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41.
Background
Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target sequence long enough to contain interfacial residues. However, too long sequences induce artifactual polymorphism: within tested modeling methods, the longer the target sequence, the more variable the secondary structure, as though the procedure were stopped before the end of the calculation (which may in fact be unreachable). Moreover, delimitation of these TMDs can produce variable results with sequence based two-dimensional prediction methods, especially for sequences showing polymorphism. To solve this problem, we developed a new modeling procedure using the PepLook method. We scanned the sequences by modeling peptides from the target sequence with a window of 19 residues.Results
Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2Rβ and IL-2Rγ TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus.Conclusions
We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. 相似文献42.
Over the past decade, there have been many reports suggesting the presence
of complex carbohydrates on nuclear and cytoplasmic proteins in mammalian
cells. Some of the most often cited of these reports deal with the
glycosylation of the high mobility group (HMG) proteins. These are
relatively abundant chromosomal proteins that are known to be associated
with nucleosomes and actively transcribed regions of chromatin. The
original report describing HMG protein glycosylation presented several
lines of evidence suggesting that these proteins are glycosylated,
including carbohydrate compositional analysis and periodic-acid Schiff
staining. We have attempted to repeat these observations with more highly
purified protein than was utilized in the original study. Using
carbohydrate compositional analysis performed by high pH anion exchange
chromatography coupled to pulsed-amperometric detection, we saw no evidence
for significant glycosylation of these proteins. In addition, we found no
evidence for the presence of O- GlcNAc, a well known form of nuclear
glycosylation. The HMG proteins did react with periodate, suggesting the
presence of a modification containing cis-diols on the protein. Several
tryptic peptides isolated from HMG 14 and 17 which retained the periodate
reactivity had in common lysine residues, suggesting a potential
modification of the straightepsilon-amino groups of lysines such as
nonenzymatic glycation. Western blot analysis of the HMG proteins using
anti-advanced glycation endproducts (AGE) antibodies confirmed the presence
of glycation products on the HMG proteins.
相似文献
43.
RS Redman 《Biotechnic & histochemistry》2013,88(3-4):103-130
Radiation therapy for cancer of the head and neck can devastate the salivary glands and partially devitalize the mandible and maxilla. As a result, saliva production is drastically reduced and its quality adversely altered. Without diligent home and professional care, the teeth are subject to rapid destruction by caries, necessitating extractions with attendant high risk of necrosis of the supporting bone. Innovative techniques in delivery of radiation therapy and administration of drugs that selectively protect normal tissues can reduce significantly the radiation effects on salivary glands. Nonetheless, many patients still suffer severe oral dryness. I review here the functional morphology and development of salivary glands as these relate to approaches to preventing and restoring radiation-induced loss of salivary function. The acinar cells are responsible for most of the fluid and organic material in saliva, while the larger ducts influence the inorganic content. A central theme of this review is the extent to which the several types of epithelial cells in salivary glands may be pluripotential and the circumstances that may influence their ability to replace cells that have been lost or functionally inactivated due to the effects of radiation. The evidence suggests that the highly differentiated cells of the acini and large ducts of mature glands can replace themselves except when the respective pools of available cells are greatly diminished via apoptosis or necrosis owing to severely stressful events. Under the latter circumstances, relatively undifferentiated cells in the intercalated ducts proliferate and redifferentiate as may be required to replenish the depleted pools. It is likely that some, if not many, acinar cells may de-differentiate into intercalated duct-like cells and thus add to the pool of progenitor cells in such situations. If the stress is heavy doses of radiation, however, the result is not only the death of acinar cells, but also a marked decline in functional differentiation and proliferative capacity of all of the surviving cells, including those with progenitor capability. Restoration of gland function, therefore, seems to require increasing the secretory capacity of the surviving cells, or replacing the acinar cells and their progenitors either in the existing gland remnants or with artificial glands. 相似文献
44.
K Ramamoorthy Subramanian Raghunandhakumar RS Anand A Paramasivam S Kamaraj S Nagaraj Devaraj Ezhilarasan Thangavelu Lakshmi Kamal Dua Dinesh Kumar Chellappan Ashokkumar Veeramuthu 《Bioinformation》2020,16(11):965
Astaxanthin (AXN) is known to have health benefits by epidemiological studies. Therefore, it is of interest to assess the effect of AXN (derived from indigenous unicellular green alga Haematococcus lacustris) to modulate cell cycle arrest, lysosomal acidification and eventually apoptosis using in vitro in A549 lung cancer cells. Natural extracts of astaxanthin were obtained by standardized methods as reported earlier and characterized by standard HPLC and MS. Treatment of A549 cells with AXN (purified fraction) showed significant reduction in cell viability (about 50%) as compared to crude extract at 50µM concentration. Thus, we show the anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris for further consideration. Together, our results demonstrated the anticancer potential of AXN from Haematococcus lacustris, which is found to be mediated via its ability to induce cell cycle arrest, lysosomal acidification and apoptotic induction. 相似文献
45.
