A word of caution about biological inference - Revisiting cysteine covalent state predictions

Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology

Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.

Chemosensors for biogenic amines and biothiols

There is burgeoning interest among supramolecular chemists to develop novel molecular systems to detect biogenic amines and bio-thiols in aqueous and non-aqueous media due to their potential role in biological processes. Biogenic amines are biologically important targets because of their involvement in the energy metabolism of human biological systems and their requirement is met through food and nutrition. However, the increasing instances of serious health problems due to food toxicity have raised the quality of food nowadays. Biogenic amines have been frequently considered as the markers or primary quality parameters of foods like antioxidant properties, freshness and spoilage. For instance, these amines such as spermine, spermidine, cadavarine, etc. may originate during microbial decarboxylation of amino acids of fermented foods/beverages. These amines may also react with nitrite available in certain meat products and concomitantly produce carcinogenic nitrosamine compounds. On the other hand, it is also well established that biothiols, particularly, thiol amino acids, provide the basic characteristics to food including flavor, color and texture that determine its acceptability. For instance, the reduction of thiol groups produces hydrogen sulfide which reduces flavour as in rotten eggs and spoiled fish, and the presence of hydrogen sulfide in fish is indicative of spoilage. Thus, biogenic amines and bio-thiols have attracted the profound interest of researchers as analytical tools for their quantification. Much scientific and technological information is issued every year, where the establishment of precise interactions of biogenic amines and bio-thiols with other molecules is sought in aqueous and non-aqueous media. This review summarizes the optical chemosensors developed for the selective detection of biogenic amines and bio-thiols.