Abstract：
:Quantitative measurements of local chromatin accessibility to DNase I in 15-day chicken embryo erythrocyte nuclei have been performed using a range of nuclease concentrations and real-time TaqMan PCR to monitor the loss of short ( approximately 80 bp) amplicons. At the beta-globin locus, well-established DNase I hypersensitive sites stand out against a background in which actively transcribed gene sequences (e.g., beta-adult and beta-hatching) are no more sensitive than the nearby constitutive heterochromatin that has previously been shown to form the 30-nm fibre structure. Similar observations were made at the lysozyme locus containing the active Gas41 gene and also at the GAPDH locus. We conclude that active genes are not continuously held in an open 'beads-on-a-string' configuration, but adopt a 30-nm-type structure most of the time. This implies that the compact nucleosomal supercoil re-forms in the wake of the polymerase complex.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Sapojnikova N,Thorne A,Myers F,Staynov D,Crane-Robinson Cdoi
10.1016/j.jmb.2008.12.048subject
Has Abstractpub_date
2009-02-20 00:00:00pages
290-9issue
2eissn
0022-2836issn
1089-8638pii
S0022-2836(08)01568-4journal_volume
386pub_type
杂志文章abstract：:A cytochrome c kinetic folding intermediate was studied by hydrogen exchange (HX) pulse labeling. Advances in the technique and analysis made it possible to define the structured and unstructured regions, equilibrium stability, and kinetic opening and closing rates, all at an amino acid-resolved level. The entire N-te...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2003.09.070
更新日期：2003-11-28 00:00:00
abstract：:The site-specific binding interaction of lac repressor with a symmetric operator sequence and of EcoRI endonuclease with its specific recognition site both exhibit a characteristic dependence of equilibrium binding constant (Kobs) on temperature, in which Kobs attains a relative maximum in the physiologically relevant...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90608-6
更新日期：1989-10-20 00:00:00
abstract：:The crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus KM1 has been solved by multiple isomorphous replacement. The enzyme is an alpha-amylase (family 13) with unique exo-amylolytic activity for glycosyltrehalosides. It cleaves the alpha-1,4 glycosidic b...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3977
更新日期：2000-08-11 00:00:00
abstract：:The structure of mucor pusillus pepsin (EC 3.4.23.6), the aspartic proteinase from Mucor pusillus, has been refined to a crystallographic R-factor of 16.2% at 2.0 A resolution. The positions of 2638 protein atoms, 221 solvent atoms and a sulphate ion have been determined with an estimated root-mean-square (r.m.s.) err...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：
更新日期：1993-03-05 00:00:00
abstract：:Filamentous bacteriophage assemble at the host membrane in a non-lytic process; the gene-3 minor coat protein (P3) is required for release from the membrane and subsequently, for recognition and infection of a new host. P3 contains at least three distinct domains: two N-terminal domains that mediate host recognition a...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(03)00950-1
更新日期：2003-09-26 00:00:00
abstract：:Allosteric communication between different subunits in metabolic enzyme complexes is of utmost physiological importance but only understood for few systems. We analyzed the structural basis of allostery in aminodeoxychorismate synthase (ADCS), which is a member of the family of glutamine amidotransferases and catalyze...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2019.05.021
更新日期：2019-07-12 00:00:00
abstract：:Muscle-specific kinase (MuSK) is a receptor tyrosine kinase expressed exclusively in skeletal muscle, where it is required for formation of the neuromuscular junction. MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. Here, we report the crystal structure of the agrin-responsive first and seco...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2006.09.019
更新日期：2006-12-01 00:00:00
abstract：:The chemotactic cytokine RANTES (Regulated on Activation, Normal T-cell Expressed and Secreted) is a potent chemoattractant and activator of a number of leukocytes, with a molecular mass of 8 kDa. Crystals of this protein have been grown from 100 mM sodium acetate buffer (pH 4.6) containing 200 mM magnesium acetate, w...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1605
更新日期：1994-09-30 00:00:00
abstract：:We describe a theoretical analysis of cation binding in the nucleosome, and in chromatin as it folds, using Manning's polyelectrolyte theory. The theory accounts remarkably well, even quantitatively, both for the interaction of histone charges with DNA in chromatin, and for the essential features of the folding proces...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(90)90081-V
更新日期：1990-02-20 00:00:00
abstract：:A gene encoding a major entomocidal polypeptide from Bacillus thuringiensis subspecies kyushuensis delta-endotoxin crystals (CytB) was cloned into Escherichia coli and sequenced. The deduced amino acid sequence gave a predicted molecular mass of 29,236 Da and showed 39% identity and 70% similarity with the 27,371 Da C...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1037
更新日期：1993-01-20 00:00:00
abstract：:The Mycobacterium leprae RuvA homologue (MlRuvA) was over-expressed in Escherichia coli and purified to homogeneity. The DNA-binding specificity and the functional interactions of MlRuvA with E. coli RuvB and RuvC (EcRuvB and EcRuvC) were examined using synthetic Holliday junctions. MlRuvA bound specifically to Hollid...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.4009
更新日期：2000-08-25 00:00:00
abstract：:A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear an...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.12.037
更新日期：2005-03-04 00:00:00
abstract：:Vascular smooth muscle cell hypertrophy and proliferation may participate in the pathophysiology of cardiovascular disease. The analysis of changes in gene expression in vascular smooth muscle cells is crucial to the understanding of the molecular biology of cardiovascular disease. An effective method for analysis of ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.1768
更新日期：1998-06-05 00:00:00