Youn Tae Kwak Alexa Raney Lillian S Kuo Sarah J Denial Brenda RS Temple J Victor Garcia John L Foster 《Retrovirology》2010,7(1):1-22
Background
The HIV-1 pathogenic factor, Nef, is a multifunctional protein present in the cytosol and on membranes of infected cells. It has been proposed that a spatial and temporal regulation of the conformation of Nef sequentially matches Nef's multiple functions to the process of virion production. Further, it has been suggested that dimerization is required for multiple Nef activities. A dimerization interface has been proposed based on intermolecular contacts between Nefs within hexagonal Nef/FynSH3 crystals. The proposed dimerization interface consists of the hydrophobic B-helix and flanking salt bridges between R105 and D123. Here, we test whether Nef self-association is mediated by this interface and address the overall significance of oligomerization.Results
By co-immunoprecipitation assays, we demonstrated that HIV-1Nef exists as monomers and oligomers with about half of the Nef protomers oligomerized. Nef oligomers were found to be present in the cytosol and on membranes. Removal of the myristate did not enhance the oligomerization of soluble Nef. Also, SIVNef oligomerizes despite lacking a dimerization interface functionally homologous to that proposed for HIV-1Nef. Moreover, HIV-1Nef and SIVNef form hetero-oligomers demonstrating the existence of homologous oligomerization interfaces that are distinct from that previously proposed (R105-D123). Intracellular cross-linking by formaldehyde confirmed that SF2Nef dimers are present in intact cells, but surprisingly self-association was dependent on R105, but not D123. SIVMAC239Nef can be cross-linked at its only cysteine, C55, and SF2Nef is also cross-linked, but at C206 instead of C55, suggesting that Nefs exhibit multiple dimeric structures. ClusPro dimerization analysis of HIV-1Nef homodimers and HIV-1Nef/SIVNef heterodimers identified a new potential dimerization interface, including a dibasic motif at R105-R106 and a six amino acid hydrophobic surface.Conclusions
We have demonstrated significant levels of intracellular Nef oligomers by immunoprecipitation from cellular extracts. However, our results are contrary to the identification of salt bridges between R105 and D123 as necessary for self-association. Importantly, binding between HIV-1Nef and SIVNef demonstrates evolutionary conservation and therefore significant function(s) for oligomerization. Based on modeling studies of Nef self-association, we propose a new dimerization interface. Finally, our findings support a stochastic model of Nef function with a dispersed intracellular distribution of Nef oligomers. 相似文献46.
Gonzalo-Ruiz J Mas R de Haro C Cabruja E Camero R Alonso-Lomillo MA Muñoz FJ 《Biosensors & bioelectronics》2009,24(6):1788-1791
A novel and rapid approach to quantify chloride concentration in sweat for early detection of cystic fibrosis (CF) is shown in this work. Disposable screen-printed sensor (SPS) devices capable to induce sweat and measure the chloride concentration are presented. Pilocarpine, which was forced into de skin by means of iontophoresis, has been used to stimulate the sweat glands. Chloride concentration has been directly measured on the skin by potentiometry. The performance of the devices has been tested in synthetic samples, obtaining good agreement with the Nernst equation. Sensors reproducibility has been analyzed in terms of residual standard deviation (RSD), obtaining a value of 8% (n=6 and alpha=0.05). Finally, the application of these sensors in several volunteers has been carried out. The results were compared with the method generally used in hospitals, obtaining deviations minor than 8%. 相似文献
47.
