当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection.

Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection.

Abstract：

:The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

van Buuren BN,Overmars FJ,Ippel JH,Altona C,Wijmenga SS

doi

10.1006/jmbi.2000.4224

keywords:

subject

Has Abstract

pub_date

2000-12-01 00:00:00

pages

371-83

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94224-4

journal_volume

304

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures.

    abstract：:Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-aver...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.05.033

    authors： Kuzmanic A,Kruschel D,van Gunsteren WF,Pannu NS,Zagrovic B

    更新日期：2011-08-05 00:00:00

  • Solution structure of R-elafin, a specific inhibitor of elastase.

    abstract：:The solution structure of r-elafin, a specific elastase inhibitor, has been determined using NMR spectroscopy. Characterized by a flat core and a flexible N-terminal extremity, the three-dimensional structure is formed by a central twisted beta-hairpin accompanied by two external segments linked by the proteinase bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.0983

    authors： Francart C,Dauchez M,Alix AJ,Lippens G

    更新日期：1997-05-09 00:00:00

  • Crystal structure of the pertussis toxin-ATP complex: a molecular sensor.

    abstract：:Pertussis toxin is a major virulence factor of Bordetella pertussis, the causative agent of whooping cough. The protein is a hexamer containing a catalytic subunit (S1) that is tightly associated with a pentameric cell-binding component (B-oligomer). In vitro experiments have shown that ATP and a number of detergents ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0277

    authors： Hazes B,Boodhoo A,Cockle SA,Read RJ

    更新日期：1996-05-17 00:00:00

  • Solution structure of a C-terminal coiled-coil domain from bovine IF(1): the inhibitor protein of F(1) ATPase.

    abstract：:Bovine IF(1) is a basic, 84 amino acid residue protein that inhibits the hydrolytic action of the F(1)F(0) ATP synthase in mitochondria under anaerobic conditions. Its oligomerization state is dependent on pH. At a pH value below 6.5 it forms an active dimer. At higher pH values, two dimers associate to form an inacti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4570

    authors： Gordon-Smith DJ,Carbajo RJ,Yang JC,Videler H,Runswick MJ,Walker JE,Neuhaus D

    更新日期：2001-04-27 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract：:The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2337

    authors： Macbeth MR,Wool IG

    更新日期：1999-01-15 00:00:00

  • Sequence context strongly modulates association of polar residues in transmembrane helices.

    abstract：:Polar residues are capable of mediating the association of membrane-embedded helices through the formation of side-chain/side-chain inter-helical hydrogen bonds. However, the extent to which native van der Waals packing of the residues surrounding the polar locus can enhance, or interfere with, the interaction of pola...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00714-9

    authors： Dawson JP,Melnyk RA,Deber CM,Engelman DM

    更新日期：2003-08-01 00:00:00

  • Leishmania mexicana glycerol-3-phosphate dehydrogenase showed conformational changes upon binding a bi-substrate adduct.

    abstract：:Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure of Leishmania mexicana GPDH (LmGPDH) with dihydroxyacetone phosphate (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00421-2

    authors： Choe J,Guerra D,Michels PA,Hol WG

    更新日期：2003-05-30 00:00:00

  • Solution structure of an EGF module pair from the Plasmodium falciparum merozoite surface protein 1.

    abstract：:The solution structure of the 96-residue C-terminal fragment of the merozoite surface protein 1 (MSP-1) from Plasmodium falciparum has been determined using nuclear magnetic resonance (NMR) spectroscopic measurements on uniformly13C/15N-labelled protein, efficiently expressed in the methylotrophic yeast Komagataella (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2753

    authors： Morgan WD,Birdsall B,Frenkiel TA,Gradwell MG,Burghaus PA,Syed SE,Uthaipibull C,Holder AA,Feeney J

    更新日期：1999-05-28 00:00:00

  • Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein.

    abstract：:FSHD region gene 1 (FRG1) is a dynamic nuclear and cytoplasmic protein that, in skeletal muscle, shows additional localization to the sarcomere. Maintaining appropriate levels of FRG1 protein is critical for muscular and vascular development in vertebrates; however, its precise molecular function is unknown. This stud...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.06.014

    authors： Sun CY,van Koningsbruggen S,Long SW,Straasheijm K,Klooster R,Jones TI,Bellini M,Levesque L,Brieher WM,van der Maarel SM,Jones PL

    更新日期：2011-08-12 00:00:00

  • The role of backbone motions in ligand binding to the c-Src SH3 domain.

