Coliphage P2 late control gene ogr. DNA sequence and product identification.

Abstract:

:The bacteriophage P2 late control gene ogr was cloned and precisely localized by deletion analysis in vitro. The DNA sequence of the ogr gene containing the ogr1 mutation was determined. The sequence translates into a basic protein of a molecular weight of 8300. Plasmids overproducing the ogr gene product were constructed, and the ogr gene product was identified by polyacrylamide gel electrophoresis.

journal_name

J Mol Biol

authors

Birkeland NK,Lindquist BH

doi

10.1016/0022-2836(86)90170-1

subject

Has Abstract

pub_date

1986-04-05 00:00:00

pages

487-90

issue

3

eissn

0022-2836

issn

1089-8638

pii

0022-2836(86)90170-1

journal_volume

188

pub_type

杂志文章
  • A model for the mechanism of polymerase translocation.

    abstract::A general mechanism for polymerase translocation is elaborated. The central feature of this mechanism is that a rapid translocational equilibrium is established after each cycle of nucleoside monophosphate incorporation such that the polymerase distributes itself by diffusional sliding between all accessible positions...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0707

    authors: Guajardo R,Sousa R

    更新日期:1997-01-10 00:00:00

  • Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.

    abstract::AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.04.026

    authors: Nishitani Y,Aono R,Nakamura A,Sato T,Atomi H,Imanaka T,Miki K

    更新日期:2013-08-09 00:00:00

  • Structure of complexes between a major protein of heterogeneous nuclear ribonucleoprotein particles and polyribonucleotides.

    abstract::We have investigated the structure of complexes formed between a series of poly(A)n (n = 30 to 480) and HD40 (helix-destabilizing protein, molecular weight of 40,000), the major protein component of 30 S heterogeneous nuclear ribonucleoprotein particles (hnRNP) from the brine shrimp Artemia salina. Protein HD40 is sim...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90039-6

    authors: Thomas JO,Glowacka SK,Szer W

    更新日期:1983-12-25 00:00:00

  • Translocation of histone proteins across lipid bilayers and Mycoplasma membranes.

    abstract::We show that the three core histones H2A, H3 and H4 can transverse lipid bilayers of large unilamellar vesicles (LUVs) and multilamellar vesicles (MLVs). In contrast, the histone H2B, although able to bind to the liposomes, fails to penetrate the unilamellar and the multilamellar vesicles. Translocation across the lip...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.10.046

    authors: Rosenbluh J,Hariton-Gazal E,Dagan A,Rottem S,Graessmann A,Loyter A

    更新日期:2005-01-14 00:00:00

  • DNA looping alters local DNA conformation during transcription.

    abstract::The effect of protein-mediated DNA looping on local DNA conformation during active transcription was studied using the lac repressor-operator system. Our results suggest that lac repressor-mediated DNA looping within a plasmid DNA molecule containing two lac repressor binding sequences in vivo effectively separates pl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90658-s

    authors: Wu HY,Liu LF

    更新日期:1991-06-20 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

  • Specific tyrosylation of the bulky tRNA-like structure of brome mosaic virus RNA relies solely on identity nucleotides present in its amino acid-accepting domain.

    abstract::Residues specifying aminoacylation by yeast tyrosyl-tRNA synthetase (TyrRS) of the tRNA-like structure present at the 3'-end of brome mosaic virus (BMV) RNA were determined by the in vitro approach using phage T7 transcripts. They correspond to nucleotides equivalent to base-pair C1-G72 and discriminator base A73 in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4654

    authors: Fechter P,Giegé R,Rudinger-Thirion J

    更新日期:2001-06-01 00:00:00

  • Mechanochemistry of a viral DNA packaging motor.

    abstract::The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage phi29 virus capsid. On the basis of the results of single-molecule experimental studies, we propose a push and roll mechanism to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while rotati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.002

    authors: Yu J,Moffitt J,Hetherington CL,Bustamante C,Oster G

    更新日期:2010-07-09 00:00:00

  • Stochastic modeling and optimization of phage display.

    abstract::Phage display, SELEX and other methods of combinatorial chemistry have become very popular means of finding ligands with high affinities to given targets. Despite their success, they suffer from numerous sources of error and bias, such as very low initial concentrations of species, non-specific binding, and the sampli...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1555

    authors: Levitan B

    更新日期:1998-04-10 00:00:00

  • Novel Insights into Cell Entry of Emerging Human Pathogenic Arenaviruses.

    abstract::Viral hemorrhagic fevers caused by emerging RNA viruses of the Arenavirus family are among the most devastating human diseases. Climate change, global trade, and increasing urbanization promote the emergence and re-emergence of these human pathogenic viruses. Emerging pathogenic arenaviruses are of zoonotic origin and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.04.026

    authors: Fedeli C,Moreno H,Kunz S

    更新日期:2018-06-22 00:00:00

  • The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation.

