Abstract:
:Replication of bacteriophage phi 29 DNA initiates at either end of its linear double-stranded DNA molecule and proceeds by a strand-displacement mechanism. In the present paper we have used an in vitro phi 29 DNA replication system to analyse by electron microscopy the replicative intermediates produced at different reaction times. Two types of replicative intermediates were observed: type I (full-length double-stranded phi 29 DNA molecules with one or more single-stranded DNA branches) and type II (full-length phi 29 DNA molecules formed by a double-stranded DNA portion of variable length from one end plus a single-stranded DNA portion spanning to the other end). Thus, the types of replicative intermediates produced in vivo were also formed in the in vitro phi 29 DNA replication system. Analysis of type I intermediates indicated that initiation of DNA replication occurs preferentially at both ends of the same DNA template, in a non-simultaneous manner. Type II intermediates appeared as early as two minutes after the reaction started, well before unit-length single-stranded phi 29 DNA molecules were synthesized. In addition, replication of recombinant phi 29 DNA templates lacking terminal protein at one end did not produce type II intermediates and led to an accumulation of full-length single-stranded phi 29 DNA molecules. These two observations strongly suggest that type II intermediates appear when two growing DNA chains, running from opposite ends, merge.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Gutiérrez C,Sogo JM,Salas Mdoi
10.1016/0022-2836(91)90589-xsubject
Has Abstractpub_date
1991-12-20 00:00:00pages
983-94issue
4eissn
0022-2836issn
1089-8638pii
0022-2836(91)90589-Xjournal_volume
222pub_type
杂志文章abstract::Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H+ and/or Na+) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH+-PPase), the VrH+-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:2019-04-05 00:00:00
abstract::Crystals have been obtained of threonyl-tRNA synthetase from the extreme thermophile Thermus thermophilus using sodium formate as a precipitant. The crystals are very stable and diffract to at least 2.4 A. The crystals belong to space group P2(1)2(1)2(1) with cell parameters a = 61.4 A, b = 156.1 A, c = 177.3 A. ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(90)90337-L
更新日期:1990-08-20 00:00:00
abstract::One to four alanines were inserted by site-directed mutagenesis at three different locations within the alpha-helix comprising residues 39 to 50 in bacteriophage T4 lysozyme. All insertion mutants were correctly folded and catalytically active although the insertions led to a thermal destabilization by 1.1 to 4.2 kcal...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1195
更新日期:1994-02-25 00:00:00
abstract::We have developed a self-assembly system for nucleosome arrays in which recombinant, post-translationally unmodified histone proteins are combined with DNA of defined-sequence to form chromatin higher-order structure. The nucleosome arrays obtained are highly homogeneous and sediment at 53S when maximally folded in 1m...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(03)00025-1
更新日期:2003-03-14 00:00:00
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
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更新日期:2002-05-17 00:00:00
abstract::We demonstrate that RecA protein-coated, short single-stranded DNA probes paired with a specific homologous DNA sequence in a linear duplex target molecule and accurately targeted the selected DNA sequence. RecA protein-coated complementary ssDNA probes were reacted with linear duplexes, and the homologously paired mo...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1431
更新日期:1993-08-05 00:00:00
abstract::The crystal structure of the glutamine-binding protein (GlnBP) from Escherichia coli in a ligand-free "open" conformational state has been determined by isomorphous replacement methods and refined to an R-value of 21.4% at 2.3 A resolution. There are two molecules in the asymmetric unit, related by pseudo 4-fold screw...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
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更新日期:1996-09-20 00:00:00
abstract::The CCAAT/enhancer-binding protein beta (C/EBPbeta) is a critical transcription factor that regulates gene expression during numerous biological processes, including differentiation, metabolism, homeostasis, proliferation, tumorigenesis, inflammation, and apoptosis. In this study, interactions between C/EBPbeta and ei...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.06.055
更新日期:2009-08-28 00:00:00
abstract::While the disulfide bridge is highly conserved within the immunoglobulin fold, a few antibody variable domains lack one of the essential cysteine residues. In the levan binding antibody ABPC48 one of the essential cysteine residues (Cys H92) of the heavy chain variable domain is replaced by tyrosine. We expressed scFv...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0726
更新日期:1997-01-17 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1995.0465
更新日期:1995-09-01 00:00:00
abstract::Nitrite reductase from Pseudomonas aeruginosa (EC 1.9.3.2), a redox enzyme synthesized by the bacterium grown in the presence of nitrate, is a soluble dimer of two identical subunits of 60 kDa, each containing one c and one d1 haem as prosthetic groups. A new crystal from of the Ps. aeruginosa nitrite reductase in the...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1659
更新日期:1994-10-21 00:00:00
abstract::The solvent-accessible surface area (As) of 46 monomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. The As of these proteins can be determined to within 1 to 2% and that of their individual residues to within 10 to 20%. The As values of proteins are corre...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(87)90038-6
更新日期:1987-08-05 00:00:00
