Abstract:
:DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groove and the convex surface of the protein secondary structure; the former changes, becoming narrower or wider so that it fits the latter. An alpha-helix, independent of which groove it binds to, tends to produce a narrow major groove and a wide minor groove. When the major groove becomes narrower, the DNA helix axis bends around the major groove. Bending of DNA, which is overall structural change, is achieved by changes in local parameters (in particular, the roll parameter) so that an intermediate feature, the groove, fits the protein surface.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Suzuki M,Yagi Ndoi
10.1006/jmbi.1996.0055subject
Has Abstractpub_date
1996-02-09 00:00:00pages
677-87issue
5eissn
0022-2836issn
1089-8638pii
S0022-2836(96)90055-8journal_volume
255pub_type
杂志文章abstract::A simple continuum model of a de novo designed model of a four-helix bundle is presented. The thermodynamics and kinetics of the model are studied using Langevin simulations. We use a three-letter minimal off-lattice representation of a de novo designed four-helix bundle protein. The native state of the model, which c...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0578
更新日期:1996-10-25 00:00:00
abstract::Lipoyl-lysine swinging arms are crucial to the reactions catalysed by the 2-oxo acid dehydrogenase multienzyme complexes. A gene encoding a putative lipoate protein ligase (LplA) of Thermoplasma acidophilum was cloned and expressed in Escherichia coli. The recombinant protein, a monomer of molecular mass 29 kDa, was c...
journal_title:Journal of molecular biology
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journal_title:Journal of molecular biology
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更新日期:2005-06-24 00:00:00
abstract::The hydroxyl radical footprint of the TATA-binding protein (TBP) bound to the high-affinity sequence TATAAAAG of the adenovirus 2 major late promoter has been quantitatively compared to a 2 ns molecular dynamics simulation of the complex in aqueous solution at room temperature using the CHARMM23 potential. The nucleot...
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pub_type: 杂志文章
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journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(83)80322-2
更新日期:1983-07-25 00:00:00
abstract::Factor B is a key component of the alternative pathway of complement and is cleaved by factor D into the Ba and Bb fragments when complexed with the activated form of C3, namely C3b. The Bb fragment contains a von Willebrand factor type A (vWF-A) domain, which is composed of an open twisted almost-parallel beta-sheet ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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abstract::Elongation factor G (EF-G) is a large, five domain GTPase that catalyses the translocation of the tRNAs on the bacterial ribosome at the expense of GTP. In the crystal structure of GDP-bound EF-G, domain 1 (G domain) makes direct contacts with domains 2 and 5, whereas domain 4 protrudes from the body of the molecule. ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:2000-07-21 00:00:00
abstract::Dystrophin Dp71 is the main product of the Duchenne muscular dystrophy gene in the brain; however, its function is unknown. To study the role of Dp71 in neuronal cells, we previously generated by antisense treatment PC12 neuronal cell clones with decreased Dp71 expression (antisense-Dp71 cells). PC12 cells express two...
journal_title:Journal of molecular biology
pub_type: 杂志文章
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pub_type: 杂志文章
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abstract::Trichorzianine A 1 is one of the main components of a mixture of related antibiotic peptides (trichorzianines) produced by the fungus Trichoderma harzianum. Good crystals were obtained and allowed X-ray diffraction up to 0.8 A resolution. The space group is orthorhombic, C222(1), Z = 8, a = 64.8 (1) A, b = 9.33 (3) A,...
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abstract::The tyrosyl-tRNA synthetases from Bacillus stearothermophilus (Bst-TyrTS) and Escherichia coli (Eco-TyrTS) are 56% identical in amino acid sequence. To map and characterize the set of interactions that makes Bst-TyrTS more stable than Eco-TyrTS, a family of nine hybrid proteins was constructed between the two enzymes....
journal_title:Journal of molecular biology
pub_type: 杂志文章
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更新日期:1993-11-05 00:00:00
abstract::Fabry disease is an X-linked lysosomal storage disease afflicting 1 in 40,000 males with chronic pain, vascular degeneration, cardiac impairment, and other symptoms. Deficiency in the lysosomal enzyme alpha-galactosidase (alpha-GAL) causes an accumulation of its substrate, which ultimately leads to Fabry disease sympt...