    abstract::Nebulin, a giant modular protein from muscle, is thought to act as a molecular ruler in sarcomere assembly. The C terminus of nebulin, located in the sarcomere Z-disk, comprises an SH3 domain, a module well known for its role in protein/protein interactions. SH3 domains are known to recognize proline-rich ligands, whi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5312

    authors: Politou AS,Spadaccini R,Joseph C,Brannetti B,Guerrini R,Helmer-Citterich M,Salvadori S,Temussi PA,Pastore A

    更新日期:2002-02-15 00:00:00

  • Identifying functionally important conformational changes in proteins: activation of the yeast α-factor receptor Ste2p.

    abstract::We have developed a procedure in which disulfide cross-links are used to identify regions of proteins that undergo functionally important intramolecular motion. The approach was applied to the identification of disulfide bonds that stabilize the active state of the yeast α-mating pheromone receptor Ste2p, a member of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.02.024

    authors: Taslimi A,Mathew E,Celić A,Wessel S,Dumont ME

    更新日期:2012-05-18 00:00:00

  • Crystal structure of the molecular chaperone HscA substrate binding domain complexed with the IscU recognition peptide ELPPVKIHC.

    abstract::HscA, a specialized bacterial Hsp70-class molecular chaperone, interacts with the iron-sulfur cluster assembly protein IscU by recognizing a conserved LPPVK sequence motif. We report the crystal structure of the substrate-binding domain of HscA (SBD, residues 389-616) from Escherichia coli bound to an IscU-derived pep...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.025

    authors: Cupp-Vickery JR,Peterson JC,Ta DT,Vickery LE

    更新日期:2004-09-24 00:00:00

  • Defining the requirements for an antibody epitope on influenza virus neuraminidase: how tolerant are protein epitopes?

    abstract::To determine the conformational requirements for antibody recognition and extent of flexibility within a protein epitope, a chimeric influenza A virus neuraminidase (NA) has been constructed in which five discontinuous polypeptide segments from a subtype N9 NA, which comprise the monoclonal antibody NC41 epitope, have...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1025

    authors: Nuss JM,Air GM

    更新日期:1994-01-14 00:00:00

  • Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses.

    abstract::A detailed phylogenetic analysis for mammalian members of the family Herpesviridae, based on molecular sequences is reported. Sets of encoded amino acid sequences were collected for eight well conserved genes that are common to mammalian herpesviruses. Phylogenetic trees were inferred from alignments of these sequence...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0152

    authors: McGeoch DJ,Cook S,Dolan A,Jamieson FE,Telford EA

    更新日期:1995-03-31 00:00:00

  • Direct phage to intrabody screening (DPIS): demonstration by isolation of cytosolic intrabodies against the TES1 site of Epstein Barr virus latent membrane protein 1 (LMP1) that block NF-kappaB transactivation.

    abstract::The expression of intracellular antibodies (intrabodies) in eukaryotic cells has provided a powerful tool to manipulate microbial and cellular signaling pathways in a highly precise manner. However, there have been several technical issues that have restricted their more widespread use. In particular, single-chain ant...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.073

    authors: Gennari F,Mehta S,Wang Y,St Clair Tallarico A,Palu G,Marasco WA

    更新日期:2004-01-02 00:00:00

  • Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.

    abstract::Biogenesis of β-barrel membrane proteins is a complex, multistep, and as yet incompletely characterized process. The bacterial porin family is perhaps the best-studied protein family among β-barrel membrane proteins that allows diffusion of small solutes across the bacterial outer membrane. In this study, we have iden...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.02.043

    authors: Naveed H,Jimenez-Morales D,Tian J,Pasupuleti V,Kenney LJ,Liang J

    更新日期:2012-05-25 00:00:00

  • Conformational isomers of a class II MHC-peptide complex in solution.

    abstract::A number of kinetic measurements of peptide dissociation from class II MHC-peptide complexes provide compelling evidence for the existence of conformational isomers in solution. There is evidence that T-lymphocytes can distinguish such isomers. However, virtually nothing is known about the structure of these isomers. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2463

    authors: Schmitt L,Boniface JJ,Davis MM,McConnell HM

    更新日期:1999-02-12 00:00:00

  • Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

    abstract::The folding of multidomain proteins often proceeds in a hierarchical fashion with individual domains folding independent of one another. A large single-domain protein, however, can consist of multiple modules whose folding may be autonomous or interdependent in ways that are unclear. We used coarse-grained simulations...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.007

    authors: Hills RD Jr,Brooks CL 3rd

    更新日期:2008-10-03 00:00:00

  • The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin.

