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PubMed1985

Phosphorylation-dependent subcellular translocation of a Ca2+/calmodulin-dependent protein kinase produces an autonomous enzyme in Aplysia neurons.

We have shown previously that the subcellular distribution of a major calmodulin-binding protein is altered under conditions causing increased synthesis of cAMP in Aplysia neurons (Saitoh, T., and J. H. Schwartz, 1983, Proc. Natl. Acad. Sci. USA, 80:6708-6712). We now provide evidence that this Mr 55,000 protein is a subunit of a Ca2+/calmodulin-dependent kinase: (a) both the Mr 55,000 calmodulin-binding protein and kinase activity are loosely attached to the membrane-cytoskeletal complex; (b) both kinase activity and the Mr 55,000 protein are translocated from the membrane-cytoskeleton complex to the cytoplasm under conditions that cause the change in the subcellular distribution of the Mr 55,000 calmodulin-binding protein; and (c) calmodulin-binding activity of the Mr 55,000 protein and the ability to carry out the Ca2+/calmodulin-dependent phosphorylation of synapsin I are purified in parallel. The subcellular localization of the Ca2+/calmodulin-dependent protein kinase appears to be under control of two second messengers: Ca2+ and cAMP. We find that the Mr 55,000 subunit is phosphorylated when the extracted membrane-cytoskeleton complex is incubated with Ca2+, calmodulin, and ATP, with the concomitant release of this phosphorylated peptide from the complex. Previously, we had found that, when translocation occurs in extracts in the presence of cAMP and ATP (but in the absence of Ca2+), there was no detectable phosphorylation of the Mr 55,000 subunit itself. The subcellular distribution of the subunit thus appears to be influenced by (a) cAMP-dependent phosphorylation, which, we infer, modifies some as yet unidentified structural component, causing the release of the enzyme; and (b) Ca2+/calmodulin-dependent phosphorylation of the Mr 55,000 subunit. These studies also suggest that phosphorylation has an important regulatory consequence: during the Ca2+/calmodulin-dependent translocation of the Mr 55,000 subunit, the kinase appears to be activated, becoming independent of added Ca2+/calmodulin.

Animals↗

PubMed1981

Analytical study of microsomes and isolated subcellular membranes from rat liver. VII. Distribution of protein-bound sialic acid.

Detailed investigations by quantitative centrifugal fractionation were conducted to determine the subcellular distribution of protein-bound sialic acid in rat liver. Homogenates obtained from perfused livers were fractionated by differential centrifugation into nuclear fraction, large granules, microsomes, and final supernate fraction, or were used to isolate membrane preparations enriched in either plasma membranes or Golgi complex elements. Large granule fractions, microsome fractions, and plasma membrane preparations were subfractionated by density equilibration in linear gradients of sucrose. In some experiments, microsomes or plasma membrane preparations were treated with digitonin before isopycnic centrifugation to better distinguish subcellular elements related to the plasma membrane or the Golgi complex from the other cell components; in other experiments, large granule fractions were obtained from Triton WR-1339-loaded livers, which effectively resolve lysosomes from mitochondria and peroxisomes in density gradient analysis. Protein-bound sialic acid and marker enzymes were assayed in the various subcellular fractions. The distributions obtained show that sialoglycoprotein is restricted to some particular domains of the cell, which include the plasma membrane, phagolysosomes, and possibly the Golgi complex. Although sialoglycoprotein is largely recovered in the microsome fraction, it has not been detected in the endoplasmic reticulum-derived elements of this subcellular fraction. In addition, it has not been detected either in mitochondria or in peroxisomes. Because the sialyltransferase activities are associated with the Golgi complex, the cytoplasm appears compartmentalized into components which biogenetically involve the Golgi apparatus and components which do not.

Animals↗

PubMed2004

ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST.

