Cloning, overexpression and purification of the terminase proteins gp16 and gp17 of bacteriophage T4. Construction of a defined in-vitro DNA packaging system using purified terminase proteins.

Abstract:

:Terminases of double-stranded DNA bacteriophages are required for packaging and generation of terminii in replicated concatemeric DNA molecules. Genetic evidence suggests that these functions in phage T4 are carried out by the products of genes 16 and 17. We cloned these T4 genes into a heat-inducible cI repressor-lambda PL promoter vector system, and overexpressed them in Escherichia coli. We developed an in-vitro DNA packaging system, which, consistent with the genetic data, shows an absolute requirement for the terminase proteins. The overexpressed terminase proteins gp16 and gp17 appear to form a specific complex and an ATP binding site is present in the gp17 molecule. We purified the terminase proteins either as individual gp16 or gp17 proteins, or as a gp16-gp17 complex. The gp16 function of the terminase complex is dispensable for packaging mature DNA, whereas gp17 is essential for packaging DNA under any condition tested. We constructed a defined in-vitro DNA packaging system with the purified terminase proteins, purified proheads and a DNA-free phage completion gene products extract. All the components of this system can be stored at -90 degrees C without loss of packaging activity. The terminase proteins, therefore, may serve as useful reagents for mechanistic studies on DNA packaging, as well as to develop T4 as a packaging-cloning vector.

journal_name

J Mol Biol

authors

Rao VB,Black LW

doi

10.1016/0022-2836(88)90537-2

subject

Has Abstract

pub_date

1988-04-05 00:00:00

pages

475-88

issue

3

eissn

0022-2836

issn

1089-8638

pii

0022-2836(88)90537-2

journal_volume

200

pub_type

杂志文章
  • Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins.

    abstract::The bacterial immunity proteins Im7 and Im9 fold with mechanisms of different kinetic complexity. Whilst Im9 folds in a two-state transition at pH 7.0 and 10 degrees C, Im7 populates an on-pathway intermediate under these conditions. In order to assess the role of sequence versus topology in the folding of these prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01249-4

    authors: Friel CT,Capaldi AP,Radford SE

    更新日期:2003-02-07 00:00:00

  • A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.

    abstract::The origin of metal ion selectivity by members of the SmtB/ArsR family of bacterial metal-sensing transcriptional repressors and the mechanism of negative allosteric regulation of DNA binding is poorly understood. Here, we report that two homologous zinc sensors, Staphylococcus aureus CzrA and cyanobacterial SmtB, are...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.007

    authors: Eicken C,Pennella MA,Chen X,Koshlap KM,VanZile ML,Sacchettini JC,Giedroc DP

    更新日期:2003-10-31 00:00:00

  • The preprotein translocase of the inner mitochondrial membrane: evolutionary conservation of targeting and assembly of Tim17.

    abstract::The preprotein translocase of the inner mitochondrial membrane has only been described in Saccharomyces cerevisiae to date. We report that the essential subunit Tim17 is highly conserved in evolution. The targeting and assembly of yeast Tim17 as well as that of human and Drosophila melanogaster Tim17 were characterize...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0522

    authors: Bömer U,Rassow J,Zufall N,Pfanner N,Meijer M,Maarse AC

    更新日期:1996-10-04 00:00:00

  • Evidence that the KH RNA-binding domains influence the action of the E. coli NusA protein.

    abstract::The NusA transcription elongation protein, which binds RNA, contains sequences corresponding to the S1 and KH classes of identified RNA binding domains. An essential function in E. coli, NusA is also one of the host factors required for action of the N transcription antitermination protein of lambda. Tandem KH domains...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00238-3

    authors: Zhou Y,Mah TF,Greenblatt J,Friedman DI

    更新日期:2002-05-17 00:00:00

  • Protein S20 binds two 16S rRNA sites as assembly is initiated.

    abstract::Ribosomal protein S20 is a primary binding protein that bridges the 5' domain and the 3' minor domain of the 16S ribosomal RNA (rRNA) in the 30S ribosomal subunit. Using time-dependent dimethyl sulfate modification, we have determined that as it is bound to 16S rRNA, protein S20 causes rapid protection of bases A246, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.06.047

    authors: Hedrick EG,Hill WE

    更新日期:2010-08-20 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

  • A single amino acid substitution in the C terminus of OmpR alters DNA recognition and phosphorylation.

    abstract::In bacteria and lower eukaryotes, adaptation to changes in the environment is often mediated by two-component regulatory systems. Such systems provide the basis for chemotaxis, nitrogen and phosphate regulation and adaptation to osmotic stress, for example. In Escherichia coli, the sensor kinase EnvZ detects a change ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3809

    authors: Tran VK,Oropeza R,Kenney LJ

    更新日期:2000-06-23 00:00:00

  • PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription.