    abstract::The Ser/Thr kinase CK2 (former name: casein kinase 2) is a heterotetrameric enzyme composed of two catalytic chains (CK2alpha) attached to a dimer of noncatalytic subunits. Together with the cyclin-dependent kinases and the mitogen-activated protein kinases, CK2alpha belongs to the CMGC family of the eukaryotic protei...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.01.008

    authors: Raaf J,Klopffleisch K,Issinger OG,Niefind K

    更新日期:2008-03-14 00:00:00

  • A thiol labelling competition experiment as a probe for sidechain packing in the kinetic folding intermediate of N-PGK.

    abstract::Protein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite this the developement of sidechain interactions during folding is not well understood. Here, the thiol-active reagent, dithio-nitrobenzoic acid (DTNB), is used to probe the exposure of the cysteine sidechain thiols in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.09.014

    authors: Cliff MJ,Alizadeh T,Jelinska C,Craven CJ,Staniforth RA,Waltho JP

    更新日期:2006-12-08 00:00:00

  • Experimental and theoretical studies of the effects of deoxyribose substitutions on the stability of the UUCG tetraloop.

    abstract::Experimental and theoretical thermodynamic studies of the consequences of 2'-hydroxyl substitution in the RNA UUCG tetraloop show distinct position dependence consistent with the diverse structural contexts of the four-loop ribose hydroxyls in this motif. The results suggest that even for simple substitutions, such as...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3547

    authors: Williams DJ,Hall KB

    更新日期:2000-03-17 00:00:00

  • E. coli transports aggregated proteins to the poles by a specific and energy-dependent process.

    abstract::Aggregation of proteins due to failure of quality control mechanisms is deleterious to both eukaryotes and prokaryotes. We found that in Escherichia coli, protein aggregates are delivered to the pole and form a large polar aggregate (LPA). The formation of LPAs involves two steps: the formation of multiple small aggre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.009

    authors: Rokney A,Shagan M,Kessel M,Smith Y,Rosenshine I,Oppenheim AB

    更新日期:2009-09-25 00:00:00

  • Partitioning protein structures into domains: why is it so difficult?

    abstract::This analysis takes an in-depth look into the difficulties encountered by automatic methods for domain decomposition from three-dimensional structure. The analysis involves a multi-faceted set of criteria including the integrity of secondary structure elements, the tendency toward fragmentation of domains, domain boun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.05.060

    authors: Holland TA,Veretnik S,Shindyalov IN,Bourne PE

    更新日期:2006-08-18 00:00:00

  • Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation.

    abstract::Autonomously folding beta-hairpins have recently emerged as powerful tools for elucidating the origins of antiparallel beta-sheet folding preferences. Analysis of such model systems has suggested four potential sources of beta-sheet stability: (1) the conformational propensity of the loop segment that connects adjacen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4349

    authors: Espinosa JF,Muñoz V,Gellman SH

    更新日期:2001-02-23 00:00:00

  • Antibody-antigen interactions: contact analysis and binding site topography.

    abstract::We have analysed antigen-contacting residues and combining site shape in the antibody Fv and Fab crystal structures now available from the Protein Data Bank. Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be propo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0548

    authors: MacCallum RM,Martin AC,Thornton JM

    更新日期:1996-10-11 00:00:00

  • NMR characterization of full-length farnesylated and non-farnesylated H-Ras and its implications for Raf activation.

    abstract::The C terminus, also known as the hypervariable region (residues 166-189), of H-, N-, and K-Ras proteins has sequence determinants necessary for full activation of downstream effectors such as Raf kinase and PI-3 kinase as well as for the correct targeting of Ras proteins to lipid rafts and non-raft membranes. There i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.08.106

    authors: Thapar R,Williams JG,Campbell SL

    更新日期:2004-11-05 00:00:00

  • Analysis of the human Alu Ya-lineage.

    abstract::The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and fo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.016

    authors: Otieno AC,Carter AB,Hedges DJ,Walker JA,Ray DA,Garber RK,Anders BA,Stoilova N,Laborde ME,Fowlkes JD,Huang CH,Perodeau B,Batzer MA

    更新日期:2004-09-03 00:00:00

  • The role of the S-S bridge in retroviral protease function and virion maturation.

    abstract::Retroviral proteases are translated as a part of Gag-related polyproteins, and are released and activated during particle release. Mason-Pfizer monkey virus (M-PMV) Gag polyproteins assemble into immature capsids within the cytoplasm of the host cells; however, their processing occurs only after transport to the plasm...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.005

    authors: Zábranská H,Tůma R,Kluh I,Svatos A,Ruml T,Hrabal R,Pichová I

    更新日期:2007-02-02 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