Automated prediction of subcellular localization of proteins is an important step in the functional annotation of genomes. The existing subcellular localization prediction methods are based on either amino acid composition or N-terminal characteristics of the proteins. In this paper, support vector machine (SVM) has been used to predict the subcellular location of eukaryotic proteins from their different features such as amino acid composition, dipeptide composition and physico-chemical properties. The SVM module based on dipeptide composition performed better than the SVM modules based on amino acid composition or physico-chemical properties. In addition, PSI-BLAST was also used to search the query sequence against the dataset of proteins (experimentally annotated proteins) to predict its subcellular location. In order to improve the prediction accuracy, we developed a hybrid module using all features of a protein, which consisted of an input vector of 458 dimensions (400 dipeptide compositions, 33 properties, 20 amino acid compositions of the protein and 5 from PSI-BLAST output). Using this hybrid approach, the prediction accuracies of nuclear, cytoplasmic, mitochondrial and extracellular proteins reached 95.3, 85.2, 68.2 and 88.9%, respectively. The overall prediction accuracy of SVM modules based on amino acid composition, physico-chemical properties, dipeptide composition and the hybrid approach was 78.1, 77.8, 82.9 and 88.0%, respectively. The accuracy of all the modules was evaluated using a 5-fold cross-validation technique. Assigning a reliability index (reliability index > or =3), 73.5% of prediction can be made with an accuracy of 96.4%. Based on the above approach, an online web server ESLpred was developed, which is available at http://www.imtech.res.in/raghava/eslpred/.

Artificial Intelligence↗

PubMed2005

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107,000 proteins from 10 model organisms (and growing), covering the major kingdoms and phyla for which annotated proteomes exist (http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB). The PA-GOSUB database effectively expands the coverage of subcellular localization and GO function annotations by a significant factor (already over five for subcellular localization, compared with Swiss-Prot v42.7), and more model organisms are being added to PA-GOSUB as their sequenced proteomes become available. PA-GOSUB can be used in three main ways. First, a researcher can browse the pre-computed PA-GOSUB annotations on a per-organism and per-protein basis using annotation-based and text-based filters. Second, a user can perform BLAST searches against the PA-GOSUB database and use the annotations from the homologs as simple predictors for the new sequences. Third, the whole of PA-GOSUB can be downloaded in either FASTA or comma-separated values (CSV) formats.

Amino Acid Sequence↗

PubMed1999

Relationship between the subcellular localization and structures of catalytic domains of FKBP-type PPIases.

The Schizosaccharomyces pombe gene, fkp39(+), encoding a homolog of FKBP(FK506 binding protein)-type peptidyl prolyl cis-trans isomerase (PPIase), was isolated and the primary structure was determined. This gene product (SpFkbp39p) showed PPIase enzymatic activity in a chymotrypsin-dependent enzyme assay involving recombinant SpFkbp39p. Comparison of the primary structures of the catalytic domains of FKBPs, including SpFkbp39p, revealed that FKBPs could be classified into four groups. This categorization corresponding to the known subcellular localization of the FKBPs, makes the prediction of the subcellular localization of FKBPs based on their primary structures feasible. SpFkbp39p was considered to be a member of the nuclear-type FKBP group from this relationship between primary structure and subcellular localization. An immunofluorescence assay against HA-epitope-tagged SpFkbp39p revealed that SpFkbp39p is localized to the nucleus, as predicted. Residues conserved in a "group-specific" manner in the catalytic domain were mapped to their corresponding three-dimensional positions; these "group-specific" residues were located in close proximity in distinct regions mostly on the protein surface, which implies the presence of "group-specific" regulatory functional regions. We also found that nuclear-type FKBPs, including SpFkbp39p, have two highly conserved domains other than catalytic ones, with further basic and acidic charged regions, especially in the case of nuclear-type FKBPs. This is the first report indicating that there is a rule for the relationship between the subcellular localization and structure of the catalytic domain of a FKBP.

Amino Acid Sequence↗

PubMed1983

Subcellular distribution of steroid delta 4-5 alpha-reductase and 3 alpha-hydroxysteroid dehydrogenase in the rat epididymis during sexual maturation.