    abstract::The NtrC-family PhhR protein of Pseudomonas putida is involved in the control of the metabolism of aromatic amino acids, and it is a dual regulatory protein. When PhhR acts as an activator, it stimulates transcription from its cognate promoters with RNA polymerase/sigma(70) rather than with sigma(54), as is the case f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.09.045

    authors: Herrera MC,Krell T,Zhang X,Ramos JL

    更新日期:2009-12-04 00:00:00

  • Nascent β Structure in the Elongated Hydrophobic Region of a Gerstmann-Sträussler-Scheinker PrP Allele.

    abstract::Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrPC). Gerstmann-Sträussler-Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human Pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.04.027

    authors: Fu ZL,Holmes PC,Westaway D,Sykes BD

    更新日期:2019-06-28 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

  • The 80's loop (residues 78 to 85) is important for the differential activity of retroviral proteases.

    abstract::The abundance of structural data available for retroviral proteases affords a unique opportunity to investigate structure activity relationships. Our approach attempts to genetically engineer an HIV (human immunodeficiency virus)-1 protease that is functionally equivalent to the HIV-2 and the SIV (simian immunodeficie...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0891

    authors: Stebbins J,Towler EM,Tennant MG,Deckman IC,Debouck C

    更新日期:1997-04-04 00:00:00

  • Molecular and functional dissection of a putative RNA-binding region in yeast mitochondrial leucyl-tRNA synthetase.

    abstract::Aminoacylation and editing by leucyl-tRNA synthetases (LeuRS) require migration of the tRNA acceptor stem end between the canonical aminoacylation core and a separate domain called CP1 that is responsible for amino acid editing. The LeuRS CP1 domain can also support group I intron RNA splicing in the yeast mitochondri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.051

    authors: Nawaz MH,Pang YL,Martinis SA

    更新日期:2007-03-23 00:00:00

  • Structure determination of the three disulfide bond isomers of alpha-conotoxin GI: a model for the role of disulfide bonds in structural stability.

    abstract::The three possible disulfide bonded isomers of alpha-conotoxin GI have been selectively synthesised and their structures determined by 1H NMR spectroscopy. alpha-Conotoxin GI derives from the venom of Conus geographus and is a useful neuropharmacological tool as it selectively binds to the nicotinic acetylcholine rece...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1701

    authors: Gehrmann J,Alewood PF,Craik DJ

    更新日期:1998-05-01 00:00:00

  • Coordinated transcriptional regulation of Hspa1a gene by multiple transcription factors: crucial roles for HSF-1, NF-Y, NF-κB, and CREB.

    abstract::Although the transcript level of inducible heat shock protein 70.3 (Hsp70.3, also known as Hspa1a) is altered in various disease states, its transcriptional regulation remains incompletely understood. Here, we systematically analyzed the Hspa1a promoter to identify major cis elements and transcription factors that may...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.09.008

    authors: Sasi BK,Sonawane PJ,Gupta V,Sahu BS,Mahapatra NR

    更新日期:2014-01-09 00:00:00

  • Reconstitution of selenocysteine incorporation reveals intrinsic regulation by SECIS elements.

    abstract::Selenoproteins are present in all three domains of life and are responsible for a major part of a cell's antioxidant defense against reactive oxygen species. Synthesis of selenoproteins requires the decoding of a UGA codon as selenocysteine (Sec) instead of translation termination. Sec is incorporated into the growing...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.04.016

    authors: Gupta N,DeMong LW,Banda S,Copeland PR

    更新日期:2013-07-24 00:00:00

  • Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase.

    abstract::An understanding of the structural basis for protein-protein interactions, and molecular recognition in general, requires complete characterization of binding energetics. Not only does this include quantification of the changes that occur in all of the thermodynamic parameters upon binding, including the enthalpy, ent...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0977

    authors: Baker BM,Murphy KP

    更新日期:1997-05-02 00:00:00

  • The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae.

    abstract::The Ri (root-inducing) plasmid in Agrobacterium rhizogenes and Ti (tumor-inducing) plasmid in Agrobacterium tumefaciens have provided the fundamental basis for the construction of plant vectors and transgenic plants. Recently, the determination of the first complete nucleotide sequence of the Ti plasmid (pTi-SAKURA) h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4488

    authors: Moriguchi K,Maeda Y,Satou M,Hardayani NS,Kataoka M,Tanaka N,Yoshida K

    更新日期:2001-03-30 00:00:00

  • The rate of polyQ-mediated aggregation is dramatically affected by the number and location of surrounding domains.

    abstract::The nine polyglutamine (polyQ) neurodegenerative diseases are caused in part by a gain-of-function mechanism involving protein misfolding, the deposition of β-sheet-rich aggregates and neuronal toxicity. While previous experimental evidence suggests that the polyQ-induced misfolding mechanism is context dependent, the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.09.014

    authors: Robertson AL,Bate MA,Buckle AM,Bottomley SP

    更新日期:2011-11-04 00:00:00

  • Dynamics of allostery in hemoglobin: roles of the penultimate tyrosine H bonds.

    abstract::The tyrosine residues adjacent to the C termini of the hemoglobin (Hb) subunits, alphaY140 and betaY145, are expected to play important structural roles, because the C termini are the loci of T-state quaternary salt-bridges, and because the tyrosine side-chains bridge the H and F helices via H bonds to the alphaV93 an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.006

    authors: Kneipp J,Balakrishnan G,Chen R,Shen TJ,Sahu SC,Ho NT,Giovannelli JL,Simplaceanu V,Ho C,Spiro TG

