Abstract：
:As a model to examine the local distribution of sequence variation within large arrays of tandemly repeated DNA in complex genomes, the long-range organization of alpha-satellite DNA from human chromosome 17 was investigated. Three individual chromosomes, representing different alpha-satellite haplotypes, were segregated into mouse and human somatic cell hybrids and their arrays sized by pulse-field gel electrophoresis. An inventory of the higher-order repeat units found in multiple separate regions of these megabase arrays was obtained using cosmid mapping and two-dimensional gel electrophoresis, a technique that combines the large-scale resolution of pulsed-field gel electrophoresis with the small-scale resolution of conventional gel electrophoresis. These analyses show that alpha-satellite arrays are characterized by the presence of localized homogeneous domains containing only one distinct type of repeat unit. These domains, which consist of sequence variants and/or higher-order repeat length variants, can be up to at least several hundred thousands of bases in length. Both abundant and rare variant repeat units can be localized in these distinct domains, which may correspond to transition states in the evolution of tandem multicopy DNA families. This description of the organization of large arrays of tandem repeats provides insight into mechanisms involved in their homogenization.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Warburton PE,Willard HFdoi
10.1016/s0022-2836(05)80056-7subject
Has Abstractpub_date
1990-11-05 00:00:00pages
3-16issue
1eissn
0022-2836issn
1089-8638pii
S0022-2836(05)80056-7journal_volume
216pub_type
杂志文章abstract：:Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing non-toxic antimicrobial agents, herbicides, and anti-parasite drugs, because the pathway is essential in the above species but is absent from mammals. The crystal structure of Mycobacterium tuberculosis SK (MtSK) in c...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/S0022-2836(02)00339-X
更新日期：2002-06-07 00:00:00
abstract：:The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.02.034
更新日期：2005-05-06 00:00:00
abstract：:Multidimensional 1H, 13C and 15N nuclear magnetic resonance spectroscopy has been used to study the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein. The 1H and the 15N spectra of the holo-protein have been almost completely assigned and so has most of the 1H spectrum of the coenzyme A part of ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1240
更新日期：1993-04-20 00:00:00
abstract：:As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2016.04.034
更新日期：2016-09-11 00:00:00
abstract：:The 64 x 10(3) Mr N-terminal breakage-reunion domain of the Escherichia coli DNA gyrase A protein was purified from an over-expressing strain. When complexed with the gyrase B protein, this truncated A protein has all of the enzymic properties of the full-length counterpart, although with reduced efficiency in some ca...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/S0022-2836(05)80162-7
更新日期：1990-10-20 00:00:00
abstract：:Homogeneous detergent-solubilized B873 light-harvesting complexes from a carotenoid-less mutant of the purple non-sulfur bacterium, Rhodospirillum rubrum G9, were reassembled spontaneously into two-dimensional (2D) hexagonal arrays during extensive and controlled dialysis. As the complexes contain only 1 to 2 mol phos...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1298
更新日期：1993-05-20 00:00:00
abstract：:The region of bacteriophage P1 DNA containing a lytic (vegetative) replicon has been identified by cloning P1 fragments into a phage lambda vector. We present the sequence of that replicon. Using a novel fusion vector containing two P1 loxP recombination sites, we have developed a transformation assay for replicon fun...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90444-0
更新日期：1989-05-05 00:00:00
abstract：:Two forms of three-dimensional crystals of the light-harvesting chlorophyll a/b protein complex from pea have been obtained. Crystals of one form grew as hexagonal plates measuring up to 150 micron across and 2 to 3 micron in thickness. Electron diffraction patterns of thin hexagonal plates showed sharp reflections to...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(87)90255-5
更新日期：1987-04-20 00:00:00
abstract：:Kinetic and crystallographic studies have characterized the effect of 2-deoxy-glucose 6-phosphate on the catalytic and structural properties of glycogen phosphorylase b. Previous work on the binding of glucose 6-phosphate, a potent physiological inhibitor of the enzyme, to T state phosphorylase b in the crystal showed...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1995.0665
更新日期：1995-12-15 00:00:00
abstract：:alpha-Synuclein is an intrinsically disordered protein that appears in aggregated forms in the brains of patients with Parkinson's disease. The conversion from monomer to aggregate is complex, and aggregation rates are sensitive to changes in amino acid sequence and environmental conditions. It has previously been obs...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.06.063
更新日期：2009-08-28 00:00:00
abstract：:The portal proteins of tailed bacteriophage and Herpesvirus capsids form dodecameric rings that occupy one capsid vertex and are incorporated during the assembly of capsid precursors called procapsids or proheads. Portals are essential and serve as the pore for DNA transit and the site of tail attachment; however, bac...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.01.022
更新日期：2020-03-27 00:00:00
abstract：:In Saccharomyces cerevisiae, the SIF2 gene product is an integral component of the Set3 complex (SET3C), an assembly of proteins with some homology to the human SMRT and N-CoR corepressor complexes. SET3C has histone deacetylase activity that is responsible for repressing a set of meiotic genes. We have determined the...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.06.025
更新日期：2005-08-26 00:00:00
abstract：:Using computational and sequence analysis of bacterial cold shock proteins, we designed a protein (CspB-TB) that has the core residues of mesophilic protein from Bacillus subtilis(CspB-Bs) and altered distribution of surface charged residues. This designed protein was characterized by circular dichroism spectroscopy, ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2003.12.058
