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Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
  • S. Negi, W. Braun
  • Biology, Medicine
  • Bioinformatics and biology insights
  • 1 January 2009
A fully automated search method, EpiSearch that predicts the possible location of conformational epitopes on the surface of an antigen, using peptide sequences from phage display experiments as input, and ranks all surface exposed patches according to the frequency distribution of similar residues in the peptides and in the patch. Expand
InterProSurf: a web server for predicting interacting sites on protein surfaces
The application of InterProSurf is illustrated to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. Expand
Conformational Flexibility of Mammalian Cytochrome P450 2B4 in Binding Imidazole Inhibitors with Different Ring Chemistry and Side Chains
The thermodynamic signature obtained for structurally similar inhibitors suggests remarkable plasticity of CYP2B4. Expand
Thermodynamics of phosphopeptide tethering to BRCT: the structural minima for inhibitor design.
Two complementary techniques are used, isothermal titration calorimetry and fluorescence polarization, to define structural minima of a BACH1 peptide, finding the minimal tetrapeptide retains low-micromolar affinity for BRCT with a thermodynamic signature comparable to the decapeptide. Expand
Rational Engineering of Human Cytochrome P450 2B6 for Enhanced Expression and Stability: Importance of a Leu264→Phe Substitution
L264F is a good candidate to further explore the unique structure-function relationships of P450 2B6 using X-ray crystallography and solution thermodynamics and made it suitable for isothermal titration calorimetry studies. Expand
Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion*
Six residues that are required specifically for signal transmission are characterized; their mutation interferes with fusion, although still allowing efficient F-protein processing and cell surface transport, and the signal receipt mechanism may be conserved among paramyxoviruses. Expand
Western Equine Encephalitis Virus: Evolutionary Analysis of a Declining Alphavirus Based on Complete Genome Sequences
It is hypothesize that an event occurred in the mid-20th century that resulted in the increased genetic diversity of WEEV in North America, followed by genetic constriction due to either competitive displacement by the B3 sublineage or stochastic events resulting from a population decline. Expand
Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts.
In immunogold double-labeling of pea leaf thin sections with antibodies raised against ferredoxin-NADP reductase and antibodies directed against the A or B subunits of the NADP-linked glyceraldehyde-3-P dehydrogenase, nearest neighbor analysis of the distribution of the gold particles indicates that FNR and the NADp-linked GAPD are co-localized, in situ. Expand
Membrane Fusion Triggering
The modular structure of the MV H-stalk is discussed in the context of membrane fusion triggering and cell entry by Paramyxoviruses and most residues in the central segment can be cross-linked by engineered disulfide bonds, and thus may be engaged in a tetrameric structure. Expand
Structural analysis of linear and conformational epitopes of allergens.
A new similarity measure, the property distance (PD) value, is developed that can be used to detect related segments in allergens with clinical observed cross-reactivity, and it is shown how sequence motifs characteristic of allergenic proteins in protein families can beused as fingerprints for allergenicity. Expand