Domain III (domain + iii)

Distribution by Scientific Domains


Selected Abstracts


Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant

FEMS MICROBIOLOGY ECOLOGY, Issue 1 2009
Babur S. Mirza
Abstract The ability of Frankia strains to grow in the rhizosphere of a nonactinorhizal plant, Betula pendula, in surrounding bulk soil and in soil amended with leaf litter was analyzed 6 weeks after inoculation of pure cultures by in situ hybridization. Growth responses were related to taxonomic position as determined by comparative sequence analysis of nifH gene fragments and of an actinomycetes-specific insertion in Domain III of the 23S rRNA gene. Phylogenetic analyses confirmed the basic classification of Frankia strains by host infection groups, and allowed a further differentiation of Frankia clusters within the Alnus host infection group. Except for Casuarina -infective Frankia strains, all other strains of the Alnus and the Elaeagnus host infection groups displayed growth in the rhizosphere of B. pendula, and none of them grew in the surrounding bulk soil that was characterized by a very low organic matter content. Only a small number of strains that all belonged to a distinct phylogenetic cluster within the Alnus host infection group grew in soil amended with ground leaf litter from B. pendula. These results demonstrate that saprotrophic growth of frankiae is a common trait for most members of the genus, and the supporting factors for growth (i.e. carbon utilization capabilities) varied with the host infection group and the phylogenetic affiliation of the strains. [source]


NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition

PROTEIN SCIENCE, Issue 6 2006
Munia Mukherjee
Abstract Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E-D3) is considered to be the primary viral determinant involved in the virus,host-cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL-2 TBE virus and is a model for the pathogenic BSL-3 and BSL-4 viruses in the serogroup. We have determined the solution structure of LGT-E-D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT-E-D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT-E-D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design. [source]


Refolding, crystallization and preliminary X-ray structural studies of the West Nile virus envelope (E) protein domain III

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005
Zhiyong Lou
Domain III of the West Nile virus envelope protein, the putative receptor-binding domain, is a major virion-surface determinant for virulence. This protein was reported to be intrinsically unstable and has defied previous crystallization attempts. It has now been purified from inclusion bodies by protein refolding and was crystallized using the hanging-drop vapour-diffusion method at 291,K. The crystals belong to space group P2221, with unit-cell parameters a = 52.6, b = 59.7, c = 95.0,┼. A complete data set was collected to 2.8,┼ at 100,K with Cu,K, X-rays from a rotating-anode generator. [source]


The calpain 1,,-actinin interaction

FEBS JOURNAL, Issue 23 2003
Resting complex between the calcium-dependant protease, its target in cytoskeleton
Calpain 1 behaviour toward cytoskeletal targets was investigated using two ,-actinin isoforms from smooth and skeletal muscles. These two isoforms which are, respectively, sensitive and resistant to calpain cleavage, interact with the protease when using in vitro binding assays. The stability of the complexes in EGTA [Kd(,Ca2+) = 0.5 ▒ 0.1 Ám] was improved in the presence of 1 mm calcium ions [Kd(+Ca2+) = 0.05 ▒ 0.01 Ám]. Location of the binding structures shows that the C-terminal domain of ,-actinin and each calpain subunit, 28 and 80 kDa, participates in the interaction. In particular, the autolysed calpain form (76/18) affords a similar binding compared to the 80/28 intact enzyme, with an identified binding site in the catalytic subunit, located in the C-terminal region of the chain (domain III,IV). The in vivo colocalization of calpain 1 and ,-actinin was shown to be likely in the presence of calcium, when permeabilized muscle fibres were supplemented by exogenous calpain 1 and the presence of calpain 1 in Z-line cores was shown by gold-labelled antibodies. The demonstration of such a colocalization was brought by coimmunoprecipitation experiments of calpain 1 and ,-actinin from C2.7 myogenic cells. We propose that calpain 1 interacts in a resting state with cytoskeletal targets, and that this binding is strengthened in pathological conditions, such as ischaemia and dystrophies, associated with high calcium concentrations. [source]


Chimeric receptor analyses of the interactions of the ectodomains of ErbB-1 with epidermal growth factor and of those of ErbB-4 with neuregulin

