Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance.

Abstract:

:Two-dimensional nuclear Overhauser enhancement spectra are presented of the complex of lac repressor headpiece with a 14 base-pair lac operator fragment. Analysis of nuclear Overhauser enhancements observed between protein and DNA shows that the second helix of the headpiece ("the recognition helix") binds in the major groove of DNA as has been suggested, but that the orientation of this helix is approximately 180 degrees different from the proposed models.

journal_name

J Mol Biol

authors

Boelens R,Scheek RM,van Boom JH,Kaptein R

doi

10.1016/0022-2836(87)90638-3

subject

Has Abstract

pub_date

1987-01-05 00:00:00

pages

213-6

issue

1

eissn

0022-2836

issn

1089-8638

pii

0022-2836(87)90638-3

journal_volume

193

pub_type

杂志文章
  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

    abstract::Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3693

    authors: Clementi C,Nymeyer H,Onuchic JN

    更新日期:2000-05-19 00:00:00

  • Structurally similar but functionally diverse ZU5 domains in human erythrocyte ankyrin.

    abstract::The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.01.041

    authors: Yasunaga M,Ipsaro JJ,Mondragón A

    更新日期:2012-04-06 00:00:00

  • Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis.

    abstract::The 69 nucleotide left-terminal domain (T(L)) of the potato spindle tuber RNA viroid (PSTVd) constitutes one of its five structural elements. Due to a twofold complementary sequence repeat, two possible conformations are proposed for the T(L) secondary structure; an elongated-rod and a bifurcated form. In the present ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.10.015

    authors: Dingley AJ,Steger G,Esters B,Riesner D,Grzesiek S

    更新日期:2003-12-05 00:00:00

  • Sigma competition: the contest between bacteriophage T4 middle and late transcription.

    abstract::In bacterial transcription, diverse sigma-family promoter recognition proteins compete for a common RNA polymerase core. Bacteriophage T4 infection ultimately reduces this competition to a duel between activated viral middle and enhanced late transcription, involving two sigma proteins, two phage-encoded activator pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2953

    authors: Kolesky S,Ouhammouch M,Brody EN,Geiduschek EP

    更新日期:1999-08-13 00:00:00

  • The hypE gene completes the gene cluster for H2-oxidation in Azotobacter vinelandii.

    abstract::The nucleotide sequence was obtained for the hypE gene in the cluster of structural and accessory genes required for the assembly and functioning of the membrane-bound, dimeric, (NiFe)hydrogenase in Azotobacter vinelandii. The hypE gene encodes a polypeptide of 341 amino acid residues which is rich in alanine, glycine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1149

    authors: Garg RP,Menon AL,Jacobs K,Robson RM,Robson RL

    更新日期:1994-02-11 00:00:00

  • The LcrG Tip Chaperone Protein of the Yersinia pestis Type III Secretion System Is Partially Folded.

    abstract::The type III secretion system (T3SS) is essential in the pathogenesis of Yersinia pestis, the causative agent of plague. A small protein, LcrG, functions as a chaperone to the tip protein LcrV, and the LcrG-LcrV interaction is important in regulating protein secretion through the T3SS. The atomic structure of the LcrG...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.07.024

    authors: Chaudhury S,de Azevedo Souza C,Plano GV,De Guzman RN

    更新日期:2015-09-25 00:00:00

  • A symmetrical model for the domain structure of type I DNA methyltransferases.

    abstract::Type I DNA methyltransferases are complex multisubunit enzymes that methylate a specific base in each half of an asymmetric bipartite DNA recognition sequence. The specificity (S) subunit contains two corresponding DNA sequence recognition domains, plus a number of conserved regions which interact with two modificatio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.1994.1624

    authors: Kneale GG

    更新日期:1994-10-14 00:00:00

  • Oligomerization of the SPP1 scaffolding protein.

    abstract::Viral scaffolding proteins direct polymerization of major capsid protein subunits into icosahedral procapsid structures. The scaffolding protein of bacteriophage SPP1 was engineered with a C-terminal hexahistidine tag (gp11-His(6)) and purified. The protein is an alpha-helical-rich molecule with a very elongated shape...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.02.028

    authors: Poh SL,el Khadali F,Berrier C,Lurz R,Melki R,Tavares P

    更新日期:2008-05-02 00:00:00

  • Three-dimensional structure of rotavirus.

    abstract::The three-dimensional structures of double and single-shelled simian rotavirus have been determined to a resolution of 40 A by image processing electron micrographs of unstained, unfixed virus particles embedded in vitreous ice. This study demonstrates that the icosahedral surface lattices in these structures have a t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90313-0

    authors: Prasad BV,Wang GJ,Clerx JP,Chiu W

    更新日期:1988-01-20 00:00:00

  • Limited proteolysis unmasks specific DNA-binding of the murine RNA polymerase I-specific transcription termination factor TTFI.

