IP blacklist

Flavivirus reveals its access code Fritz et al. have identifi ed an amino acid switch that fl aviviruses fl ip to gain access to cells. Flaviviruses such as tick-borne encephalitis virus (TBEV), yellow fever, and dengue are dangerous human pathogens. These membrane-encircled viruses enter cells by being gobbled up into endosomes and fusing their membrane with that of the endosome. Fusion is triggered by the endosome's acidic environment. Low pH prompts the aptly named fusion protein, on the virus's outer membrane, to change shape and grab hold of the endosome membrane, bringing the two membranes together. In their search for possible pH sensors, researchers have focused on fi ve highly conserved histidine residues in the fl avivirus fusion protein. The chemical properties of histidines make them prime candidates—they switch from uncharged to having a double positive charge upon acidifi cation of their environment, such as that in endosomes. Fritz et al. replaced each of the fi ve histidines of the TBEV fusion protein with alternative residues and observed the virus's fusion ability. Given the conservation of the fi ve histidines, the team was surprised, that mutation of one of the histidines, His323, was suffi cient to completely abolish fusion. Individual mutation of three of the others had no effect on fusion whatsoever, and mutation of the fourth led to an untestable ill-formed fusion protein. The team went on to show that mutation of the crucial His323 interfered with the pH-induced shape change of the fusion protein. Like gatecrashers at a celebrity party, there are proteins that turn up in immunoprecipitation (IP) experiments despite having no real association with the A-list protein of interest. But now, researchers-cum-bouncers, Trinkle-Mulcahy et al. are armed with a list of repeat gatecrashers to look out for. One way to lessen the chance of uninvited proteins turning up in your IP is to increase the stringency of purifi cation methods; however, this is also likely to remove low affi nity, low abundance and yet genuine interaction partners. To keep stringency low but cope with the large number of co-precipitating proteins, researchers have developed a mass spectrometry approach called SILAC (stable isotope labeling with amino acids in culture) that identifi es and quantifi es all precipitated proteins. Trinkle-Mulcahy and colleagues now describe an optimized methodology for the technique with the important addition of a " bead proteome " —a blacklist of proteins that bind nonspecifi cally to …