Software

Refinement and prediction of protein prenylation motifs

Sebastian Maurer-Stroh and Frank Eisenhaber

IMP - Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria

author email corresponding author email

Genome Biology 2005, 6:R55doi:10.1186/gb-2005-6-6-r55

Published:	27 May 2005

Subject areas: Bioinformatics, Molecular biology

Abstract

We refined the motifs for carboxy-terminal protein prenylation by analysis of known substrates for farnesyltransferase (FT), geranylgeranyltransferase I (GGT1) and geranylgeranyltransferase II (GGT2). In addition to the CaaX box for the first two enzymes, we identify a preceding linker region that appears constrained in physicochemical properties, requiring small or flexible, preferably hydrophilic, amino acids. Predictors were constructed on the basis of sequence and physical property profiles, including interpositional correlations, and are available as the Prenylation Prediction Suite (PrePS, http://mendel.imp.univie.ac.at/sat/PrePS webcite) which also allows evaluation of evolutionary motif conservation. PrePS can predict partially overlapping substrate specificities, which is of medical importance in the case of understanding cellular action of FT inhibitors as anticancer and anti-parasite agents.