Expression vectors for the V domain of Alix (pcGNM2/hAlix(364–716) have been described

[54]. The EIAV Gag expression vector (pPRE/GagEIAV) has been described [71]. Metabolic labeling and immunoprecipitation The protocol for radiolabeling and immunoprecipitation of cell and virus lysates has been described in detail previously [72]. Briefly, transfected cells were starved for 30 min in RPMI medium lacking Met and Cys. Thereafter, cells were incubated for 2–3 h in RPMI medium supplemented with FBS and [35S]Met/Cys. Culture supernatants were filtered and subjected to ultracentrifugation at 100,000 x g for 45 min. Cell and virion samples see more were lysed in cell lysis buffer (0.5% Triton X-100, 300 mM NaCl, 50 mM Tris [pH 7.5] containing protease inhibitors [Complete; Roche]). Thereafter, they were immunoprecipitated either with

HIV-Ig (Kindly Smad activation provided by the NIH AIDS research and reference reagent program) or anti-WNV serum (Kindly provided by Dr. Robert B. Tesh, University of Texas Medical Branch, Galveston) coated Protein A beads. Immunoprecipitated cell lysates were washed three times in RIPA buffer and once with SDS-DOC wash (0.1% sodium dodecyl sulfate, 300 mM NaCl, 50 mM Tris [pH 7.5], 2.5 mM deoxycholic acid), resolved by SDS-PAGE followed by PhosphorImager analysis. Virus release efficiency was calculated as ratio of virion associated versus total cell plus virion associated HIV-1 Gag or WNV E protein. Renilla based virus release

assay The overall strategy for this assay is summarized in Figure 2A. 293T cells were transfected with CprME and WNV Ren/Rep plasmids [46]. Culture supernatants were harvested 24 h post check details transfection and cells lysed and read for ren-luc activity using the Dual Glo luciferase assay substrate (Promega). Equal volume of the harvested supernatants were then used to infect 293T cells, cells lysed and read for luciferase activity (virion-associated) 24 h post infection. Virus release was calculated as ratio of virion associated ren-luc/(cell+virion associated ren-luc) activity. The overall strategy is summarized in Figure 2A. Sequence analysis Selected Flavivirus proteins were downloaded from NCBI [42]. The NCBI database was searched for sequences for complete or almost full length (>3300 amino acids) polyproteins from Flaviviruses ADP ribosylation factor and selected the ones with species name including West Nile Virus. If multiple sequences were available per virus name, only the longest sequence was considered. This yielded 11 different West Nile virus sequences with separate strain designations (strain name and GI numbers shown in alignment). The downloaded sequences were aligned with MAFFT [43] and the respective motif regions visualized in Jalview [44] using ClustalX-like coloring based on physicochemical properties and conservation. To systematically count the frequency of YCYL and PAAP motif variants in WNV, we first identified significant protein hits (E<0.