FEBS JOURNAL, Issue 9 2002
Jae-Hoon Kim
A series of chimeric receptors was generated between the epidermal growth factor (EGF) receptor, ErbB-1, and its homologue, ErbB-4, to investigate the roles of the extracellular domains (I,IV) in the ligand specificities. As compared with ErbB-1 and the chimeras with both domains I and III of ErbB-1, the chimeras with only one of these domains exhibited reduced binding of 125I-labeled EGF. Particularly, the contribution of domain III was appreciably larger than that of domain I of ErbB-1 in 125I-labeled EGF binding. Nevertheless, the chimeras with domain III of ErbB-1 and domain I of ErbB-4 were prevented from binding to 125I-labeled EGF competitively by the ErbB-4 ligand, neuregulin (NRG). On the other hand, NRG did not compete with 125I-labeled EGF for binding to the chimeras with the ErbB-1 domain I and the ErbB-4 domain III. Therefore, NRG binding to ErbB-4 depends much more on domain I than on domain III. With respect to autophosphorylation and subsequent ERK activation, EGF activated the chimeras with either domain I or III of ErbB-1. In contrast, NRG activated the chimeras with the ErbB-4 domain I and the ErbB-1 domain III, but not those with the ErbB-1 domain,I and the ErbB-4 domain III. Therefore, the relative contributions between domains I and III of ErbB-4 in the NRG signaling are different from those of ErbB-1 in the EGF signaling. [source]


Cloning and Expression of Low Molecular Weight Glutenin Genes from the Chinese Elite Wheat Cultivar "Xiaoyan 54"

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 2 2006
Xin-Yu Wang
Abstract The low molecular weight (LMW) glutenin subunits account for 40% of wheat gluten protein content by mass and these proteins are considered to significantly affect dough quality characteristics. Five new full-length LMW glutenin genes (designated LMW-5, LMW-7, LMW-42, LMW-58, and LMW-34) were isolated from the Chinese elite wheat cultivar "Xiaoyan 54" by PCR amplification of genomic DNA using a pair of degenerate primers designed from the conserved sequences of the N- and C-terminal regions of published LMW glutenin genes. Deduced amino acid sequence analysis showed that LMW-5 belongs to the LMW-i type genes and that the other four belong to LMW-m type genes. Sequence comparisons revealed that point mutations occasionally occurred in signal peptide and N-terminus domains and often existed in domain III and domain V. Small insertions and deletions are represented in the repetitive domain. There is a stop codon after amino acid position 110 in the repetitive domain of LMW-34, indicating that it is a pseudogene. The other four genes have complete open reading frames and the putative mature regions of these genes were subcloned into pET-30a expression vector and successfully expressed in Escherichia coli. Protein sodium dodecyl sulfate-polyacrylamide gel electro-phoresis analysis showed that all proteins expressed in E. coli by the four genes could be related to B-group LMW glutenin subunits of wheat. (Managing editor: Li-Hui Zhao) [source]


NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition

PROTEIN SCIENCE, Issue 6 2006
Munia Mukherjee
Abstract Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E-D3) is considered to be the primary viral determinant involved in the virus,host-cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL-2 TBE virus and is a model for the pathogenic BSL-3 and BSL-4 viruses in the serogroup. We have determined the solution structure of LGT-E-D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT-E-D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT-E-D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design. [source]


Refolding, crystallization and preliminary X-ray structural studies of the West Nile virus envelope (E) protein domain III

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005
Zhiyong Lou
Domain III of the West Nile virus envelope protein, the putative receptor-binding domain, is a major virion-surface determinant for virulence. This protein was reported to be intrinsically unstable and has defied previous crystallization attempts. It has now been purified from inclusion bodies by protein refolding and was crystallized using the hanging-drop vapour-diffusion method at 291,K. The crystals belong to space group P2221, with unit-cell parameters a = 52.6, b = 59.7, c = 95.0,┼. A complete data set was collected to 2.8,┼ at 100,K with Cu,K, X-rays from a rotating-anode generator. [source]


THE EPITHELIAL BRUSH BORDER Na+/H+ EXCHANGER NHE3 ASSOCIATES WITH THE ACTIN CYTOSKELETON BY BINDING TO EZRIN DIRECTLY AND VIA PDZ DOMAIN-CONTAINING Na+/H+ EXCHANGER REGULATORY FACTOR (NHERF) PROTEINS

CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 8 2008
Boyoung Cha
SUMMARY 1The Na+/H+ exchanger NHE3 associates with the actin cytoskeleton by binding ezrin both directly and indirectly. Both types of interaction are necessary for acute regulation of NHE3. Most acute regulation of NHE3 occurs by changes in trafficking via effects on exocytosis and/or endocytosis. However, NHE3 activity can also be regulated without changing the surface expression of NHE3 (change in turnover number). 2A positive amino acid cluster in the a-helical juxtamembrane region in the COOH-terminus of NHE3 (amino acids K516, R520 and R527) is necessary for binding to the protein 4.1, ezrin, radixin, moesin (FERM) domain III of ezrin. Direct binding of NHE3 to ezrin is necessary for many aspects of basal trafficking, including basal exocytosis, delivery from the synthetic pathway and movement of NHE3 in the brush border (BB), which probably contributes to endocytosis over a prolonged period of time. 3In addition, NHE3 binds indirectly to ezrin. The PDZ domain-containing proteins Na+/H+ exchanger regulatory factor (NHERF) 1 and NHERF2, as intermediates in linking NHE3 to ezrin, are necessary for many aspects of NHE3 regulation. The binding of NHERF,ezrin/radixin/moesin to NHE3 occurs in the cytosolic domain of NHE3 between amino acids 475 and 689. This NHERF binding is involved in the formation of the NHE3 complex and restricts NHE3 mobility in the BB. However, it is dynamic; for example, changing in some cases of signalling. Furthermore, NHERF binding is necessary for lysophosphatidic acid stimulation of NHE3 and inhibition of NHE3 by Ca2+, cAMP and cGMP. [source]


The central domain of bovine submaxillary mucin consists of over 50 tandem repeats of 329 amino acids

FEBS JOURNAL, Issue 8 2000
Chromosomal localization of the BSM1 gene, porcine counterparts, relations to ovine
We previously elucidated five distinct protein domains (I,V) for bovine submaxillary mucin, which is encoded by two genes, BSM1 and BSM2. Using Southern blot analysis, genomic cloning and sequencing of the BSM1 gene, we now show that the central domain (V) consists of ,,55 tandem repeats of 329 amino acids and that domains III,V are encoded by a 58.4-kb exon, the largest exon known for all genes to date. The BSM1 gene was mapped by fluorescence in situ hybridization to the proximal half of chromosome 5 at bands q2.2,q2.3. The amino-acid sequence of six tandem repeats (two full and four partial) were found to have only 92,94% identities. We propose that the variability in the amino-acid sequences of the mucin tandem repeat is important for generating the combinatorial library of saccharides that are necessary for the protective function of mucins. The deduced peptide sequences of the central domain match those determined from the purified bovine submaxillary mucin and also show 68,94% identity to published peptide sequences of ovine submaxillary mucin. This indicates that the core protein of ovine submaxillary mucin is closely related to that of bovine submaxillary mucin and contains similar tandem repeats in the central domain. In contrast, the central domain of porcine submaxillary mucin is reported to consist of 81-amino-acid tandem repeats. However, both bovine submaxillary mucin and porcine submaxillary mucin contain similar N-terminal and C-terminal domains and the corresponding genes are in the conserved linkage regions of the respective genomes. [source]


F90927: A New Member in the Class of Cardioactive Steroids

CARDIOVASCULAR THERAPEUTICS, Issue 3 2007
Markus Keller
ABSTRACT F90927 is a newly developed cardioactive drug with a steroid-like structure. It acts directly and agonistically on the cardiac L-type Ca2+ channel by shifting its voltage-dependent activation toward more negative potentials. This leads to an increased influx of Ca2+ and, therefore, to a stronger contraction; however, no arrhythmias occur. Calcium current stimulation can already be observed at nanomolar concentrations, but higher concentrations of F90927 elevate intracellular Ca2+ concentration, causing a reduction of the myocardial compliance and an increased diastolic blood pressure. Vessels also react to F90927 and contract in its presence. Binding of F90927 with the L-type Ca2+ channel presumably occurs in the vicinity of the transmembrane domains III and IV of the ,1 subunit. F90927 exhibits no use dependence and interacts with Ca2+ channel inhibitors of all three known classes of channel modulators (dihydropyridines, phenylalkylamines, and benzothiazepines), suggesting that it is a member of a new class of Ca2+ channel modulators. Due to its adverse effects on blood pressure and vessel contraction, F90927 is not an ideal drug candidate. It has, however, some unique properties, which makes it a promising tool to study the function of the L-type Ca2+ channel. [source]