Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

Discovery of discontinuous B-cell epitopes is a major challenge in vaccine design. Previous epitope prediction methods have mostly been based on protein sequences and are not very effective. Here, we present DiscoTope, a novel method for discontinuous epitope prediction that uses protein three-dimensional structural data. The method is based on amino acid statistics, spatial information, and surface accessibility in a compiled data set of discontinuous epitopes determined by X-ray crystallography of antibody/antigen protein complexes. DiscoTope is the first method to focus explicitly on discontinuous epitopes. We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15.5% of residues located in discontinuous epitopes with a specificity of 95%. At this level of specificity, the conventional Parker hydrophilicity scale for predicting linear B-cell epitopes identifies only 11.0% of residues located in discontinuous epitopes. Predictions by the DiscoTope method can guide experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification.     

Evaluation of the Hydrophobicity of Bacterial Cells by Measuring Their Adherence to Chloroform Drops

A simple method for measuring the hydrophobicity of bacterial cells is proposed, which is based on the spectrophotometric evaluation of cell adherence to chloroform drops in a biphasic water–chloroform mixture.     

Enhancement of biodegradation of 2,7-dichlorodibenzo-p-dioxin by addition of fungal culture filtrate

The hydrophilicity of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD), a model dioxin compound, increased when incubated with the culture filtrates of several strains of fungi. The possibility that the addition of these filtrates could enhance the biodegradation of 2,7-DCDD by the white-rot basidiomycetous fungus Phanerochaete sordida YK-624 was examined. The decrease of 2,7-DCDD after 3 weeks incubation in a YK-624 culture containing these filtrates was greater (30%) than that in the culture of YK-624 alone (15%). This is the first report describing the enhancement of dioxin decrease by the addition of a fungal filtrate.     

A synthetic complement C1q-like peptide selectively interacts with immune complexes

A water-soluble peptide possessing an immune complex selective affinity was synthesized and its primary structure established as: Leu-Glu-Gln-Gly-Glu-Asn-Val-Phe-Leu-Gln-Ala-Thr-Ser-Asp-Asp-Cys. This peptide, designated as C1q-like peptide (CLP), represents a possible immune complex binding epitope of complement C1q. CLP has a hydrophilicity value of 0.21. At 0.5 M, it inhibited by 50% natural human C1q from binding to horseradish peroxidase-rabbit anti-peroxidase immune complex. CLP failed to inhibit Staphylococcus aureus protein A from binding monomeric IgG. When coated to a microplate, CLP showed selective binding to the immune complex, and could be used for application in immunochemical detection of immune complex. © Rapid Science Ltd. 1998     

Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity

X-ray crystallographic protein structures often contain disordered regions that are observed as missing electron density. Diffraction data may give little or no direct evidence as to the specific nature of disordered regions. We have developed a weighted window-based disorder predictor optimized using crystallographic data. Performance of a predictor is strongly influenced by chain termini. Optimized score adjustment values for amino- and carboxy-terminal positions demonstrate a simple, monotonic relationship between disorder and residue distance from termini. This optimized disorder predictor performs similarly to DISOPRED2 on crystallographically disordered regions. Data-optimized residue disorder propensities show strong linear correlation with experimentally determined amino acid transfer energies between water and hydrogen-bonding organic solvents, which primarily reflect residue hydrophobicity (exemplified by the Nozaki-Tanford hydrophobicity scale). Disorder propensities do not correlate as well with transfer energies between water and apolar solvents, which primarily reflect a different hydropathic property: residue hydrophilicity (also reflected by the Kyte-Doolittle hydropathy scale). Our results suggest that while hydrophobic side-chain interactions are primarily involved in determining stability of the folded conformation, hydrogen bonding, and similar polar interactions are primarily involved in conformational and interaction specificity.     

Molecular heterogeneity of the isolated surface glycoprotein from variant AnTat 1.1 of Trypanosoma brucei brucei

Variant surface glycoprotein (VSG) of Trypanosoma brucei brucei AnTat 1.1 was released by means of the procedure described by Baltz et al. ([1976], Ann. Immunol. [Inst. Pasteur] 127C, 761-774). The concanavalin-A chromatography yielded 3 VSG fractions according to the addition, in the elution buffer, of alpha-methyl-D-mannopyranoside, beta-mercaptoethanol, and sodium dodecyl sulfate. These VSG fractions showed heterogeneous behaviour on reverse-phase high performance liquid chromatography. The 3 VSG fractions as well as the myristylated VSG of AnTat 1.1 essentially consist of dimer VSG forms linked through a disulfide bridge, as judged by sodium dodecyl sulfate polyacrylamide gel electrophoresis, under reducing and nonreducing conditions.     

Surface hydrophobicity causes SO2 tolerance in lichens

BACKGROUND AND AIMS: The superhydrophobicity of the thallus surface in one of the most SO(2)-tolerant lichen species, Lecanora conizaeoides, suggests that surface hydrophobicity could be a general feature of lichen symbioses controlling their tolerance to SO(2). The study described here tests this hypothesis. METHODS: Water droplets of the size of a raindrop were placed on the surface of air-dry thalli in 50 lichen species of known SO(2) tolerance and contact angles were measured to quantify hydrophobicity. KEY RESULTS: The wettability of lichen thalli ranges from strongly hydrophobic to strongly hydrophilic. SO(2) tolerance of the studied lichen species increased with increasing hydrophobicity of the thallus surface. Extraction of extracellular lichen secondary metabolites with acetone reduced, but did not abolish the hydrophobicity of lichen thalli. CONCLUSIONS: Surface hydrophobicity is the main factor controlling SO(2) tolerance in lichens. It presumably originally evolved as an adaptation to wet habitats preventing the depression of net photosynthesis due to supersaturation of the thallus with water. Hydrophilicity of lichen thalli is an adaptation to dry or humid, but not directly rain-exposed habitats. The crucial role of surface hydrophobicity in SO(2) also explains why many markedly SO(2)-tolerant species are additionally tolerant to other (chemically unrelated) toxic substances including heavy metals.