To yield the three structural proteins capsid, pre-membrane and envelope and the nonstructural proteins, NS1, NS2A, NS2B, NS3, NS4A, 2K, NS4B and NS5. Replication of the DENV genome occurs in intimate association with perinuclear ER membranes which are modified to form characteristic structures during virus infection. High-throughput RNA interference studies have shown that DENV depends heavily on the cellular machinery for replication. However the mechanisms by which DENV interacts with cellular pathways and the viral and cellular proteins involved, largely remain to be determined. Comparative analysis of the gene expression profiles of a range of cell types infected with DENV in vitro and cells isolated from the blood of DENV infected individuals has identified a number of genes and cellular signaling pathways that are specifically dysregulated in DENV infection and may be Sipeimine involved in pathogenesis. In addition, high-throughput interaction studies have identified a number of interactions between DENV and cellular proteins that may play a role in replication or avoiding host defense mechanisms. By contrast to gene expression studies, the analysis of the host response to either DENV or flavivirus infection at the proteomic level is more limited. The standard approach of two-dimensional PAGE combined with the identification of specific proteins by mass spectrometry has been used to 
detect proteins that are altered in amount in DENV infected mammalian cells, insect cells and in sera from DENV infected patients and resulted in the identification of a number of cellular proteins potentially relevant to pathogenesis. However this type of analysis is limited by the resolution and sensitivity of 2D-PAGE. In recent years, advances in the sensitivity of MS, coupled with high-throughput protein identification has made it feasible to quantify global Ursolic-acid changes in cellular protein levels in response to viral infection. The use of stable isotope labeling techniques to distinguish proteins derived from different cell populations, either by metabolic labeling of proteins or chemical modification of peptides, in combination with quantitative MS, provides the most sensitive means of accurately analyzing the proteome of a cell currently available. By combining differential labeling techniques with subcellular fractionation and quantitative MS, it is possible not only to measure changes in the amounts of proteins, but also to study changes in the cellular distribution of proteins, even if the total protein levels have not altered significantly. This approach is well suited to the comparative analysis of cell populations such as control and virus infected cells, but surprisingly there are very few reports of the application of these techniques to study viral pathogenesis and none for DENV. In this study we investigated the effects of DENV-2 infection on the host cell proteome of human A549 cells using SILAC in combination with high throughput liquid chromatography MS/MS. The mock and infected A549 cells were fractionated into nuclear and cytoplasmic extracts before analysis to identify proteins that redistribute between cellular compartments during infection and reduce the complexity of the analysis. We identified proteins that both increased and decreased in response to DENV2 infection.