abstract：:It has been suggested that modified nucleosides of the xm5(s2)U(m)34-type restrict the wobble capacity of the base, and that their function is to prevent misreading in the third position of the codon in mixed codon family boxes that encode two different amino acids. In this study in Escherichia coli, the misreading in...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.2162
更新日期：1998-11-20 00:00:00
abstract：:Protein-primed DNA polymerases form a subgroup of the eukaryotic-type DNA polymerases family, also called family B or alpha-like. A multiple amino acid sequence alignment of this subgroup of DNA polymerases led to the identification of two insertions, TPR-1 and TPR-2, in the polymerisation domain. We showed previously...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(03)00788-5
更新日期：2003-08-22 00:00:00
abstract：:Thermodynamic analysis by differential scanning calorimetry shows that the folding/unfolding transition of staphylococcal nuclease is consistent with the two-state process. Stopped-flow kinetic measurements, monitoring the Trp140 fluorescence and covering five decades in time (2 ms to 300 s), indicate that the unfoldi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90116-n
更新日期：1991-08-05 00:00:00
abstract：:Mannan-binding lectin (MBL) is the archetypical pathogen recognition molecule of the innate immune defense. Upon binding to microorganisms, reactions leading to the destruction of the offender ensue. MBL is an oligomer of structural subunits each composed of three identical polypeptides. We used atomic force microscop...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.05.083
更新日期：2009-08-07 00:00:00
abstract：:Single crystals of the Fab fragment of a murine A/J anti-azophenylarsonate monoclonal antibody have been prepared by the vapor diffusion method. Antibody 3A7 uses the same combination of variable region gene segments (VK, JK, VH, JH) as do anti-azophenylarsonate antibodies bearing a predominant cross-reactive idiotype...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90587-1
更新日期：1989-04-20 00:00:00
abstract：:The expression of xylose utilization in Bacillus subtilis is regulated at the level of transcription by xylose dependent Xyl repressor-xyl operator interaction. We have structurally and functionally characterized the binding sites of Xyl repressor in the xyl regulatory region. Methylation and hydroxyl radical protecti...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1669
更新日期：1994-10-28 00:00:00
abstract：:Three viral proteins participate directly in transcription of bacteriophage T4 late genes: the sigma-family protein gp55 provides promoter recognition, gp33 is the co-activator, and gp45 is the activator of transcription; gp33 also represses transcription in the absence of gp45. Transcriptional activation by gp45, the...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(02)00732-5
更新日期：2002-08-30 00:00:00
abstract：:Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by bind...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1144
更新日期：1997-08-01 00:00:00
abstract：:The effect of temperature on the velocity of rhodamine phalloidin-labelled F-actin moving in vitro on rabbit skeletal myosin has been studied. Translating actin filaments were visualized by epi-fluorescence in an inverted microscope, equipped with temperature control (+/- 0.2 K) of the stage and objective. Images were...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(92)90467-x
更新日期：1992-04-20 00:00:00
abstract：:The effect of divalent cations on the self-association of high molecular weight subfragment-2 (long S-2) and low molecular weight subfragment-2 (short S-2) of rabbit skeletal muscle myosin has been investigated. In the presence of millimolar concentrations of Ca2+ or Mg2+ long S-2 associates at neutral pH to form orde...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(83)80015-1
更新日期：1983-08-05 00:00:00
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
更新日期：2000-05-19 00:00:00
abstract：:This work describes the isolation of mutations in infC, the structural gene for IF3, using different genetic screens. Among 21 mutants characterised, seven were shown to produce stable variant IF3 proteins unable to fully complement a strain carrying a chromosomal deletion of the infC gene. The mutants were also shown...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.2737
更新日期：1999-05-21 00:00:00
abstract：:We report the first protein phase-diagram characterized by a combination of volumetric, calorimetric, and spectroscopic techniques. More specifically, we use ultrasonic velocimetry, densimetry, and differential scanning calorimetry, in conjunction with UV absorbance and CD spectroscopy to detect and to characterize th...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1394
更新日期：1997-11-28 00:00:00
abstract：:Natural killer (NK) cells play a crucial role in the detection and destruction of virally infected and tumor cells during innate immune responses. The cytolytic activity of NK cells is regulated through a balance of inhibitory and stimulatory signals delivered by NK receptors that recognize classical major histocompat...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(02)00498-9
更新日期：2002-07-12 00:00:00
abstract：:Disulfide bonds play an important role in protein stability and function. Here, we describe a general procedure for generating disulfide-linked dimers and multimers of proteins of known crystal structures. An algorithm was developed to predict sites in a protein compatible with intermolecular disulfide formation with ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.07.033
更新日期：2007-10-05 00:00:00
abstract：:Small RNAs were selected from a highly degenerate library on the basis of their ability to bind tightly to Escherichia coli phenylalanyl-tRNA synthetase (FRS). The 63 nucleotide library consisted of the acceptor stem and portions of the D and T stems of E. coli tRNA(Phe) flanking a 32 nucleotide randomized region. Bec...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1571
更新日期：1994-09-23 00:00:00
abstract：:Binding of the TATA-binding protein (TBP) to the "TATA" sequences present in the promoters of eukaryotic class II genes is the first step in the sequential assembly of transcription pre-initiation complexes. Myriad structural changes, including severe bending of the DNA, accompany TBP-TATA complex formation. A detaile...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.2835
更新日期：1999-06-25 00:00:00