Decaro N Camero M Greco G Zizzo N Tinelli A Campolo M Pratelli A Buonavoglia C 《The new microbiologica》2004,27(2):177-181
An outbreak of canine distemper in a kennel of German shepherds in the province of Bari is reported. Six 42-day-old pups developed typical signs of canine distemper (fever, conjunctivitis, respiratory distress and enteritis) and died within 7-10 days. Neurological symptoms were observed only in one pup. Four additional pups, which had shown no sign of illness, were separated and vaccinated, but two of these developed a severe, fatal nervous form 15 days later. Post-mortem examination, carried out on two pups which died without neurological signs, showed pneumonia and enteritis, more severe in one of the two examined pups. Smears from the brain and the conjunctiva of both dogs tested positive for canine distemper virus (CDV) by an immunofluorescent assay, confirmed by the identification of viral RNA using RT-PCR. Bordetella bronchiseptica and a canine adenovirus strain, characterized as canine adenovirus type 2 by a differential PCR assay, were isolated from the lungs of the pup showing the most pronounced lesions. Furthermore, canine coronavirus was detected by PCR in the intestinal content of this pup, suggesting a multifactorial aetiology of the outbreak. 相似文献
48.
The performance of fungal xylan-degrading enzyme preparations in elemental chlorine-free bleaching for Eucalyptus pulp 总被引:2,自引:0,他引:2
Medeiros RG Silva FG Salles BC Estelles RS Filho EX 《Journal of industrial microbiology & biotechnology》2002,28(4):204-206
Cellulase-free xylan-degrading enzyme preparations from Acrophialophora nainiana, Humicola grisea var. thermoidea and two Trichoderma harzianum strains were used as bleaching agents for Eucalyptus kraft pulp, prior to a chlorine dioxide and alkaline bleaching sequence. In comparison to the control sequence (performed
without xylanase pretreatment), the sequence incorporating enzyme treatment was more effective. Removal of residual lignin
was indicated by a reduction in kappa number. Overall, enzyme preparations from T. harzianum were marginally more effective in reducing pulp viscosity and chlorine chemical consumption and improving the brightness
of the kraft pulp. However, the highest reduction in pulp viscosity was mediated by the xylanase preparation from A. nainiana. Xylanase pretreatment compares very favorably with that of chemical pulping. Journal of Industrial Microbiology & Biotechnology (2002) 28, 204–206 DOI: 10.1038/sj/jim/7000227
Received 27 April 2001/ Accepted in revised form 03 November 2001 相似文献
49.
Evaluation of the innate immune response in pups during canine parvovirus type 1 infection 总被引:1,自引:0,他引:1
Decaro N Altamura M Pratelli A Pepe M Tinelli A Casale D Martella V Tafaro A Camero M Elia G Tempesta M Jirillo E Buonavoglia C 《The new microbiologica》2002,25(3):291-298
In two pups (A and B) naturally infected with canine parvovirus type 1 (CPV1) phagocytic responses were evaluated over a period of two weeks (day 0 = T0; day 3 = T1; day 7 = T2; day 14 = T3). CPV1 infection led to a marked reduction of monocyte (MO) phagocytosis in both pups. Also MO killing was impaired and in pup B this function was totally absent. Polymorphonuclear (PMN) phagocytosis values of both pups fluctuated within normal ranges, as well as PMN killing of pup A. In pup B, killing exerted by PMN was absent at T0, then increased but again dropped below normal ranges at T3. The described alterations of phagocytic functions may be regarded as possible viral mechanisms of immune evasion. 相似文献
50.
Regier JC; Fang QQ; Mitter C; Peigler RS; Friedlander TP; Solis MA 《Molecular biology and evolution》1998,15(9):1172-1182
Evolution and phylogenetic utility of the period gene are explored through
sequence analysis of a relatively conserved 909-bp fragment in 26
lepidopteran species. Taxa range from tribes to superfamilies, primarily
within the putative clade Macrolepidotera plus near outgroups, and include
both strongly established and problematic groupings. Their divergence dates
probably range from the late Cretaceous through much of the Tertiary.
Comparisons within the same set of closely related species show that amino
acid substitutions in period occur 4.9 and 44 times as frequently as they
do in two other nuclear genes--dopa decarboxylase and elongation factor-1
alpha, respectively. In contrast, rates of observed synonymous substitution
are within 60% of each other for these three genes. Synonymous changes in
period approach saturation by the family level, whereas nonsynonymous and
amino acid divergences across the Macrolepidoptera are less than half the
maximal values reported for this gene. Phylogenetic analyses of period
strongly supported groupings at the family level and below. In contrast to
previous analyses at this level with other nuclear genes, much of the
information lies in nonsynonymous change. Relationships up to the
superfamily level were recovered with decreasing effectiveness, and little,
if any, signal was apparent regarding relationships among superfamilies.
This could reflect rapid radiation of the superfamilies, however, rather
than saturation in the period locus; thus, period, in combination with
other genes, remains a plausible candidate for approaching the difficult
problems of lepidopteran family and superfamily relationships.
相似文献