The curve of the specific activity of rat epididymal nuclear delta 4-5 alpha-reductase is bell shaped as a function of age, whereas that of cytoplasmic 3 alpha-hydroxysteroid dehydrogenase does not change significantly with age. The present study examines the subcellular distribution of delta 4-5 alpha-reductase and 3 alpha-hydroxysteroid dehydrogenase in the caput-corpus and cauda epididymidis during development. A 5-step discontinuous sucrose gradient was developed for fractionation of epididymal homogenates. By using enzyme markers specific for different subcellular organelles, the five different subcellular fractions obtained were shown to be of cytoplasmic, microsomal, mitochondrial, nuclear and spermatozoal origin. 3 alpha-Hydroxysteroid dehydrogenase activity was associated only with the cytoplasmic fraction. The activity of the enzyme did not change significantly with age in either the caput-corpus or cauda epididymidis. delta 4-5 alpha-Reductase activity was found in fractions containing microsomal and nuclear markers. delta 4-5 alpha-Reductase activity in the nuclear fraction of the caput-corpus epididymidis was evident in the youngest age group (Day 25), increased 4-fold and peaked in the next age group (Day 35), and declined with each successive age group: Day 45 (60% of maximum), Day 60 (20% of maximum), Day 75 (15% of maximum) and Day 105 (10% of maximum). In contrast, microsomal delta 4-5 alpha-reductase activity increased successively from Day 25 to Day 105; enzyme activity doubled between these two ages. The ratio of nuclear to microsomal delta 4-5 alpha-reductase activity from the caput-corpus epididymidis thus changed markedly with age: Day 25:1.32; Day 35:3.76; Day 45:2.44; Day 60:1.03; Day 75:0.41; and Day 105:0.21. In the cauda epididymidis nuclear delta 4-5 alpha-reductase activity was only evident at Day 35 and Day 45; in microsomal fractions, activity was first found at Day 35 and did not subsequently change with age. These results demonstrate that: 1) epididymal 3 alpha-hydroxysteroid dehydrogenase activity is found only in the cytoplasmic fraction; 2) delta 4-5 alpha-reductase activity is found in nuclear and microsomal fractions; and 3) the subcellular distribution of delta 4-5 alpha-reductase activity changes markedly with age and epididymal section, suggesting differential regulation of nuclear and microsomal delta 4-5 alpha-reductase activities.

3-Hydroxysteroid Dehydrogenases↗

PubMed1967

Senescence: action of auxin and kinetin in control of RNA and protein synthesis in subcellular fractions of bean endocarp.

A comparative study was made of the effects of auxin (alpha-naphthalene acetic acid), kinetin (6-furfurylaminopurine) and a mixture of auxin and kinetin applied in vivo on synthesis of RNA and protein and the distribution of such synthesis amongst the subcellular fractions of sections of endocarp from Kentucky Wonder pole beans (Phaseolus vulgaris, L.). Auxin caused considerable enhancement of incorporation of labeled precursors into RNA and protein of all subcellular fractions, and induced net synthesis of RNA and protein. That auxin-induced net synthesis of protein is repressed by actinomycin D indicates that auxin acts primarily to stimulate synthesis of RNA, as a result of which synthesis of protein is enhanced. The effect of kinetin alone on synthesis of RNA, or of kinetin on auxin-induced synthesis of RNA was variable, with either stimulation or inhibition observed in different experiments. Kinetin-enhancement of synthesis of both RNA and protein in subcellular fractions also varied, with enhancement of synthesis in 1 or all subcellular fractions among different experiments. The variable effect of kinetin did not seem to be related to the amount of endogenous or added auxin. The mode of action of kinetin is discussed.

Journal Article↗

PubMed1992

Subcellular Distribution of O-Acetylserine(thiol)lyase in Cauliflower (Brassica oleracea L.) Inflorescence.

The subcellular localization of O-acetyiserine(thiol)lyase (EC 4.2.99.8) in nongreen tissue from higher plants has been studied using purified proplastids, mitochondria, and protoplasts from cauliflower (Brassica oleracea L.) buds as a source of subcellular fractions. O-Acetylserine(thiol)lyase has been detected in both organelles (proplastids and mitochondria) and a cytosolic extract obtained by protoplast fractionation. We confirmed these observations, demonstrating that a form of the enzyme different in global charge and separated from others by anion-exchange chromatography corresponded to each subcellular location. Our observations are consistent with the need for cysteine biosynthesis in each subcellular compartment where the synthesis of proteins occurs.

Journal Article↗

PubMed1990

Two Closely Related Wheat Storage Proteins Follow a Markedly Different Subcellular Route in Xenopus laevis Oocytes.

