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Finding nuclear localization signals.

M Cokol·R Nair·B Rost
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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.

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AnimalsCell NucleusComputer SimulationCytoplasmDNADNA-Binding ProteinsDatabases, FactualGenomeHumansModels, BiologicalMutagenesisNuclear Localization SignalsProtein TransportRNASoftwareJournal Article

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M Cokol, R Nair, B Rost. 2000. Finding nuclear localization signals.. https://doi.org/10.1093/embo-reports%2Fkvd092

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