当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

Abstract：

:The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inconsistent with other evidence from hybridisation and NMR studies of P-containing oligonucleotides, which suggests that, while P can form stable base-pairs with either A or G, thymine-like properties are more pronounced. Thermal denaturation experiments over a range of solution pH values indicate that protonation of the P.A base-pairs is unlikely to be responsible for the anomalous behaviour. No specific crystal packing effects can be identfied as an explanation, and it is concluded that base stacking and other interactions between nucleotide residues in Z-DNA are responsible.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Schuerman GS,Van Meervelt L,Loakes D,Brown DM,Kong Thoo Lin P,Moore MH,Salisbury SA

doi

10.1006/jmbi.1998.2080

subject

Has Abstract

pub_date

1998-10-09 00:00:00

pages

1005-11

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(98)92080-0

journal_volume

282

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Molecular symmetry of the ClpP component of the ATP-dependent Clp protease, an Escherichia coli homolog of 20 S proteasome.

    abstract：:The ClpP component Clp protease from Escherichia coli has been crystallized and examined by X-ray crystallography and self-rotation function calculations. The crystal belongs to the monoclinic space group P2(1) with unit cell dimensions of a = 196.9 A, b = 104.3 A, c = 162.4 A and beta = 98.3 degrees. The X-ray diffra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0499

    authors： Shin DH,Lee CS,Chung CH,Suh SW

    更新日期：1996-09-20 00:00:00

  • Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition.

    abstract：:Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0553

    authors： Heyman T,Agoutin B,Friant S,Wilhelm FX,Wilhelm ML

    更新日期：1995-10-20 00:00:00

  • Crystal structure and comparative functional analyses of a Mycobacterium aldo-keto reductase.

    abstract：:Aldo-keto reductases (AKRs) are a large superfamily of NADPH-dependent enzymes that catalyze the reduction of aldehydes, aldoses, dicarbonyls, steroids, and monosaccharides. While their precise physiological role is generally unknown, AKRs are nevertheless involved in the detoxification of a broad range of toxic metab...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.02.021

    authors： Scoble J,McAlister AD,Fulton Z,Troy S,Byres E,Vivian JP,Brammananth R,Wilce MC,Le Nours J,Zaker-Tabrizi L,Coppel RL,Crellin PK,Rossjohn J,Beddoe T

    更新日期：2010-04-23 00:00:00

  • Congenital Cataract-Causing Mutation G129C in γC-Crystallin Promotes the Accumulation of Two Distinct Unfolding Intermediates That Form Highly Toxic Aggregates.

    abstract：:Cataract is a lens opacification disease prevalent worldwide. Cataract-causing mutations in crystallins generally lead to the formation of light-scattering particles in the lens. However, it remains unclear for the detailed structural and pathological mechanisms of most mutations. In this study, we showed that the G12...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.07.001

    authors： Xi YB,Chen XJ,Zhao WJ,Yan YB

    更新日期：2015-08-28 00:00:00

  • In vitro protein-primed initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3' nucleotide of the linear template: a stepwise sliding-back mechanism.

    abstract：:Phage Cp-1 from Streptoccocus pneumoniae makes use of a protein-priming mechanism to start replication of its linear DNA: the first reaction consists of the addition of 5' dAMP to a molecule of the primer protein, an initiation event occurring at both DNA ends. After elongation of the initiation complex, the primer pr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0407

    authors： Martín AC,Blanco L,García P,Salas M,Méndez J

    更新日期：1996-07-19 00:00:00

  • Structure of tubulin rings studied by X-ray scattering using synchrotron radiation.

    abstract：:X-ray patterns have been obtained from solutions of microtubules and tubulin rings using synchrotron radiation. They are interpreted on the basis of the oriented fiber X-ray diagram of microtubules, and by comparing them with the calculated scattering traces of model structures. The data are consistent with models in ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80040-0

    authors： Mandelkow E,Mandelkow EM,Bordas J

    更新日期：1983-06-15 00:00:00

  • Monomers of the Escherichia coli SSB-1 mutant protein bind single-stranded DNA.

    abstract：:The Escherichia coli wild-type single strand binding (SSB) protein is a stable tetramer that binds to single-stranded (ss) DNA in its role in DNA replication, recombination and repair. The ssb-1 mutation, a substitution of tyrosine for histidine-55 within the SSB-1 protein, destabilizes the tetramer with respect to mo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90611-9

    authors： Bujalowski W,Lohman TM

    更新日期：1991-01-05 00:00:00

  • The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA.

    abstract：:We have used gel electrophoresis to measure the progress of local denaturation in closed circular pBR322 DNA as a function of temperature and linking deficiency, delta Lk. Local denaturation is closely coupled to supercoiling in closed DNA, requiring statistical mechanical methods for analysis. We have applied these m...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1669

    authors： Bauer WR,Benham CJ

    更新日期：1993-12-20 00:00:00

  • Towards elucidation of the mechanism of UV1C, a deoxyribozyme with photolyase activity.