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更新日期:2004-03-19 00:00:00
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journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2012.09.019
更新日期:2012-12-14 00:00:00
abstract::Recent studies on iron-loaded transferrins have revealed a conformational change upon binding iron due to a domain closure. It has been suggested that the domain closure may be the key for the receptor recognition of the metal loaded transferrin (Grossmann et al., 1992). Small angle X-ray scattering has been used to p...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1063
更新日期:1993-02-05 00:00:00
abstract::Using site-specific fluorescence probes and cross-linking we demonstrated that cofilin (ADF), a key regulator of actin cellular dynamics, weakens longitudinal contacts in F-actin in a cooperative manner. Differential scanning calorimetry detected a dual nature of cofilin effects on F-actin conformation. At sub-stoichi...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.11.072
更新日期:2006-02-17 00:00:00
abstract::Using a lacI-Z fusion system, we have determined the efficiency of suppression of nonsense codons in the I gene of Escherichia coli by assaying beta-galactosidase activity. We examined the efficiency of four amber suppressors acting on 42 different amber (UAG) codons at known positions in the I gene, and the efficienc...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(83)90087-6
更新日期:1983-02-15 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::The induction of effector genes that encode enzymes is often controlled by the protein product of a regulator gene that is directly involved in the control of its own expression. This coupling of elementary gene circuits can lead to three patterns of regulator and effector gene expression. As effector gene expression ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0011
更新日期:1996-01-12 00:00:00
abstract::Pancreatic amyloid is found in more than 95 % of type II diabetes patients. Pancreatic amyloid is formed by the aggregation of islet amyloid polypeptide (hIAPP or amylin), which is a 37-residue peptide. Because pancreatic amyloid is cytotoxic, it is believed that its formation is directly associated with the developme...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1999.3422
更新日期:2000-01-28 00:00:00
abstract::Clusters of complement-type ligand-binding repeats (CRs) in the low-density lipoprotein receptor (LDLR) family are thought to mediate the interactions with their various ligands. Apolipoprotein E (ApoE), a key ligand for cholesterol homeostasis, has been shown to interact with LDLR-related protein 1 (LRP) through thes...
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journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
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更新日期:2019-10-17 00:00:00
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
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更新日期:2001-03-23 00:00:00
abstract::Oncogenes may play a crucial role in the genetic program of cellular differentiation; even, probably, at a very early stage in this program, which can be described as pre-commitment. We have investigated the variation in, and the control level of, the accumulation of the transformation-associated cellular protein p53 ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(88)90333-6
更新日期:1988-03-05 00:00:00
abstract::The single mutation L30 K in the Hu-Yap65 WW domain increased the stability of the complex with the peptide GTPPPPYTVG (K(d)=40(+/-5) microM). Here we report the refined solution structure of this complex by NMR spectroscopy and further derived structure-activity relationships by using ligand peptide libraries with tr...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2000.5199
更新日期:2001-12-14 00:00:00
abstract::In order to colonize a niche and compete for scarce resources, microorganisms have evolved means to adjust the expression levels of their biosynthetic enzymes in response to the changing levels of metabolites available to them. To do so, they often rely on transcription factors or structured RNAs that directly sense t...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
doi:10.1016/j.jmb.2016.04.019
更新日期:2016-05-22 00:00:00
abstract::Mycobacterium tuberculosis (Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2008.06.030
更新日期:2008-09-12 00:00:00
abstract::Cre recombinase uses two pairs of sequential cleavage and religation reactions to exchange homologous DNA strands between 34 base-pair (bp) LoxP recognition sequences. In the oligomeric recombination complex, a switch between "cleaving" and "non-cleaving" subunit conformations regulates the number, order, and regio-sp...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/S0022-2836(02)00246-2
更新日期:2002-05-24 00:00:00
abstract::Crystals of a relatively unspecific NAD(P)H dehydrogenase from human erythrocytes suitable for X-ray analysis have been grown. They belong to space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2 with unit cell dimensions: a = b = 79.3 A and c = 38.1 A. The asymmetric unit contains one molecule of Mr 18,000. ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(84)90093-7
更新日期:1984-04-25 00:00:00
abstract::Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repulsion between two approaching phosphate groups at the site of strand exchange is commonly supposed to have a negative influence on the thermodynamic stability of the fully stacked...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0518
更新日期:1996-09-27 00:00:00
abstract::The three-dimensional structure of the membrane glycoprotein neuraminidase of an escape mutant of the influenza virus strain A/Tokyo/3/67 has been determined to 3 A (1 A = 0.1 nm) resolution by X-ray diffraction. The mutant virus, selected by growing the virus in the presence of a monoclonal antibody to the neuraminid...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(88)90344-0
更新日期:1988-03-05 00:00:00