The Kahn Dynamic Proteomics Database

Alon lab, Weizmann Institute of Science

 

The Kahn Dynamic Proteomics project aims at monitoring the position and amounts of endogenous proteins in individual living human cells. This is based on the Library of Annotated Reporter Cell-clones (LARC). Each cell-line clone contains an endogenous protein fused to yellow fluorescent protein (YFP), expressed from its endogenous chromosomal location with its natural regulation. Labeling with YFP was done by exon-tagging (also known as CD-tagging), where YFP, flanked by splice signals, was delivered into the genome using a retrovirus. YFP is then spliced into the protein as a new exon. Protein identity was established by sequencing the cDNA. The cell line used is the H1299 non-small lung cell carcinoma line which stably expressed the viral receptor. This is a robust cell-line with a nicely spread cell morphology that is highly photogenic for microscopy purposes. Several lines of evidence indicate that over 2/3 of the tagged proteins retain their proper functionality and localization.

The amount and location of each tagged protein is monitored by means of automated time-lapse fluorescence microscopy in controlled CO2 and humidity conditions. Movies of the cells are automatically processed using dedicated image analysis software. This yields quantitative traces of protein amounts and localization over time for each individual cell in a response to the chemotheraphy drug Camptothecin (C9911 Sigma).

This site contains a database of the proteins tagged by YFP. Each protein entry includes detailed sequence and functional annotation, images of protein localization, movies and protein dynamics and links to other databases: InterPro, GeneCards, Ensembl, Entrez, UniProt. Sequence Analysis tools are available for up to 70 sequences provided by a user within all the cDNA sequences in the database. The Search and Comparison of protein dynamics are offered for all unique proteins with high-quality time-lapse fluorescence movies available in the database. The site is updated regularly as new clones are added to the protein library.

Supported by the Kahn Family Foundation.