    更新日期:2006-02-17 00:00:00

  • Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism.

    abstract::Previous work used hydrogen exchange (HX) experiments in kinetic and equilibrium modes to study the reversible unfolding and refolding of cytochrome c (Cyt c) under native conditions. Accumulated results now show that Cyt c is composed of five individually cooperative folding units, called foldons, which unfold and re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.04.035

    authors: Krishna MM,Maity H,Rumbley JN,Lin Y,Englander SW

    更新日期:2006-06-23 00:00:00

  • Mediator Architecture and RNA Polymerase II Interaction.

    abstract::Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.01.028

    authors: Plaschka C,Nozawa K,Cramer P

    更新日期:2016-06-19 00:00:00

  • Zooming in on Transcription Preinitiation.

    abstract::Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotei...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.04.003

    authors: Gupta K,Sari-Ak D,Haffke M,Trowitzsch S,Berger I

    更新日期:2016-06-19 00:00:00

  • M-LDH serves as a regulatory subunit of the cytosolic substrate-channelling complex in vivo.

    abstract::Nucleoside diphosphate kinase A (NDPK-A) regulates the alpha1 isoform of the AMP-activated protein kinase (AMPK alpha1) selectively, independent of [AMP] and surrounding [ATP], by a process termed substrate channelling. Here, we show, using a range of empirically validated biochemical techniques, that the muscle form ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.05.081

    authors: Jovanović S,Jovanović A,Crawford RM

    更新日期:2007-08-10 00:00:00

  • Crystallization and preliminary X-ray analysis of human alpha-galactosidase A complex.

    abstract::Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22), the glycosylated lysosomal enzyme deficient in Fabry disease, has been crystallized as a complex with the inhibitor N-6-aminohexanoyl-alpha-D-galactopyranosylamine. The "hanging drop" method of vapor diffusion was used to grow crystals fr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1397

    authors: Murali R,Ioannou YA,Desnick RJ,Burnett RM

    更新日期:1994-06-17 00:00:00

  • Crystal structure of the C-terminal domain of S.cerevisiae eIF5.

    abstract::eIF5, a GTPase-activating protein (GAP) specific for eIF2, plays a critical role in pre-initiation complex assembly and correct AUG selection during eukaryotic translation initiation. eIF5 is involved in the formation of the multifactor complex (MFC), an important intermediate of the 43S pre-initiation complex. The C-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.03.037

    authors: Wei Z,Xue Y,Xu H,Gong W

    更新日期:2006-05-26 00:00:00

  • Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA.

    abstract::Here, we describe a structure-based approach to reduce the size of an antigen protein for a subunit vaccine. Our method consists of (i) determining the three-dimensional structure of an antigen, (ii) identifying protective epitopes, (iii) generation of an antigen fragment that contains the protective epitope, and (iv)...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.066

    authors: Koide S,Yang X,Huang X,Dunn JJ,Luft BJ

    更新日期:2005-07-08 00:00:00

  • Architecture and flexibility of the yeast Ndc80 kinetochore complex.

    abstract::Kinetochores mediate microtubule-chromosome attachment and ensure accurate segregation of sister chromatids. The highly conserved Ndc80 kinetochore complex makes direct contacts with the microtubule and is essential for spindle checkpoint signaling. It contains a long coiled-coil region with globular domains at each e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.077

    authors: Wang HW,Long S,Ciferri C,Westermann S,Drubin D,Barnes G,Nogales E

    更新日期:2008-11-21 00:00:00

  • Exploring conformational space with a simple lattice model for protein structure.

    abstract::We present a low resolution lattice model for which we can exhaustively generate all possible compact backbone conformations for small proteins. Using simple structural and energetic criteria, for a variety of proteins, we can select for lattice structures that have significant similarities with their known native str...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90040-x

    authors: Hinds DA,Levitt M

    更新日期:1994-11-04 00:00:00

  • Analysis of the CYT-18 protein binding site at the junction of stacked helices in a group I intron RNA by quantitative binding assays and in vitro selection.

    abstract::The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active structure of the intron RNA. Previous studies showed that CYT-18 binds with high affinity to the P4-P6 domain of the catalytic core and that there is...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0439

    authors: Saldanha R,Ellington A,Lambowitz AM

    更新日期:1996-08-09 00:00:00

  • Crystal structure of rat intestinal fatty-acid-binding protein. Refinement and analysis of the Escherichia coli-derived protein with bound palmitate.

    abstract::Rat intestinal fatty-acid-binding protein (I-FABP) is a small (15,124 Mr) cytoplasmic polypeptide that binds long-chain fatty acids in a non-covalent fashion. I-FABP is a member of a family of intracellular binding proteins that are thought to participate in the uptake, transport and/or metabolic targeting of hydropho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90392-6

    authors: Sacchettini JC,Gordon JI,Banaszak LJ

    更新日期:1989-07-20 00:00:00