    abstract：:The Src homology 3 (SH3) domain of pp60(c-src) (Src) plays dual roles in signal transduction, through stabilizing the repressed form of the Src kinase and through mediating the formation of activated signaling complexes. Transition of the Src SH3 domain between a variety of binding partners during progression through ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5083

    authors： Wang C,Pawley NH,Nicholson LK

    更新日期：2001-11-02 00:00:00

  • The crystal structure of affinity-matured human growth hormone at 2 A resolution.

    abstract：:A variant of human growth hormone (hGH), in which 15 mutations were introduced with phage display mutagenesis to improve receptor binding affinity by 400-fold, yielded two related crystal forms diffracting to high resolution. The structure of this variant was determined in both crystal forms, one at 2.0 A resolution a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1135

    authors： Ultsch MH,Somers W,Kossiakoff AA,de Vos AM

    更新日期：1994-02-11 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

  • Activation of calpain by Ca2+: roles of the large subunit N-terminal and domain III-IV linker peptides.

    abstract：:The calpains are a family of cysteine proteases with closely related amino acid sequences, but a wide range of Ca(2+) requirements (K(d)). For m-calpain, K(d) is approximately 325microM, for mu-calpain it is approximately 50microM, and for calpain 3 it is not strictly known but may be approximately 0.1microM. On the b...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.08.073

    authors： Hosfield CM,Elce JS,Jia Z

    更新日期：2004-10-29 00:00:00

  • NMR structure of the integral membrane protein OmpX.

    abstract：:The structure of the integral membrane protein OmpX from Escherichia coli reconstituted in 60 kDa DHPC micelles (OmpX/DHPC) was calculated from 526 NOE upper limit distance constraints. The structure determination was based on complete sequence-specific assignments for the amide protons and the Val, Leu, and Ile(delta...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.09.014

    authors： Fernández C,Hilty C,Wider G,Güntert P,Wüthrich K

    更新日期：2004-03-05 00:00:00

  • Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.

    abstract：:The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with (1)H NMR spectroscopy by utilizing distance restraints from total relaxation m...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4498

    authors： Isaacs RJ,Spielmann HP

    更新日期：2001-03-23 00:00:00

  • Bile acid interactions with rabbit ileal lipid binding protein and an engineered helixless variant reveal novel ligand binding properties of a versatile beta-clam shell protein scaffold.

    abstract：:The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.024

    authors： Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

    更新日期：2007-08-31 00:00:00

  • Single fibril growth kinetics of α-synuclein.

    abstract：:Neurodegenerative disorders associated with protein misfolding are fatal diseases that are caused by fibrillation of endogenous proteins such as α-synuclein (α-syn) in Parkinson's disease (PD) or amyloid-β in Alzheimer's disease. Fibrils of α-syn are a major pathological hallmark of PD and certain aggregation intermed...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.01.020

    authors： Wördehoff MM,Bannach O,Shaykhalishahi H,Kulawik A,Schiefer S,Willbold D,Hoyer W,Birkmann E

    更新日期：2015-03-27 00:00:00

  • A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core.

    abstract：:The folding thermodynamics and kinetics of the alpha-spectrin SH3 domain with a redesigned hydrophobic core have been studied. The introduction of five replacements, A11V, V23L, M25V, V44I and V58L, resulted in an increase of 16% in the overall volume of the side-chains forming the hydrophobic core but caused no remar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00273-0

    authors： Cobos ES,Filimonov VV,Vega MC,Mateo PL,Serrano L,Martínez JC

    更新日期：2003-04-18 00:00:00

  • The recognition of distorted DNA structures by HMG-D: a footprinting and molecular modelling study.

    abstract：:The high mobility group (HMG) domain is a DNA binding motif found in some eukaryotic chromosomal proteins and transcription factors. This domain binds in the minor groove of DNA inducing a sharp bend and also preferentially binds to certain distorted DNA structures. Although structures of sequence-specific HMG domains...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3246

    authors： Payet D,Hillisch A,Lowe N,Diekmann S,Travers A

    更新日期：1999-11-19 00:00:00

  • The SOCS box domain of SOCS3: structure and interaction with the elonginBC-cullin5 ubiquitin ligase.

