,Anderson E,Margalit D,Holmes SG

    更新日期：2007-04-13 00:00:00

  • Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril.

    abstract：:The beta-lactamases are involved in bacterial resistance to penicillin and related compounds. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are thus becoming of major clinical importance. The structures of the Zn-beta-lactamase from Fluoribacter gormanii (FEZ-1) in the native and in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01271-8

    authors： García-Sáez I,Mercuri PS,Papamicael C,Kahn R,Frère JM,Galleni M,Rossolini GM,Dideberg O

    更新日期：2003-01-24 00:00:00

  • Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri.

    abstract：:3-Methylitaconate-Delta-isomerase (Mii) participates in the nicotinate fermentation pathway of the anaerobic soil bacterium Eubacterium barkeri (order Clostridiales) by catalyzing the reversible conversion of (R)-3-methylitaconate (2-methylene-3-methylsuccinate) to 2,3-dimethylmaleate. The enzyme is also able to catal...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.052

    authors： Velarde M,Macieira S,Hilberg M,Bröker G,Tu SM,Golding BT,Pierik AJ,Buckel W,Messerschmidt A

    更新日期：2009-08-21 00:00:00

  • E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA.

    abstract：:The rpsO mRNA of E. coli encoding ribosomal protein S15 is destabilized by poly(A) tails posttranscriptionally added by poly(A)polymerase I. We demonstrate here that polyadenylation also contributes to the rapid degradation of mRNA fragments generated by RNase E. It was already known that an RNase E cleavage occurring...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2547

    authors： Hajnsdorf E,Régnier P

    更新日期：1999-03-05 00:00:00

  • Crystallization and preliminary X-ray analysis of papaya mosaic virus coat protein.

    abstract：:Papaya mosaic virus coat protein has been treated with trypsin and a large fragment of the intact protein has been crystallized in space group P3(1)21 or P3(2)21 (unit cell dimensions: a = b = 110 A, c = 237 A). The crystals diffract to 3.5 A resolution. Crystals of the untreated protein have also been grown. The untr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1634

    authors： Zhang H,Todderud E,Stubbs G

    更新日期：1993-12-05 00:00:00

  • Attachment of tail fibers in bacteriophage T4 assembly. Identification of the baseplate protein to which tail fibers attach.

    abstract：:A phage-neutralizing rabbit antiserum collected after immunization with tail-fiberless bacteriophage T4 particles was adsorbed with complete T4 phage. The resulting adsorbed serum inhibited tail fiber attachment in vitro. To identify the antigens against which this inhibitory activity was directed, blocking experiment...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80059-x

    authors： Urig MA,Brown SM,Tedesco P,Wood WB

    更新日期：1983-09-15 00:00:00

  • The role of the L-chain in ferritin iron incorporation. Studies of homo and heteropolymers.

    abstract：:Mammalian ferritins are 24-meric proteins composed of variable proportions of H and L-subunits. The L-chain, in contrast to the H-chain, lacks detectable ferroxidase activity, and its role in ferritin iron incorporation is unclear. In this study, apoferritins were subjected to iron loading with large iron increments t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1325

    authors： Levi S,Santambrogio P,Cozzi A,Rovida E,Corsi B,Tamborini E,Spada S,Albertini A,Arosio P

    更新日期：1994-05-20 00:00:00

  • Rapid creation of a novel protein function by in vitro coevolution.

    abstract：:We have developed a simple and efficient method for creation of novel protein functions in an existing protein scaffold. The in vitro coevolution method involves design of a hypothetical pathway for the target function followed by stepwise directed evolution of the corresponding protein along the pathway. As a test ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.02.070

    authors： Chen Z,Zhao H

    更新日期：2005-05-20 00:00:00

  • Solution structure of GDP-tubulin double rings to 3 nm resolution and comparison with microtubules.

    abstract：:GDP liganded tubulin, which is inactive in microtubule assembly, polymerizes into rings more readily than the active GTP liganded protein. The structure of double rings made of highly purified GDP-tubulin has been characterized to 3 nm resolution with synchrotron X-ray solution scattering. The scattering profile has c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1282

    authors： Díaz JF,Pantos E,Bordas J,Andreu JM

    更新日期：1994-04-29 00:00:00

  • Refined structure of rat Clara cell 17 kDa protein at 3.0 A resolution.

    abstract：:The rat Clara cell 17 kDa protein (previously referred to as the rat Clara cell 10 kDa protein) has been reported to inhibit phospholipase A2 and papain, and to also bind progesterone. It has been isolated from rat lung lavage fluid and crystallized in the space group P6(5)22. The structure has been determined to 3.0 ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)91006-b

    authors： Umland TC,Swaminathan S,Furey W,Singh G,Pletcher J,Sax M

    更新日期：1992-03-20 00:00:00

  • Molecular Highways-Navigating Collisions of DNA Motor Proteins.

    abstract：:Fundamental biological processes require concurrent sharing of DNA by numerous motor proteins and complexes. Thus, collision, congestion, and roadblocks are inescapable on these busy "molecular highways." The consequences of these traffic problems are diverse, resulting in complex cellular mechanisms to resolve threat...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.08.006

    authors： Le TT,Wang MD

    更新日期：2018-10-26 00:00:00

  • The oligomeric structure of vaccinia viral envelope protein A27L is essential for binding to heparin and heparan sulfates on cell surfaces: a structural and functional approach using site-specific mutagenesis.

    abstract：:The soluble domain of the self-assembly vaccinia virus envelope protein A27L, sA27L-aa, consists of a flexible extended coil at the N terminus and a rigid hydrophobic coiled-coil region at the C terminus. In the former, a basic strip of 12 residues is responsible for binding to cell-surface heparan sulfates. Although ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.04.024

    authors： Ho Y,Hsiao JC,Yang MH,Chung CS,Peng YC,Lin TH,Chang W,Tzou DL

    更新日期：2005-06-24 00:00:00

  • Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease.

    abstract：:Chagasin is a protein produced by Trypanosoma cruzi, the parasite that causes Chagas' disease. This small protein belongs to a recently defined family of cysteine protease inhibitors. Although resembling well-known inhibitors like the cystatins in size (110 amino acid residues) and function (they all inhibit papain-li...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.005

    authors： Ljunggren A,Redzynia I,Alvarez-Fernandez M,Abrahamson M,Mort JS,Krupa JC,Jaskolski M,Bujacz G

    更新日期：2007-08-03 00:00:00

  • Folding amphipathic helices into membranes: amphiphilicity trumps hydrophobicity.

    abstract：:High amphiphilicity is a hallmark of interfacial helices in membrane proteins and membrane-active peptides, such as toxins and antimicrobial peptides. Although there is general agreement that amphiphilicity is important for membrane-interface binding, an unanswered question is its importance relative to simple hydroph...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.016

    authors： Fernández-Vidal M,Jayasinghe S,Ladokhin AS,White SH

    更新日期：2007-07-13 00:00:00