Locating-proteins-in-the-cell-using-TargetP，-SignalP-and-related-tools.pdfVIP

PROTOCOL Locating proteins in the cell using TargetP, SignalP and related tools 1 2 3 2 Olof Emanuelsson , Søren Brunak , Gunnar von Heijne Henrik Nielsen 1Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden. 2Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark. 3Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden. Correspondence should be addressed to H.N. (hnielsen@cbs.dtu.dk). Published online 19 April 2007; doi:10.1038/nprot.2007.131 s Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe l o c the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and o t chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other o r p sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization e r u prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of t a n the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological / m o Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular c . localization predictors. Finally, we di