Cover Picture: Proteomics 3/2008

In this issue of Proteomics you will find the following highlighted articles: Once upon a complex busy Once upon a complex busy spied CN Pang et al. who found a doozy: proteins partnered for tours of duty and lived lives measured by general utility. All right, enough is enough, back to work. From a variety of studies, particularly in yeast, it is now apparent that specific protein complexes form and disperse as needed or not, in solution or membrane‐associated. A common general structure has been proposed: core proteins associated with functional modules and attachment mediators. This paper is an analysis of data from five quantitative studies of protein characteristics and complexes in yeast, including role in complexes, protein abundance and half‐life. With three types of proteins there are six pair‐wise interactions. Attachment proteins were the most abundant, modules were the longest lived, and core proteins exhibit the most significant changes after changes in growth medium. Pang, C. N. I. et al. , Proteomics 2008, 8 , 425–434. Express yourself through another species, array yourself on an explosive sheet. What a life The wonder and the headache of modern life science is how little it takes to have a measurable effect on the behavior of a cell or an organism. Thus, the continuing demand for molecular amplification schemes. In their study of Johne’s disease, a bacterial infection of cattle, sheep, goats and a number of wild species, Bannantine et al. used an E. coli expression system. Selected genes from Mycobacterium paratuberculosis were cloned into a tagging vector, over‐expressed in E. coli , affinity‐purified, and spotted on nitrocellulose membranes. Of 50 expression clones, 43 yielded tagged fusion protein and 31 (62%) produced satisfactory amounts of protein to study. The arrayed proteins were used to evaluate antibody profiles in lab animals and cattle, both naturally infected and experimentally infected. Although the naturally infected animals exhibited symptoms of Johne’s disease and the experimentally infect­ed ones did not, both populations had essentially the same antibody profile. Bannantine, J. P. et al., Proteomics 2008, 8 , 463–474. Fishing for fucosyl (and other) transferases Catching the elusive glycosyltransferases is a sporting scientist’s challenge: they come in over 80 multimember families that are structurally similar, there are relatively few copies per cell, and they live in the tangles of the Golgi membranes. Given the impact of post‐translational glycosylation on protein function, understanding the regulation of these enzymes is important. Transcriptional regulation is not as sensitive or subtle as required. Lin et al. developed a concentration/purification scheme to improve the chances of catching the transferases of interest. The key step is concentrating transferases in a Golgi extract by chromatography on a UDP‐ or GDP‐affinity column. The subsequent step cleans the sample up by electrophoresing the sample just to the top edge of the separating gel. After in‐gel digestion and LC/MS, secure identification of the transferases is fairly straightforward. They also describe sensitive fluorescent transferase activity assays. Lin, C.‐H. et al., Proteomics 2008, 8 , 475–483.