Prediction of Nuclear Proteins with a Charge Periodicity of 28 Residues in Eukaryote Genomes

Abstract

Recently, we found that approximately 3% of all amino acid sequences from the human genome show a significant charge periodicity of 28 residues [1]. The largest fraction of proteins with a charge periodicity of 28 residues (PCP28) was nuclear proteins, although many PCP28 were poorly identified. Another category of PCP28 was motor proteins which have located in the cytoplasm. We investigated the difference in the physicochemical properties of amino acid sequences between the nuclear and cytoplasmic PCP28 for developing a prediction system to classify of PCP28. First we extracted PCP28 from all amino acid sequences in the public database of Swiss-Prot release 48.7. Then we classified PCP28 into two categories: proteins in the nucleus and those in the cytoplasm. Second, the physicochemical properties of the two PCP28 categories were compared, allowing calculation of two discrimination scores from entire amino acid sequences as well as from the local regions around clusters of positive charges which are characteristic of nuclear localization signals. Finally, using the scores from the global and local parameters, the prediction system was developed with a sensitivity of 92% and specificity of 88% [2]. Then, to study a biological meaning of PCP28, we discriminated nuclear PCP28 from other types of PCP28 in eukaryote genomes by this prediction system. We compared the number of all nuclear PCP28 in vertebrate and invertebrate genomes. The results showed that nuclear PCP28 is specifically increased in vertebrate genomes and that the ratio of other types of PCP28 is almost constant in all eukaryote genomes [3]. These findings strongly suggest that nuclear PCP28 is an essential protein for vertebrate organisms.