The Burnham Institute's Adam Godzik is the senior author on a paper appearing this week in PLoS Biology that attempted to map the "dark matter of protein space," or uncharacterized proteins with domains of unknown function of which there are about 2,200 families. Upon analyzing the structures of 248 of these families, Godzik's team found that two-thirds of the DUF families are "remote homologs of already known protein families." This suggests that "the protein universe is made up of a relatively small and stable number of 'extended neighborhoods' that bring together distantly related protein families."
José Peregrín-Alvarez at the Hospital for Sick Children in Toronto is first author on work that studied protein interactions in the E. coli proteome. In this "important step towards a 'systems view of E. coli," as the abstract says, the scientists blended experimental and computational interaction data to build a network of almost 4,000 interactions between almost 2,000 proteins. Then, they pinpointed groups of proteins that could fit into about 300 "modules ... that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes," they say. Their work was published in PLoS Computational Biology this week.
PLoS Genetics tackles the debate over if – and how – GWAS data should be made publicly available in order to both protect study participants' privacy and allow researchers to advance the field. Weighing in are the Public Population Project in Genomics, which advocates for "a universal researcher ID with an access permit mechanism for bona fide researchers"; Catherine Heeney, Naomi Hawkins, Jantina de Vries, Paula Boddington, and Jane Kaye of the University of Oxford Ethox Centre; Harvard's George Church, who promotes full disclosure; the University of Cambridge's Martin Bobrow; and Bruce Weir at the University of Washington.
Researchers at the University of Illinois at Urbana-Champaign, National University of Singapore, A*STAR, and KAIST in South Korea used quantitative data to study the large-scale organization of N-linked glycosylation pathways in mammalian cells. They found that the pathways are "extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis." Although enzymes that attach glycans to their binding partners can act on many different glycans, cross-talk between pathways is limited, they found. Their work appears in PLoS One.