abstract::Haloacid dehalogenases catalyse the removal of halides from organic haloacids and are of interest for bioremediation and for their potential use in the synthesis of industrial chemicals. We present the crystal structure of the homodimer DehI from Pseudomonas putida strain PP3, the first structure of a group I alpha-ha...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2008.02.035
更新日期:2008-04-18 00:00:00
abstract::Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:2019-09-06 00:00:00
abstract::Gap junction channels are intercellular channels that form by docking the extracellular loops of connexin protein subunits. While the structure and function of gap junctions as intercellular channels have been characterized using different techniques, the physics of the inter-connexin interaction remain unknown. Moreo...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2011.07.013
更新日期:2011-09-09 00:00:00
abstract::The group I intron from Tetrahymena thermophila is able to catalyze its own excision from a precursor RNA. The intron recognizes the splice sites through an intron-encoded sequence called the internal guide sequence, or IGS. The 5' and 3' exons are thought to align on the IGS and form a pseudoknot structure consisting...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1541
更新日期:1993-10-20 00:00:00
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
更新日期:1983-12-25 00:00:00
abstract::An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1991-10-05 00:00:00
abstract::The eukaryotic 26S proteasome is a large multisubunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle and the 20S core particle. Most substrates are first covalently modified by ubiquitin, which the...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
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journal_title:Journal of molecular biology
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abstract::Single crystals of the RNase inhibitor from porcine liver have been obtained from 30 to 34% saturated ammonium sulphate solutions at pH 6.0 to 7.2, containing 20 mM dithiothreitol, at room temperature over a period of two to three weeks. Because the inhibitor contains 30 1/2-cystinyl residues, all of which occur in th...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1299
更新日期:1993-05-20 00:00:00
abstract::The 1.94 A resolution three-dimensional structure of oxidized horse heart cytochrome c has been elucidated and refined to a final R-factor of 0.17. This has allowed for a detailed assessment of the structural features of this protein, including the presence of secondary structure, hydrogen-bonding patterns and heme ge...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(90)90200-6
更新日期:1990-07-20 00:00:00
abstract::Site-directed mutagenesis has been used to change individual amino acids of the larvicidal 27,000 Mr delta-endotoxin of Bacillus thuringiensis var. israelensis. Basic and acidic residues have been systematically replaced by alanine, and the resulting mutant polypeptides analysed for cytolytic and larvicidal activity, ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1988-08-05 00:00:00
abstract::We have examined the nuclease sensitivity of the 5' flanking region of the rabbit beta 1 globin gene in bone marrow nuclei and in supercoiled plasmids. A DNase I hypersensitive site was found about 100 base-pairs 5' to the cap site in bone marrow nuclei. S1 nuclease can introduce a specific double-strand cut in the DN...
journal_title:Journal of molecular biology
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doi:10.1016/0022-2836(85)90373-0
更新日期:1985-07-20 00:00:00
abstract::The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA that resides in the HDV genome and regulates its replication. The native fold of the ribozyme is complex, having two pseudoknots. Earlier work implicated four non-native pairings in slowing pseudoknot formation: Alt 1, Alt 2, Alt 3, and Alt P1. The goal o...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.05.071
更新日期:2004-08-13 00:00:00
abstract::Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP...
journal_title:Journal of molecular biology
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更新日期:2003-02-28 00:00:00
abstract::An analysis by electron microscopy in amorphous ice and X-ray diffraction of four types of three-dimensional crystals of adenovirus fibre is presented. Fibre from adenovirus type 2 (Ad2) crystallizes in two forms depending on whether it is native or cleaved near the N terminus at Tyr17. Fibre from Ad5 also crystallize...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1990-10-20 00:00:00
abstract::Members of the Bcl-2 protein family regulate apoptosis by controlling the release of apoptogenic proteins such as cytochrome c from the mitochondrial intermembrane space. Proapoptotic members induce release by increasing outer membrane permeability, while antiapoptotic members prevent this. The activity of Bcl-2 prote...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2003.10.028
更新日期:2004-01-02 00:00:00
abstract::The accessory gene regulatory (agr) operon of the opportunistic human pathogen Staphylococcus aureus is a prime pathogenesis factor in this bacterium. The agr operon consists of two transcription units, RNAII and RNAIII, which are transcribed from divergent promoters, P2 and P3, respectively. RNAII encodes a quorum-se...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:2011-10-07 00:00:00
abstract::The nuclear receptors peroxisome proliferator-activated receptors (PPARs) are known for their critical role in the metabolic syndrome. Here, we show that they are direct regulators of the family of pyruvate dehydrogenase kinase (PDK) genes, whose products act as metabolic homeostats in sensing hunger and satiety level...
journal_title:Journal of molecular biology
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doi:10.1016/j.jmb.2007.06.091
更新日期:2007-09-14 00:00:00