[alpha]-Gliadins and [gamma]-gliadins are two closely related wheat storage proteins that evolved from a common ancestral gene. However, synthesis of [alpha]-gliadins and [gamma]-gliadins in Xenopus laevis oocytes revealed striking differences in their subcellular routing. The major portion of [alpha]-gliadin accumulated inside the oocyte, whereas most of the [gamma]-gliadin was secreted. Disruption of the Golgi apparatus by monensin revealed that the major part of secretion of [gamma]-gliadin is Golgi mediated. The difference in the subcellular route between [alpha]-gliadin and [gamma]-gliadin may be attributed to differential transport from the endoplasmic reticulum to the Golgi apparatus, a process that is generally the rate-limiting step in protein secretion. Coinjection of the two mRNAs had no effect on their routing, indicating no interaction between them. Our results support the hypothesis that subcellular transport of gliadins in wheat endosperm occurs in two separate routes; one is Golgi mediated, and the other is not. We also show that the subcellular transport may be markedly affected by small structural variations within closely related storage proteins.

Journal Article↗

PubMed2004

Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions.

Gram-negative bacteria have five major subcellular localization sites: the cytoplasm, the periplasm, the inner membrane, the outer membrane, and the extracellular space. The subcellular location of a protein can provide valuable information about its function. With the rapid increase of sequenced genomic data, the need for an automated and accurate tool to predict subcellular localization becomes increasingly important. We present an approach to predict subcellular localization for Gram-negative bacteria. This method uses the support vector machines trained by multiple feature vectors based on n-peptide compositions. For a standard data set comprising 1443 proteins, the overall prediction accuracy reaches 89%, which, to the best of our knowledge, is the highest prediction rate ever reported. Our prediction is 14% higher than that of the recently developed multimodular PSORT-B. Because of its simplicity, this approach can be easily extended to other organisms and should be a useful tool for the high-throughput and large-scale analysis of proteomic and genomic data.

Artificial Intelligence↗

PubMed2006

Subcellular localization of mammalian type II membrane proteins.

Application of a computational membrane organization prediction pipeline, MemO, identified putative type II membrane proteins as proteins predicted to encode a single alpha-helical transmembrane domain (TMD) and no signal peptides. MemO was applied to RIKEN's mouse isoform protein set to identify 1436 non-overlapping genomic regions or transcriptional units (TUs), which encode exclusively type II membrane proteins. Proteins with overlapping predicted InterPro and TMDs were reviewed to discard false positive predictions resulting in a dataset comprised of 1831 transcripts in 1408 TUs. This dataset was used to develop a systematic protocol to document subcellular localization of type II membrane proteins. This approach combines mining of published literature to identify subcellular localization data and a high-throughput, polymerase chain reaction (PCR)-based approach to experimentally characterize subcellular localization. These approaches have provided localization data for 244 and 169 proteins. Type II membrane proteins are localized to all major organelle compartments; however, some biases were observed towards the early secretory pathway and punctate structures. Collectively, this study reports the subcellular localization of 26% of the defined dataset. All reported localization data are presented in the LOCATE database (http://www.locate.imb.uq.edu.au).

Animals↗

PubMedDate not supplied

Effects of inhibitors of RNA and protein synthesis on the subcellular distribution of the eukaryotic translation initiation factor, eIF-5A, and the HIV-1 Rev protein.

The subcellular distributions of the endogenous eukaryotic translation initiation factor, eIF-5A, and Rev, a protein of the human immunodeficiency virus proposed to interact with eIF-5A, were studied in COS-7 cells treated with inhibitors of RNA or protein synthesis. We have previously shown that transiently expressed Rev is localized in the nucleolus, whereas eIF-5A is primarily in the cytoplasm. The subcellular localization of Rev was not affected by treatment with protein synthesis inhibitors (cycloheximide, CHX, 10 micrograms/ml; puromycin, 10 micrograms/ml), although its location changed from predominantly the nucleolus to the cytoplasm after treatment with RNA synthesis inhibitors (actinomycin D, 4 micrograms/ml, and 5,6-dichloro-1 beta-D-ribofuranosylbenzimidazole, DRB; 0.1 mM), as previously reported. In contrast, none of the RNA synthesis inhibitors (alpha-amanitin, 10 micrograms/ml; actinomycin D, 4 micrograms/ml, and DRB, 0.1 mM) caused any significant changes in the subcellular distribution pattern of eIF-5A. However, treatment with puromycin, a protein synthesis inhibitor known to dissociate ribosomes, dramatically altered the subcellular distribution pattern of eIF-5A in 30% of the cell population. In these cells, the staining of eIF-5A was changed from an endoplasmic reticulum (ER) net work-like perinuclear structure to a patched dotted pattern dispersed throughout the cytoplasm. This change was not observed in the same cells stained for calnexin, an ER resident protein, nor in cells treated with CHX, which freezes the ribosomes to block protein synthesis. Our data suggest that eIF-5A does not shuttle between the nucleus and cytoplasm in the same way as Rev. Our findings are consistent with our previous conclusion that eIF-5A is associated with the ER through ribosomes and support a role for eIF-5A in protein synthesis.