    abstract::Previously we have shown that nuclear extracts from mouse cells contain a heterogeneous group of polypeptides (p65, p80, p90, p100) which form distinct DNA-protein complexes on the 18 base-pair sequence element (termed Sal-box), which constitutes the murine rDNA transcription termination signal. These distinct protein...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90213-4

    authors: Smid A,Finsterer M,Grummt I

    更新日期:1992-10-05 00:00:00

  • Single-stranded DNA binding properties of the UvsX recombinase of bacteriophage T4: binding parameters and effects of nucleotides.

    abstract::Bacteriophage T4 provides an important model for the biochemistry and genetics of DNA metabolism. Phage-encoded proteins conduct all essential steps of T4 DNA replication, repair, and recombination. Central to these three processes is the T4 UvsX protein, a member of the filamentous, ATP-dependent class of general rec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2124

    authors: Ando RA,Morrical SW

    更新日期:1998-11-06 00:00:00

  • A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction.

    abstract::RNase MRP is a ribonucleoprotein endoribonuclease involved in eukaryotic pre-rRNA processing. The enzyme possesses a putatively catalytic RNA subunit, structurally related to that of RNase P. A thorough structure analysis of Saccharomyces cerevisiae MRP RNA, entailing enzymatic and chemical probing, mutagenesis and th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.076

    authors: Walker SC,Avis JM

    更新日期:2004-08-06 00:00:00

  • Local and global cooperativity in the human alpha-lactalbumin molten globule.

    abstract::NMR spectroscopy has been used to follow the urea-induced unfolding of the low pH molten globule states of a single-disulfide variant of human alpha-lactalbumin ([28-111] alpha-LA) and of two mutants, each with a single proline substitution in a helix. [28-111] alpha-LA forms a molten globule very similar to that form...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.02.045

    authors: Quezada CM,Schulman BA,Froggatt JJ,Dobson CM,Redfield C

    更新日期:2004-04-16 00:00:00

  • The SH3-fold family: experimental evidence and prediction of variations in the folding pathways.

    abstract::To investigate the relationships between protein topology, amino acid sequence and folding mechanisms, the folding transition state of the Sso7d protein has been characterised both experimentally and theoretically. Although Sso7d protein has a similar topology to that of the SH3 domains, the structure of its transitio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4234

    authors: Guerois R,Serrano L

    更新日期:2000-12-15 00:00:00

  • New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.

    abstract::A bank of 13,563 loops from three to eight amino acid residues long, representing motifs between two consecutive regular secondary structures, has been derived from protein structures presenting less than 95 % sequence identity. Statistical analyses of occurrences of conformations and residues revealed length-dependen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2826

    authors: Wojcik J,Mornon JP,Chomilier J

    更新日期:1999-06-25 00:00:00

  • Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.

    abstract::The role of an 18-residue ion-pair network, that is present in the glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus, in conferring stability to other, less stable homologous enzymes, has been studied by introducing four new charged amino acid residues into the subunit interface of glutam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2779

    authors: Lebbink JH,Knapp S,van der Oost J,Rice D,Ladenstein R,de Vos WM

    更新日期:1999-06-04 00:00:00

  • Prediction of functionally important residues based solely on the computed energetics of protein structure.

    abstract::Catalytic and other functionally important residues in proteins can often be mutated to yield more stable proteins. Many of these residues are charged residues that are located in electrostatically unfavorable environments. Here it is demonstrated that because continuum electrostatics methods can identify these destab...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5009

    authors: Elcock AH

    更新日期:2001-09-28 00:00:00

  • The crystal structure of C2a, the catalytic fragment of classical pathway C3 and C5 convertase of human complement.

    abstract::The multi-domain serine protease C2 provides the catalytic activity for the C3 and C5- convertases of the classical and lectin pathways of complement activation. Formation of these convertases requires the Mg(2+)-dependent binding of C2 to C4b, and the subsequent cleavage of C2 by C1s or MASP2, respectively. The C-ter...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.039

    authors: Krishnan V,Xu Y,Macon K,Volanakis JE,Narayana SV

    更新日期:2007-03-16 00:00:00

  • Mycobacterium tuberculosis Hsp16.3 nonamers are assembled and re-assembled via trimer and hexamer intermediates.

    abstract::Hsp16.3, a small heat shock protein from Mycobacterium tuberculosis proposed to form specific trimer-of-trimers structures, acts as a molecular chaperone in vitro. The assembly and re-assembly mechanisms of this oligomeric protein were studied and compared using in vitro transcription/translation and denaturization/re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00018-4

    authors: Abulimiti A,Fu X,Gu L,Feng X,Chang Z

    更新日期:2003-02-28 00:00:00

  • Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus.

