Abstract
The nucleus is the largest and the highly organized organelle of eukaryotic cells. Within nucleus exist a number of pseudo-compartments, which are not separated by any membrane, yet each of them contains only a specific set of proteins. Understanding protein sub-nuclear localization can hence be an important step towards understanding biological functions of the nucleus. Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins. This method predicts protein localization for 10 different sub-nuclear locations sequentially by combining presence or absence of unique Pfam domain and amino acid composition based SVM model. The prediction accuracy during leave-one-out cross-validation for centromeric proteins was 85.05%, for chromosomal proteins 76.85%, for nuclear speckle proteins 81.27%, for nucleolar proteins 81.79%, for nuclear envelope proteins 79.37%, for nuclear matrix proteins 77.78%, for nucleoplasm proteins 76.98%, for nuclear pore complex proteins 88.89%, for PML body proteins 75.40% and for telomeric proteins it was 83.33%. Comparison with other reported methods showed that SubNucPred performs better than existing methods. A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at http://14.139.227.92/mkumar/subnucpred/. Standalone version of SubNucPred can also be downloaded from the web-server.
Highlights
Nuclear proteins are produced in cytoplasm from where they are transported to the nucleus
Knowledge of proteins sub-nuclear localization is essential for understanding the cellular processes and genomic regulation and to understand the clinico-pathological manifestations caused due to mis-localized nuclear proteins
We developed a combined method, SubNucPred, for predicting the sub-nuclear location of nuclear proteins with high accuracy by combining Pfam domain information and Support Vector Machine (SVM) score
Summary
Nuclear proteins are produced in cytoplasm from where they are transported to the nucleus. At present several experimental methods like co-expression of fluorescent proteins [1], electron and fluorescence microscopy [2,3], immuno-fluorescence labeling [4,5], photo-activated localization microscopy [6], liquid-chromatography-tandem mass spectrometry [7,8] etc are available to study protein localization. Alterations in gene expression of proteins located in different sub-nuclear locations may cause cancer and other genetic diseases [9,10]. The prediction of protein localization at the sub-nuclear level is difficult compared to the generalized subcellular level due to (i) absence of physical barrier or membrane within the cell nucleus [11] and (ii) dynamic nature of protein complexes within the nucleus [12]
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