更新日期：2004-02-27 00:00:00
abstract：:Mammalian lipoxygenases form a heterogeneous family of lipid peroxidizing enzymes, which have been implicated in synthesis of inflammatory mediators, in cell development and in the pathogenesis of various diseases (atherosclerosis, osteoporosis) with major health political importance. The crystal structures of two pla...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.08.076
更新日期：2004-10-29 00:00:00
abstract：:Selective autophagy is the capture of specific cytosolic contents in double-membrane vesicles that subsequently fuse with the vacuole or lysosome, thereby delivering cargo for degradation. Selective autophagy receptors (SARs) mark the cargo for degradation and, in yeast, recruit Atg11, the scaffolding protein for sele...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.08.025
更新日期：2020-10-02 00:00:00
abstract：:The molten globule has been assumed to be a major intermediate state of protein folding. To extend our understanding of protein folding it is important to elucidate the thermodynamic mechanism of conformational stability of the molten globule. To clarify the role of electrostatic charge repulsion in the stability of t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90504-y
更新日期：1991-12-05 00:00:00
abstract：:Although many putative heme transporters have been discovered, it has been challenging to prove that these proteins are directly involved with heme trafficking in vivo and to identify their heme binding domains. The prokaryotic pathways for cytochrome c biogenesis, Systems I and II, transport heme from inside the cell...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2018.01.022
更新日期：2018-04-13 00:00:00
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
更新日期：2010-08-20 00:00:00
abstract：:Here, we show that in the chicken genome, the domain of alpha-globin genes is preceded by a CpG island of which the downstream part ( approximately 0.65 kbp) is heavily methylated in lymphoid cells; it is either non-methylated or undermethylated in erythroid cells. Recombinant plasmids were constructed with the corres...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3775
更新日期：2000-06-16 00:00:00
abstract：:The molecular chaperone Hsp90 and its cofactor Cdc37 are required for the stability of protein kinases in the cellular environment. Upon pharmacological inhibition of Hsp90, the Hsp90-dependent kinases are degraded quickly by the proteasome. Clear physiological evidence for the formation of heterooligomeric complexes ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2016.09.002
更新日期：2016-10-09 00:00:00
abstract：:Hyaluronan (HA), an extracellular linear polysaccharide of alternating N-acetyl-glucosamine and glucuronic acid residues, is ubiquitously expressed in vertebrates, where it affects a broad spectrum of physiological processes, including cell adhesion, migration and differentiation. The HA polymer is synthesized on the ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2012.01.053
更新日期：2012-04-20 00:00:00
abstract：:This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3836
更新日期：2000-08-04 00:00:00
abstract：:An analysis was performed on 335 pairs of structurally aligned proteins derived from the structural classification of proteins (SCOP http://scop.mrc-lmb.cam.ac.uk/scop/) database. These similarities were divided into analogues, defined as proteins with similar three-dimensional structures (same SCOP fold classificatio...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1019
更新日期：1997-06-13 00:00:00
abstract：:DNase I digestion of unlabelled chromatin has been used to determine the orientation of nucleosomes in the higher-order structure of chromatin. DNA digestion patterns were analysed quantitatively and compared with simulation curves that were generated with the experimentally obtained rate constants for cutting inside ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.1777
更新日期：1998-05-29 00:00:00
abstract：:The RhaS and RhaR regulatory proteins are encoded in the Escherichia coli L-rhamnose gene cluster. We used complementation analysis and DNA mobility shift assays to show that RhaR is not the direct activator of the L-rhamnose catabolic operon, rhaBAD. An in-frame deletion of rhaS (rhaS-rhaR+) eliminated expression fro...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1565
更新日期：1993-11-05 00:00:00
abstract：:We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The on...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2019.01.026
更新日期：2019-03-15 00:00:00
abstract：:The rate of ligation of DNA molecules into circular forms depends on the ring closure probability, commonly called the j-factor, which is a sensitive measure of the extent to which thermal fluctuations contribute to bending and twisting of DNA molecules in solution. We present a theoretical treatment of the cyclizatio...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(86)90381-5
更新日期：1986-05-05 00:00:00
abstract：:Collagens contain sequence- and conformation-dependent epitopes responsible for their digestion by collagenases at specific loci. A synthetic heterotrimer construct containing the collagenase cleavage site of collagen type I was found to mimic perfectly native collagen in terms of selectivity and mode of enzymatic deg...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/S0022-2836(02)00365-0
更新日期：2002-06-21 00:00:00
abstract：:The Escherichia coli wild-type single strand binding (SSB) protein is a stable tetramer that binds to single-stranded (ss) DNA in its role in DNA replication, recombination and repair. The ssb-1 mutation, a substitution of tyrosine for histidine-55 within the SSB-1 protein, destabilizes the tetramer with respect to mo...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90611-9
更新日期：1991-01-05 00:00:00
abstract：:Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid residues. The wild-type AB heterodimer is produced by proteolytic rem...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.4105
更新日期：2000-09-29 00:00:00
