Sequence homologies analysis

In vitro assays to assess allergenicity (source of the protein, amino acid sequence homology analysis, physicochemical properties)... 

No sequence homologies can be detected. This is, perhaps, not surprising. The X-ray structure analysis of lysozyme by Phillips has shown that the polypeptide chain is folded in a way which puts none of the amino acids in sequential vicinity of the catalytic Asp-52 and Glu-37 that are near to the bound substrate. Comparable folding patterns can probably be realized with widely differing arrangements of amino acids, and thus the apparent lack of homologies. 

Henrissat, B. (1990) Weak sequence homologies among chitinases detected by clustering analysis. Protein Sequence Data Analysis 3, 523-526. 

In addition to bcl-2, another hitherto completely unexpected target for the actions of chronic lithium and VPA has been identified from the mRNA RT-PCR DD study described above. Another clone, also derived from a transcript whose levels were increased by both lithium and VPA, shows very strong homology to a human mRNA-binding protein, the AUH protein ([54, 55] Genbank accession number X79888). BESTFIT analysis revealed 83.2% sequence homology between this rodent clone and the human AUH protein [54—56]. 

In summary, it is reasonable to conclude that bioinformatic analysis of structural similarities to, or of sequence homology with, known protein allergens, and evaluation of stability with SGF, can both contribute, if interpreted cautiously, to an overall assessment of sensitizing hazard. However, these analyses, neither alone nor in combination, provide a definitive answer regarding allergenic potential, and for this reason there has been interest in exploring a more holistic approach (and more definitive assessment) that may be provided by suitable animal models. 

Figure 10.1. The membrane topology proposed for D. vulgaris Hildenborough DcrH based on hydrophathy analysis and sequence homologies to other bacterial chemoreceptors (Deckers and Voordouw 1996). Shaded boxes, putative membrane-spanning (residues 9-30 and 422 31), excitation (residues 653-692), and methylation (residues 757-764) regions. The C-terminal box (residues 824-959) indicates the Hr-like region. Reprinted with permission from Xiong et al. (2000), copyright 2000 American Chemical Society.

Much of the FLS biochemical and structure/fimction analysis has focused on a protein from C. unshiu (mandarin). A cDNA was isolated based on sequence homology to an Arabidopsis FLS EST (153O10T7) and used as a probe to determine regulation of gene expression [92]. Higher expression was observed in young leaf, flower, peel, and juice sac/segment epidermis tissues. Expression decreased with tissue age, as has been observed for citrus CHS, CHI, and F3H [57]. Southern analysis... 

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