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An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum 总被引:2,自引:0,他引:2
A graphic program has been developed to calculate the secondarystructure content of proteins from their circular dichroismspectrum. All the information concerning analysis and resultsare given on a single screen. The actual and the theoreticalspectra are plotted to allow visual inspection of the fit quality.The percentages of secondary structure and statistical parameters(r. m. s., residuals) are provided. The program is fully interactivefor spectra analysis. Moreover, cursors driven by a mouse orarrow keys are moveable onto spectra yielding all the informationconcerning a given wavelength, such as the theoretical and experimentalellipticities, wavelength, values of reference model for -helix,ß-sheet and ß-turn. Interfaces are providedfor the CONTIN program ofProvencher and Glockner. 相似文献
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Potential for Virus Endogenization in Humans through Testicular Germ Cell Infection: the Case of HIV
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Identification of antigenic regions of duck hepatitis B virus core protein with antibodies elicited by DNA immunization and chronic infection
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Thermet A Robaczewska M Rollier C Hantz O Trepo C Deleage G Cova L 《Journal of virology》2004,78(4):1945-1953
The induction of humoral response in ducks by DNA-based immunization against duck hepatitis B virus (DHBV) core protein (DHBc) was investigated. In addition, the amino acid specificity of the induced response was compared by using peptide scanning to that elicited either by protein immunization or during chronic DHBV infection. Immunization of ducks with a plasmid expressing DHBc protein led to the induction of a long-lasting antibody response able to specifically recognize viral protein in chronically infected duck livers. Peptide scanning analysis of anti-DHBc response induced during chronic DHBV infection allowed us to identify six major antigenic regions (AR1 to AR6). The reactivity spectrum of duck sera elicited by protein immunization appeared narrower and was restricted to only four of these antigenic regions in spite of higher anti-DHBc antibody titers. Interestingly, anti-DHBc antibodies induced by DNA-based immunization recognized five of six antigenic regions, and the epitope pattern was broader and more closely related to that observed in chronic viral infections. To gain more insight into the location of antigenic regions, we built a three-dimensional (3-D) model of DHBc protein based on human and duck core sequence alignment data and the HBc 3-D crystal structure. The results suggest that two identified antigenic regions (AR2, amino acids [aa] (64)T-P(84), and AR5, aa (183)A-R(210)) are located at positions on the protein surface equivalent to those of the two HBc major epitopes. Moreover, we identified another antigenic region (AR3, aa (99)I-I(112)) that was recognized by all sera from chronically infected, DNA- or protein-immunized ducks within the large 45-aa insertion in DHBc protein, suggesting that this region, which lacks HBc, is externally exposed. 相似文献
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Luca Micci Xavier Alvarez Robin I. Iriele Alexandra M. Ortiz Emily S. Ryan Colleen S. McGary Claire Deleage Brigitte B. McAtee Tianyu He Cristian Apetrei Kirk Easley Savita Pahwa Ronald G. Collman Cynthia A. Derdeyn Miles P. Davenport Jacob D. Estes Guido Silvestri Andrew A. Lackner Mirko Paiardini 《PLoS pathogens》2014,10(10)
In rhesus macaques (RMs), experimental depletion of CD4+ T-cells prior to SIV infection results in higher viremia and emergence of CD4-independent SIV-envelopes. In this study we used the rhesus recombinant anti-CD4 antibody CD4R1 to deplete RM CD4+ T-cells prior to SIVmac251 infection and investigate the sources of the increased viral burden and the lifespan of productively infected cells. CD4-depleted animals showed (i) set-point viral load two-logs higher than controls; (ii) macrophages constituting 80% of all SIV vRNA+ cells in lymph node and mucosal tissues; (iii) substantial expansion of pro-inflammatory monocytes; (iv) aberrant activation and infection of microglial cells; and (v) lifespan of productively infected cells significantly longer in comparison to controls, but markedly shorter than previously estimated for macrophages. The net effect of CD4+ T-cell depletion is an inability to control SIV replication and a shift in the tropism of infected cells to macrophages, microglia, and, potentially, other CD4-low cells which all appear to have a shortened in vivo lifespan. We believe these findings have important implications for HIV eradication studies. 相似文献
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Deleage Gilbert; Clerc Francois F.; Roux Bernard; Gautheron Daniele C. 《Bioinformatics (Oxford, England)》1988,4(3):351-356
A simple microcomputer package is described to make the theoreticalanalysis of protein sequences. Several methods designed to comparetwo sequences, to model proteolytic reactions and to predictthe secondary structure, the hydro-phobic/hydrophilic regionsand the potential antigenic sites of proteins have been includedin an Apple II microcomputer software. The package comprises21 programs as well as the secondary structure database of Kabschand Sander (1983).
Received on November 24, 1987; accepted on March 8, 1988 相似文献
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Laurent Houzet Claire Deleage Anne-Pascale Satie Laetitia Merlande Dominique Mahe Nathalie Dejucq-Rainsford 《PloS one》2015,10(6)
PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA) is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP) based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening. 相似文献
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Bernocco S Steiglitz BM Svergun DI Petoukhov MV Ruggiero F Ricard-Blum S Ebel C Geourjon C Deleage G Font B Eichenberger D Greenspan DS Hulmes DJ 《The Journal of biological chemistry》2003,278(9):7199-7205
Procollagen C-proteinase enhancer (PCPE) is an extracellular matrix glycoprotein that can stimulate the action of tolloid metalloproteinases, such as bone morphogenetic protein-1, on a procollagen substrate, by up to 20-fold. The PCPE molecule consists of two CUB domains followed by a C-terminal NTR (netrin-like) domain. In order to obtain structural insights into the function of PCPE, the recombinant protein was characterized by a range of biophysical techniques, including analytical ultracentrifugation, transmission electron microscopy, and small angle x-ray scattering. All three approaches showed PCPE to be a rod-like molecule, with a length of approximately 150 A. Homology modeling of both CUB domains and the NTR domain was consistent with the low-resolution structure of PCPE deduced from the small angle x-ray scattering data. Comparison with the low-resolution structure of the procollagen C-terminal region supports a recently proposed model (Ricard-Blum, S., Bernocco, S., Font, B., Moali, C., Eichenberger, D., Farjanel, J., Burchardt, E. R., van der Rest, M., Kessler, E., and Hulmes, D. J. S. (2002) J. Biol. Chem. 277, 33864-33869) for the mechanism of action of PCPE. 相似文献
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Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins 总被引:3,自引:0,他引:3
A computer module that includes multiple alignments, secondarystructure prediction, and site and pattern search has been developedand integrated into our ANTHEPROT software for protein sequenceanalysis. All the programs can be invokeed from within any routine,thus yielding multiple path to obtain final results. All theresults are graphically displayed. The main feature of thismodule is that all methods are connected in an interactive graphicmaimer. This module has been designed to display easily thepotential sites with conserved predicted structures. 相似文献