An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data

Abstract

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

Figure 1.

Visualization of 3D structure of SARS-CoV PLP protease (nsp3d). The key active site residues of PLP, and a nearby tryptophan proposed to stabilize the tetrahedral intermediate in the catalytic cycle, are illustrated in the annotation for the 3D structure that is viewable at RC. The 3D structure is fully interactive and different views are obtained by clicking on the buttons associated with the views’ description. The different views illustrate features described by Ratia et al. (31).

Figure 2.

Experiment and annotation data of Mouse Mitogen-activated gene. (A) search result; (B) mitogen-activated protein profile of macrophages under B. anthracis infection; (C) mitogen-activated protein profile of Nramp1-posititve and Nramp1-negative macrophages under S. typhimurium infection; (D) mitogen-activated gene expression profile of macrophages under different treatments.

Figure 3.

The studied Chaperone protein having a peptide signal feature. (A) search result by entering chaperone and signal keywords; (B) the summary information of Chaperone stored in the RC system; (C) the comprehensive annotation data of the chaperone protein.