    abstract::Staphylococcus aureus A70 produces a heat-stable bacteriocin designated aureocin A70. Aureocin A70 is encoded within a mobilisable 8 kb plasmid, pRJ6, and is active against Listeria monocytogenes. Experiments of transposition mutagenesis and gene cloning had shown that aureocin A70 production and immunity were associa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4885

    authors: Netz DJ,Sahl HG,Marcelino R,dos Santos Nascimento J,de Oliveira SS,Soares MB,do Carmo de Freire Bastos M

    更新日期:2001-08-31 00:00:00

  • Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase.

    abstract::Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and its complexes with panose, maltotetraose and isopanose were determined at resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two carbohydrates are substrates of this enzyme, a deactivated mutant at the catalytic residue Glu35...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01402-x

    authors: Hondoh H,Kuriki T,Matsuura Y

    更新日期:2003-02-07 00:00:00

  • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI.

    abstract::The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.053

    authors: Wood KM,Daniels LE,Halford SE

    更新日期:2005-07-08 00:00:00

  • BolA inhibits cell elongation and regulates MreB expression levels.

    abstract::The morphogene bolA is a general stress response gene in Escherichia coli that induces a round morphology when overexpressed. Results presented in this report show that increased BolA levels can inhibit cell elongation mechanisms. MreB polymerization is crucial for the bacterial cell cytoskeleton, and this protein is ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.12.026

    authors: Freire P,Moreira RN,Arraiano CM

    更新日期:2009-02-06 00:00:00

  • Importance of the 5 S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli.

    abstract::A specific complex of 5 S rRNA and several ribosomal proteins is an integral part of ribosomes in all living organisms. Here we studied the importance of Escherichia coli genes rplE, rplR and rplY, encoding 5 S rRNA-binding ribosomal proteins L5, L18 and L25, respectively, for cell growth, viability and translation. U...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.097

    authors: Korepanov AP,Gongadze GM,Garber MB,Court DL,Bubunenko MG

    更新日期:2007-03-02 00:00:00

  • The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction.

    abstract::Polycystin-1 is a large membrane-associated protein that interacts with polycystin-2 in the primary cilia of renal epithelial cells to form a mechanosensitive ion channel. Bending of the cilia induces calcium flow into the cells, mediated by the polycystin complex. Antibodies to polycystin-1 and polycystin-2 abolish t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.008

    authors: Forman JR,Qamar S,Paci E,Sandford RN,Clarke J

    更新日期:2005-06-17 00:00:00

  • Crystallization and preliminary crystallographic data of the Fab fragment of an anti-phenylalanine hydroxylase monoclonal antibody.

    abstract::Two crystal habits, one rod shaped and the other square prismatic, of the Fab fragment of a monoclonal anti-phenylalanine hydroxylase antibody have been grown using the method of vapour phase diffusion against polyethylene glycol 6000. The square prisms diffract to better than 2.8 A, belong to the space group P1 and h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90121-4

    authors: Guddat LW,Cowan SW,Machin KJ,Isaacs NW,Cotton RG

    更新日期:1985-11-20 00:00:00

  • The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.

    abstract::Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completene...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3404

    authors: Kawano Y,Kumagai T,Muta K,Matoba Y,Davies J,Sugiyama M

    更新日期:2000-01-28 00:00:00

  • Functional hydration and conformational gating of proton uptake in cytochrome c oxidase.

    abstract::Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel, a 25-A-long cavity, provides the principal pathway for the uptake of chemical and pumped protons. A water chain is thought to mediate the relay of protons via a Grotthuss mechanism through the D...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.02.042

    authors: Henry RM,Yu CH,Rodinger T,Pomès R

    更新日期:2009-04-17 00:00:00

  • Interaction of monomeric and dimeric kinesin with microtubules.

    abstract::The binding stoichiometry of kinesin to microtubules was determined using several biochemical and biophysical approaches (chemical crosslinking, binding assays, scanning transmission electron microscopy (STEM), image reconstruction, and X-ray scattering). The results show that each tubulin dimer associates with one ki...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1503

    authors: Thormählen M,Marx A,Müller SA,Song Y,Mandelkow EM,Aebi U,Mandelkow E

    更新日期:1998-02-06 00:00:00

  • Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

    abstract::Foot-and-mouth disease virus (FMDV), a non-enveloped picornavirus, is sensitive to acidic conditions. At pH values below 7 the icosahedral virus capsid, formed from 60 copies of a protomer containing four polypeptides (VP1 to 4), dissociates into 12 pentamers, releasing the viral RNA. Evidence suggests that this acid ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1418

    authors: van Vlijmen HW,Curry S,Schaefer M,Karplus M

    更新日期:1998-01-16 00:00:00