Animals↗

PubMed1983

[Effect of the linolenic acid content of the mother's diet on the polyunsaturated fatty acid composition of subcellular fractions in brain development in the rat].

In order to determine precisely the respective roles of linolenic acid and linoleic acid in the maternal diet on rat brain subcellular fractions during development, we used two diets with different percentages of linolenic acid (18:3 n-3). The animals were fed peanut oil (group A) or soybean oil (group B) during pregnancy and throughout lactation. Nature and amount of essential fatty acids had no incidence on saturated and monounsaturated fatty acid distributions in myelin, synaptosomal, mitochondrial and microsomal fractions. In adult rats, all subcellular fractions are marked by an increase of n-3 fatty acid and a decrease of n-6 fatty acid levels in group B compared to group A. In 15-day-old animals, on the contrary, only the synaptosomal fractions are significantly affected by the diet. Independent of diet, brain development is marked by a decrease of n-6 fatty acids in all subcellular fractions; on the other hand, the n-3 fatty acid level is increased in the synaptosomal and mitochondrial fractions, and decrease in the myelin and microsomal fractions. The sum of (n-3 + n-6) fatty acids remains constant in group B and in group A in all subcellular fractions. Finally, under our experimental conditions, we found no marked effect of diet composition upon linoleic acid conversion to arachidonic acid; only the delta 4-7-10-13-16-docosapentaenoic acid (22:5 n-6) level decreased in group B. delta 7-10-13-16-19-Docosapentaenoic acid (22:5 n-3) seemed to be a better substrate for delta 4 desaturase than delta 7-10-13-16-docosatetraenoic acid (22:4 n-6).

Animals↗

PubMed2003

Organelle proteomics: implications for subcellular fractionation in proteomics.

Functional proteome analysis is not restricted to the sequence information but includes the broad spectrum of structural modifications and quantitative changes of proteins to which they are subjected in different tissues and cell organelles and during the development of an organism. Cell biology has provided the means required for the analysis of the composition and properties of purified cellular elements. Subcellular fractionation is an approach universal across all cell types and tissues, including cardiac and vascular system. Subcellular fractionation and proteomics form an ideal partnership when it comes to enrichment and analysis of intracellular organelles and low abundant multiprotein complexes. Subcellular fractionation is a flexible and adjustable approach resulting in reduced sample complexity and is most efficiently combined with high-resolution 2D gel/mass spectrometry analysis as well as with gel-independent techniques. In this study we introduce state of the art subcellular fractionation techniques and discuss their suitability, advantages, and limitations for proteomics research.

Animals↗

PubMed1994

Modulation of Ca2+ release in cultured neonatal rat cardiac myocytes. Insight from subcellular release patterns revealed by confocal microscopy.

It is well established that in heart muscle the influx of Ca2+ through Ca2+ channels during the action potential is the main trigger for Ca2+ release from the sarcoplasmic reticulum (SR), but intact cardiac tissue and single myocytes are also known to exhibit spontaneous Ca2+ release from the SR under a variety of circumstances. Although conditions favoring spontaneous activity have been examined extensively, mechanisms modulating or regulating spontaneous as well as triggered Ca2+ release are still largely unknown. Using the high spatial and temporal resolution of laser-scanning confocal microscopy, we investigated subcellular aspects of spontaneous and triggered Ca2+ release in isolated rat neonatal myocytes loaded with the Ca(2+)-sensitive fluorescent dye fluo 3. Three distinct patterns of spontaneous Ca2+ release were identified: (1) a homogeneous Ca2+ release, presumably corresponding to Ca2+ release during a spontaneous action potential, (2) a focal or spatially restricted Ca2+ release with no or only limited subcellular propagation, and (3) a Ca2+ release propagating as a wave throughout the entire cell. Pharmacologic tools that interfere with the SR revealed that all release types were critically dependent on the Ca2+ release and uptake function of the SR. From our results we conclude that the probability, extent, and pattern of Ca2+ release are modulated on the subcellular level. The observed spectrum of release patterns can be explained by a space- and time-dependent variability in the positive feedback of the Ca(2+)-induced Ca(2+)-release mechanism within an individual myocyte. Presumably, this variability depends on the existence of subcellular functional elements of the SR. The actual degree of positive feedback may be modulated locally by the Ca(2+)-loading state of each SR element.

