Finding nuclear localization signals

TitleFinding nuclear localization signals
Publication TypeJournal Article
Year of Publication2000
AuthorsCokol, M, Nair, R, Rost, B
JournalEMBO Rep
Volume1
Pagination411-5
KeywordsAnimals Cell Nucleus/metabolism Computer Simulation Cytoplasm/metabolism DNA/metabolism DNA-Binding Proteins/chemistry Databases, Biological Mutagenesis *Nuclear Localization Signals Protein Transport RNA/metabolism Software, Factual Genome Humans Models
Abstract

A variety of nuclear localization signals (NLSs) are experimentally known although only one motif was available for database searches through PROSITE. We initially collected a set of 91 experimentally verified NLSs from the literature. Through iterated 'in silico mutagenesis' we then extended the set to 214 potential NLSs. This final set matched in 43% of all known nuclear proteins and in no known non-nuclear protein. We estimated that >17% of all eukaryotic proteins may be imported into the nucleus. Finally, we found an overlap between the NLS and DNA-binding region for 90% of the proteins for which both the NLS and DNA-binding regions were known. Thus, evolution seemed to have used part of the existing DNA-binding mechanism when compartmentalizing DNA-binding proteins into the nucleus. However, only 56 of our 214 NLS motifs overlapped with DNA-binding regions. These 56 NLSs enabled a de novo prediction of partial DNA-binding regions for approximately 800 proteins in human, fly, worm and yeast.