    abstract：:Among the unexpected chemistries that can be catalyzed by nucleic acid enzymes is photochemistry. We have reported the in vitro selection of a small, cofactor-independent deoxyribozyme, UV1C, capable of repairing thymine dimers in a DNA substrate, most optimally with light at a wavelength of >300 nm. We hypothesized t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.10.062

    authors： Chinnapen DJ,Sen D

    更新日期：2007-02-02 00:00:00

  • An additional dimer linkage structure in Moloney murine leukemia virus RNA.

    abstract：:We have identified an additional dimerization linkage structure in the genome of Moloney murine leukemia virus (MoMLV). Retroviral genomes have long been known to be linked at their 5' ends to form dimers. In MoMLV, a hairpin loop functioning as a dimer linkage structure (DLS) has previously been identified at nucleot...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2984

    authors： Oroudjev EM,Kang PC,Kohlstaedt LA

    更新日期：1999-08-20 00:00:00

  • A short DNA sequence from lambda phage inhibits protein synthesis in Escherichia coli rap.

    abstract：:The Escherichia coli rap mutant inhibits vegetative growth of bacteriophage lambda. Phage mutations termed bar, which overcome the rap defect, have been mapped to three genetic loci in the pL operon. Plasmids with a lambda wild-type bar DNA segment cloned downstream from an active promoter cannot be maintained in rap ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80316-x

    authors： Pérez-Morga D,Guarneros G

    更新日期：1990-11-20 00:00:00

  • Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3'-terminal intron alterations on cleavage at the 5' and 3' splice site.

    abstract：:A shortened derivative of the group IIA intron from the mitochondrial cytochrome-c-oxidase subunit I gene (COI I1) of the ascomycete Podospora anserina can undergo self-splicing in vitro. When compared to self-splicing group IIB introns from yeast mitochondria (aI5c, bI1) the autocatalytic reaction shows a lower effic...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1309

    authors： Schmidt U,Sägebarth R,Schmelzer C,Stahl U

    更新日期：1993-06-05 00:00:00

  • phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP complex ligand and in protein-primed initiation.

    abstract：:DNA polymerases require two acidic residues to coordinate metal ions A and B at their polymerisation active site during catalysis of nucleotide incorporation. Crystallographic resolution of varphi29 DNA polymerase ternary complex showed that metal B coordination also depends on the carbonyl group of Val250 that belong...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.10.061

    authors： Pérez-Arnaiz P,Lázaro JM,Salas M,de Vega M

    更新日期：2010-01-15 00:00:00

  • Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

    abstract：:The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(94)90042-6

    authors： Kraulis PJ

    更新日期：1994-11-04 00:00:00

  • A Theoretical Framework for Evolutionary Cell Biology.

    abstract：:One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2020.02.006

    authors： Lynch M,Trickovic B

    更新日期：2020-03-27 00:00:00

  • Efficient recovery of high-affinity antibodies from a single-chain Fab yeast display library.

    abstract：:Yeast display is a powerful technology for the isolation of monoclonal antibodies (mAbs) against a target antigen. Antibody libraries have been displayed on the surface of yeast as both single-chain variable fragment (scFv) and antigen binding fragment (Fab). Here, we combine these two formats to display well-characte...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.04.019

    authors： Walker LM,Bowley DR,Burton DR

    更新日期：2009-06-05 00:00:00

  • Evolution of protein binding modes in homooligomers.

    abstract：:The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.10.052

    authors： Dayhoff JE,Shoemaker BA,Bryant SH,Panchenko AR

    更新日期：2010-01-29 00:00:00

  • Refined crystal structure of the catalytic domain of dihydrolipoyl transacetylase (E2p) from Azotobacter vinelandii at 2.6 A resolution.

    abstract：:Dihydrolipoyl transacetylase (E2p) is both structurally and functionally the central enzyme of the pyruvate dehydrogenase multienzyme complex. The crystal structure of the catalytic domain, i.e. residues 382 to 637, of Azotobacter vinelandii E2p (E2pCD) was solved by multiple isomorphous replacement and refined by ene...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1235

    authors： Mattevi A,Obmolova G,Kalk KH,Westphal AH,de Kok A,Hol WG

    更新日期：1993-04-20 00:00:00

  • Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation.

    abstract：:The capsid protein of tomato bushy stunt virus (TBSV) has two antiparallel beta-sheet domains with the so-called jellyroll conformation. Contrary to previous analyses, we note that these domains are non-superimposable topologies. The TBSV shell (S) domain topology is common to many other proteins but the protruding (P...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90298-Z

    authors： Gibson TJ,Argos P

    更新日期：1990-03-05 00:00:00

  • E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase.

    abstract：:NusG is an essential transcription factor in Escherichia coli that is capable of increasing the overall rate of transcription. Transcript elongation by RNA polymerase (RNAP) is frequently interrupted by pauses of varying durations, and NusG is known to decrease the occupancy of at least some paused states. However, it...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.03.051

    authors： Herbert KM,Zhou J,Mooney RA,Porta AL,Landick R,Block SM

    更新日期：2010-05-28 00:00:00

  • Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.