    abstract：:Suppressor of cytokine signalling 3 (SOCS3) is responsible for regulating the cellular response to a variety of cytokines, including interleukin 6 and leukaemia inhibitory factor. Identification of the SOCS box domain led to the hypothesis that SOCS3 can associate with functional E3 ubiquitin ligases and thereby induc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.06.038

    authors： Babon JJ,Sabo JK,Soetopo A,Yao S,Bailey MF,Zhang JG,Nicola NA,Norton RS

    更新日期：2008-09-12 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

  • Structural and functional characterisation of a conserved archaeal RadA paralog with antirecombinase activity.

    abstract：:DNA recombinases (RecA in bacteria, Rad51 in eukarya and RadA in archaea) catalyse strand exchange between homologous DNA molecules, the central reaction of homologous recombination, and are among the most conserved DNA repair proteins known. RecA is the sole protein responsible for this reaction in bacteria, whereas ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.04.060

    authors： McRobbie AM,Carter LG,Kerou M,Liu H,McMahon SA,Johnson KA,Oke M,Naismith JH,White MF

    更新日期：2009-06-19 00:00:00

  • The refined crystal structure of toxic shock syndrome toxin-1 at 2.07 A resolution.

    abstract：:The pyrogenic toxin toxic shock syndrome toxin-1 from Staphylococcus aureus is a causative agent of the toxic shock syndrome disease. It belongs to a family of proteins known as superantigens that cross-link major histocompatibility class II molecules and T-cell receptors leading to the activation of a substantial num...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0421

    authors： Papageorgiou AC,Brehm RD,Leonidas DD,Tranter HS,Acharya KR

    更新日期：1996-07-26 00:00:00

  • Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

    abstract：:The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90391-4

    authors： Namba K,Pattanayek R,Stubbs G

    更新日期：1989-07-20 00:00:00

  • Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.

    abstract：:Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four memb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00596-5

    authors： Kreusch A,Spraggon G,Lee CC,Klock H,McMullan D,Ng K,Shin T,Vincent J,Warner I,Ericson C,Lesley SA

    更新日期：2003-07-04 00:00:00

  • RNA editing in Drosophila 4f-rnp gene nuclear transcripts by multiple A-to-G conversions.

    abstract：:Pre-mRNA editing results in production of transcripts having nucleotide sequences differing from that of the DNA template. We describe the first example of RNA editing in the fruitfly Drosophila melanogaster. This editing occurs in an alternatively spliced adult head transcript arising from the single-copy nuclear 4f-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0365

    authors： Petschek JP,Mermer MJ,Scheckelhoff MR,Simone AA,Vaughn JC

    更新日期：1996-06-28 00:00:00

  • Growth-rate-dependent accumulation of twelve tRNA species in Escherichia coli.

    abstract：:We have previously shown that in Escherichia coli the accumulation of five leucine and three methionine tRNA species is regulated so that those tRNA species that translate major codons increase while those that translate minor codons decrease as the growth rate increases. Here, we have analyzed the growth-rate-depende...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1165

    authors： Emilsson V,Näslund AK,Kurland CG

    更新日期：1993-03-20 00:00:00

  • Binding of Escherichia coli RNA polymerase to a promoter carrying mutations that stop transcription initiation.

    abstract：:The gal P2 promoter can be inactivated by point mutations located in the -10 hexamer sequence or immediately upstream from it. Mutations at either site reduce expression in vivo and prevent the formation, in vitro, of tight complexes with RNA polymerase that give a strong footprint and can initiate transcription. Howe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90194-x

    authors： Johnston F,Ponnambalam S,Busby S

    更新日期：1987-06-05 00:00:00

  • Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases.

    abstract：:TrmD and Trm5 are, respectively, the bacterial and eukarya/archaea methyl transferases that catalyze transfer of the methyl group from S-adenosyl methionine (AdoMet) to the N1 position of G37 in tRNA to synthesize m1G37-tRNA. The m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.08.010

    authors： Christian T,Hou YM

    更新日期：2007-10-26 00:00:00

  • Requirement of 3'-terminal guanosine in (-)-stranded RNA for in vitro replication of cucumber mosaic virus satellite RNA by viral RNA-dependent RNA polymerase.

    abstract：:The 3' terminus of the (-) RNA strand in the replicative forms of several (+)-stranded RNA viruses possesses an unpaired guanosine with unknown function. This unpaired guanosine is also found at the 3' terminus of the (-) strand in the double-stranded form of two cucumoviral satellite RNAs. Using a cucumber mosaic vir...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1326

    authors： Wu G,Kaper JM

    更新日期：1994-05-20 00:00:00