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A correlation of the localization of functionally important regions with places having low and high values on twelve profiles built on a basis of amino acid sequences was analysed using a broad set of proteins. The profiles of hydrophilicity, resemblance to the sequences of human proteins, flexibility, mutability and others were considered. The resemblance profile was plotted by the program fixing short similar fragments in the testing protein and 92 human ones. The active centres were shown to be located in the primary structure regions having relatively low values on the resemblance profiles. Similar effect was observed in the mutability and alpha-helicity profiles. The potential functionally important sites of the human leukocyte interferon and interleukin-2 isolated on the basis of the analysis of this profiles were in accord with the available literary data. 相似文献
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Karpenko LI Ivanisenko VA Pika IA Chikaev NA Eroshkin AM Veremeiko TA Ilyichev AA 《Amino acids》2000,18(4):329-337
Summary. Hepatitis B core antigen is one of the most promising protein carriers of foreign epitopes of various human and animal pathogens.
Chimeric HBcAg particles can be used as effective artificial immunogenes. Unfortunately, not all chimeric proteins are able
to be particulated. The dependence of correct or incorrect folding of chimeric proteins on physical and chemical properties
of inserts was studied with the help of ProAnalyst, SALIX and QSARPro computer programs. We have found that insertion of amino
acids with high hydrophobicity, large volume, and high β-strand index prevent self-assembling chimeric proteins. These factors are most important for the C-termini of inserts. Recommendations
for obtaining correct folding of chimeric HBcAg particles have been given.
Received August 8, 1999, Accepted September 26, 1999 相似文献
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A.?V.?BayramovEmail author F.?M.?Eroshkin N.?Y.?Martynova E.?E.?Orlov A.?V.?Borodulin A.?G.?ZaraiskyEmail author 《Russian Journal of Bioorganic Chemistry》2017,43(2):216-219
The protein Noggin4 of the African clawed frog Xenopus laevis has been shown to act as a modulator of the “noncanonical” Wnt/PCP-signaling pathway that plays an important role in the regulation of cell motility. Induction of disturbances in the expression of Noggin4 led to the activation of Wnt/PCP-pathway and the related anomalies of early embryonic development. The Noggin4 protein can bind the Wnt11 protein that normally contributes to the activation of the Wnt/PCP-pathway and of enhancing the activator effect of this protein in luciferase assays. Thus, Noggin4 can be used as a tool for specific experimental regulation of the activity of the Wnt/PCP pathway. 相似文献
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Based on the protein sequence data bank (PIR), the "variable fragment" bank, comprising pairs of closely related proteins, containing one or more strongly differing sites of primary structures was formed. The bank includes 465 "variable fragments" of 383 protein pairs. Amino acid residues composition of "variable fragments" was examined and indexes of potential amino acid residues variability was formed. An analysis of amino acid fragments replaceability was carried out by substituting the N-, C-terminal, or middle part of a chain), the fragments length differences and physico-chemical properties of residues, such as volume, hydrophobicity, polarity, isoelectric point, etc. Some general empirical rules of peptide insertions in carrier-proteins were created based on these analyses. The rules are directed for performing modifications maintaining the common structure and function of the carrier-protein molecule. The selection scheme for determining the regions suitable for modification and the criteria for defining the width of acceptable modifications in this regions were suggested. The use of potential variability profile for detecting regions suitable for peptide insertion was considered on the model of hepatitis B surface protein. 相似文献
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Enoksson M Li J Ivancic MM Timmer JC Wildfang E Eroshkin A Salvesen GS Tao WA 《Journal of proteome research》2007,6(7):2850-2858
The identification of natural substrates and their cleavage sites is pivotal to defining proteolytic pathways. Here we report a novel strategy for the identification of the signature of proteolytic cleavage events based on quantitative proteomics. Lysine residues in proteins are blocked by guanidination so that free N-terminals can be labeled with amine-specific iTRAQ reagents. The quantitative nature of iTRAQ reagents allows us to distinguish N-terminals newly formed by proteolytic treatment (neoepitopes) from original N-terminals in proteins. Proteins are digested with trypsin and analyzed using MALDI-TOF/TOF mass spectrometry. Peptides labeled with iTRAQ reagents are distinguished from other peptides by exhibiting intense signature ions in tandem mass spectrometry analysis. A corresponding data acquisition strategy was developed to specifically analyze iTRAQ tagged N-terminal peptides. To validate the procedure, we examined a set of recombinant Escherichia coli proteins that have predicted caspase-3 cleavage motifs. The protein mixture was treated with active or inactive caspase-3 and subsequently labeled with two different iTRAQ reagents. Mass spectrometric analysis located 10 cleavage sites, all corresponding to caspase-3 consensus. Spiking caspase-cleaved substrate into a human cell lysate demonstrated the high sensitivity of the procedure. Moreover, we were able to identify proteolytic cleavage products associated with the induction of cell-free apoptosis. Together, these data reveal a novel application for iTRAQ technology for the detection of proteolytic substrates. 相似文献
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