    abstract：:The multidomain Mac-2 binding protein (M2BP) is present in serum and in the extracellular matrix in the form of linear and ring-shaped oligomers, which interact with galectin-3, fibronectin, collagens, integrins and other large glycoproteins. Domain 1 of M2BP (M2BP-1) shows homology with the cysteine-rich SRCR domain ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2996

    authors： Müller SA,Sasaki T,Bork P,Wolpensinger B,Schulthess T,Timpl R,Engel A,Engel J

    更新日期：1999-08-27 00:00:00

  • Effect of organic co-solvents on the dimer/tetramer equilibrium of human haemoglobin.

    abstract：:We have studied the effect of organic co-solvents (monohydric alcohols and formamide) on the dimer-tetramer equilibrium of human haemoglobin by measuring the dependence of oxygen affinity upon haemoglobin concentration over a 100-fold concentration range and analysing the data with a modified Monod-Wyman-Changeux mode...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90514-0

    authors： Cupane A,Vitrano E,Cordone L

    更新日期：1986-05-20 00:00:00

  • Conformational properties of the iso-1-cytochrome C denatured state: dependence on guanidine hydrochloride concentration.

    abstract：:Production of seven single surface histidine variants of yeast iso-1-cytochrome c allowed measurement of the apparent pK(a), pK(a)(obs), for histidine-heme loop formation for loops of nine to 83 amino acid residues under varying denaturing conditions (2 M to 6 M guanidine hydrochloride, gdnHCl). A linear correlation b...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(04)00331-6

    authors： Wandschneider E,Bowler BE

    更新日期：2004-05-21 00:00:00

  • Islet amyloid polypeptide inserts into phospholipid monolayers as monomer.

    abstract：:Amyloid deposits in the pancreatic islets of Langerhans are thought to be a main factor responsible for death of the insulin-producing islet beta-cells in type 2 diabetes. It is hypothesized that beta-cell death is related to interaction of the 37 amino acid residue human islet amyloid polypeptide (hIAPP), the major c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.020

    authors： Engel MF,Yigittop H,Elgersma RC,Rijkers DT,Liskamp RM,de Kruijff B,Höppener JW,Antoinette Killian J

    更新日期：2006-02-24 00:00:00

  • Interdomain contact regions and angles between adjacent short consensus repeat domains.

    abstract：:The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.017

    authors： Lehtinen MJ,Meri S,Jokiranta TS

    更新日期：2004-12-10 00:00:00

  • Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces.

    abstract：:Building on the substantial progress that has been made in using free energy perturbation (FEP) methods to predict the relative binding affinities of small molecule ligands to proteins, we have previously shown that results of similar quality can be obtained in predicting the effect of mutations on the binding affinit...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.02.003

    authors： Clark AJ,Negron C,Hauser K,Sun M,Wang L,Abel R,Friesner RA

    更新日期：2019-03-29 00:00:00

  • The denatured state under native conditions: a non-native-like collapsed state of N-PGK.

    abstract：:The guanidinium-denatured state of the N-domain of phosphoglycerate kinase (PGK) has been characterized using solution NMR. Rather than behaving as a homogenous ensemble of random coils, chemical shift changes for the majority of backbone amide resonances indicate that the denatured ensemble undergoes two definable eq...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.080

    authors： Reed MA,Jelinska C,Syson K,Cliff MJ,Splevins A,Alizadeh T,Hounslow AM,Staniforth RA,Clarke AR,Craven CJ,Waltho JP

    更新日期：2006-03-24 00:00:00

  • Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site.

    abstract：:The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs). To examine th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.01.032

    authors： Middleton AJ,Marshall CB,Faucher F,Bar-Dolev M,Braslavsky I,Campbell RL,Walker VK,Davies PL

    更新日期：2012-03-09 00:00:00

  • Tryptophan supports interaction of transmembrane helices.

    abstract：:Interactions of transmembrane helices play an important role in folding and oligomerization of integral membrane proteins. The interfacial residues of these helices frequently correspond to heptad repeat motifs. In order to uncover novel mechanisms underlying these interactions, we randomised a heptad repeat pattern w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.09.084

    authors： Ridder A,Skupjen P,Unterreitmeier S,Langosch D

    更新日期：2005-12-09 00:00:00

  • C--H...O hydrogen bond involving proline residues in alpha-helices.

    abstract：:Despite proline being assumed to be a helix-breaker, a large number of alpha-helices are found to contain Pro in globular as well as membrane proteins. Proline has no free NH group and therefore cannot form the conventional intra-helical NH.O=C hydrogen bond. An analysis of known protein structures has shown that the ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2199

    authors： Chakrabarti P,Chakrabarti S

    更新日期：1998-12-11 00:00:00