Action Potentials↗

PubMed1992

Subcellular visualization of light microscopic specimens by laser scanning microscopy and computer analysis: a new application of image analysis.

To identify subcellular organelles or to observe their pathological changes in sections prepared for light microscopy, immuno- and/or enzyme histochemical staining for the marker substances or enzymes of those subcellular organelles are frequently employed. With conventional light microscopes (CLM), however, it is hardly possible to determine whether or not the target organelles are properly stained and to confirm their fine structure. In the present study, the laser scanning microscope (LSM) was employed to obtain highly contrasted images of histochemically stained subcellular organelles at the limit of resolution in light microscopy. To refine or characterize those images, images built up as electronic signals in LSM were further processed in the Image Analysis System (IAS) with pipeline. Thus, the approximate figures of subcellular organelles such as microtubules, endoplasmic reticula, secretory granules, and mitochondria were visualized in brightfield on sections prepared for light microscopy (paraffin, frozen sections and cultured living cells). The validity of the images obtained by LSM or LSM-IAS was confirmed by immunoelectron microscopy when possible. The LSM images of histochemically stained suborganelles of various cells were definitely improved (refined and/or strengthened) by processing them with IAS.

Endoplasmic Reticulum↗

PubMed2005

Direct template matching reveals a host subcellular membrane gyroid cubic structure that is associated with SARS virus.

Viral infection can result in alterations to the host subcellular membrane. This is often reported when using transmission electron microscopy (TEM), resulting in a description of tubuloreticular membrane subcellular ultrastructure rather than a definition based on 3-D morphology. 2-D TEM micrographs depicting subcellular membrane changes are associated with subcellular SARS virion particles [Goldsmith CS, Tatti KM, Ksiazek TG et al. Ultra-structural characterization of SARS coronavirus. Emerg Infect Dis 2004; 10: 320-326]. In the present study, we have defined the 2-D membrane pattern and shape associated with the SARS virus infection. This is by using a direct template matching method to determine what the 3-D structure of the SARS virus associated host membrane change would be. The TEM image for our purposes is defined on 2-D information, such as the membrane having undergone proliferation and from pattern recognition suggesting that the membrane-described pattern is possibly a gyroid type of membrane. Features of the membrane were used to compute and match the gyroid structure with an existing 2-D TEM micrograph, where it was revealed that the membrane structure was indeed a gyroid-based cubic membrane. The 2-D gyroid computer-simulated image that was used to match the electron micrograph of interest was derived from a mathematically well-defined 3-D structure, and it is from this 3-D derivative that allows us to make inferences about the 3-D structure of this membrane. In conclusion, we demonstrate that a 3-D structure can be defined from a 2-D membrane patterned image and that a SARS viral associated membrane change has been identified as cubic membrane morphology. Possible mechanisms for this cubic membrane change are discussed with respect to viral severity, persistence and free radical production.

Cell Membrane↗

PubMed2006

Predicting the subcellular localization of viral proteins within a mammalian host cell.

BACKGROUND: The bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms. However, this is not the case for viruses whose proteins are often involved in extensive interactions at various subcellular localizations with host proteins. RESULTS: Here, we investigate the extent of utilization of human cellular localization mechanisms by viral proteins and we demonstrate that appropriate eukaryotic subcellular localization predictors can be used to predict viral protein localization within the host cell. CONCLUSION: Such predictions provide a method to rapidly annotate viral proteomes with subcellular localization information. They are likely to have widespread applications both in the study of the functions of viral proteins in the host cell and in the design of antiviral drugs.

Computational Biology↗