Focus Forming Unit (FFU) Reduction Assay
FFU reduction assays were performed as previously described [14]. Approximately 200 FFU of virus were incubated with peptide in serum-free DMEM for 1 hr at room temperature before infecting LLC-MK2 cell monolayers for 1 hr at 37uC, and overlaying with media containing 0.85% (w/v) Sea-Plaque Agarose (Cambrex Bio Science, Rockland, ME). Infected cells were incubated at 37uC with 5% CO2 for 2 days (yellow fever virus), 3 days (dengue virus 3 and 4, Russian spring summer encephalitis virus and Central European encephalitis virus) or 5 days (dengue virus 1and 2). Infected cultures were fixed with 10% (v/v) formalin, permeablized with 70% (v/v) ethanol, and foci were detected using mouse monoclonal antibodies against yellow fever virus (Chemicon, Temecula, CA), dengue (E60), or polyclonal anti-Kumlinge virus rED3 antisera, followed by horseradish peroxidase-conjugated goat anti-mouse immunoglobulin (Pierce, Rockford, IL), and developed using AEC chromogen substrate (Dako, Carpinteria, CA) as previously described [15,29].

Virus Inhibition on C6/36 Cells
C6/36 monolayers were infected with approximately 7,600 FFU of dengue virus 2 at 37uC for 1 hr before being aspirated, complete culture media added, and incubated at 37uC and 5% CO2. After 72 hrs, RNA was isolated from cells using an RNeasy Mini Kit (Qiagen, Valencia, CA). qRT-PCR was performed as previously described [18].Materials and Methods Viruses and Cells
Dengue virus 1 (HI-1), dengue virus 2 (NGC-2), dengue virus 3 (H-78), dengue virus 4 (H-42), and yellow fever virus (17-D) were propagated in LLC-MK2 cells (American Type Culture Collection (ATCC), Manassas, VA, cat. no. CCL-7) [15]. Russian spring summer encephalitis virus (Sofjin), and Central European encephalitis virus (Hypr) were propagated in BHK-21 cells (ATCC, cat. no. CCL-10). C6/36 cells (ATCC, cat. no. CRL1660) were maintained in Dulbecco’s modified eagle medium (DMEM) with 10% fetal bovine serum (FBS), 100 mM Nonessential amino acids, 2 mM Glutamax, 100 U/ml penicillin G, 100 mg/ml streptomycin and 0.25 mg/ml amphotericin B, at 30uC with 5% CO2. For the cryo-electron microscopy studies, dengue virus 2 (16681) was grown in C6/36 cells and the tissue culture supernatant was collected on day 3-4, spun at 2,7046g for 10 minutes at 4uC. 8% PEG in NTE (120 mM NaCl, 12 mM Tris, pH 8.0, 1 mM EDTA) was added to the tissue culture supernatant and mixed. The solution was then allowed to sit overnight before the PEG precipitated virus was centrifuged at 14,6366g for 1 hr. The pellet was resuspended in 1 ml NTE buffer, loaded onto a 24% (w/v) sucrose cushion and centrifuged at 175,5876g for 90 min. Pellets were resuspended overnight in NTE before being loaded onto a 10-30% (w/v) potassium sodium tartrate step gradient and centrifuged at 175,5876g for 2 hrs. Purified virus was collected from the 20% potassium-tartrate fraction.

Cryo-electron Microscopy
1 mM DN59 in 10% (v/v) DMSO was mixed with 18 ml of mature dengue virus to give a final DN59 concentration of 100 mM with 1% (v/v) DMSO. The mixture was incubated at 37uC for 30 min, then 4uC for 2 hrs and frozen on holey carbon grids. Dengue virus without peptide and dengue virus incubated with DMSO only controls were also frozen. Images were collected with a Philips CM200 cryo-electron microscope using 200 KV, a magnification of 50,000, an electron dose of 25 e2/A2, and taken at about 4.3 to 7 mm out-of-focus. Thirty-eight DN59 treated dengue virus particles were selected for three-dimensional (3D) image reconstruction. Initial models for 3D reconstructions were generated using the program starticos in EMAN [30]. This program correlates each image with itself after rotating by 72u, 120u and the starting model is essentially a random model based on combining the three orientations related by icosahedral symmetry. Subsequently, thirty iterations were performed in which the orientation of each of the raw images was determined relative to the current model from the previous cycle using the program SPIDER [31]. The images were split into two groups for resolution estimation, by observing the point at which the Fourier shell coefficient fell below 0.5 [32].(Figure S3). Contours were chosen to only just avoid opening a hole in the capsid other than at the five-fold vertices.RNase Assay and qRT-PCRApproximately 1.4-2.96104 FFU of dengue virus 2 was incubated with DN59 for 1 hr at room temperature and then digested with micrococcal nuclease (New England BioLabs, Ipswich, MA) for 1 hr at 37uC.PBS, with 15 minutes of equilibration after each titration before measurements were made. Binding curves were obtained by taking the intensity at 335 nm for each spectra, minus the intensity of the appropriate peptide-free control sample.

Liposome Vesicle Leakage
The fluorescent dye 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS) and its obligate quencher p-xylene-bis-pyridinium bromide (DPX) were purchased from Invitrogen (Carlsbad, CA). Vesicles were prepared with ANTS/DPX entrapped inside where DPX quenches ANTS fluorescence [34]. Lipids were hydrated with buffer containing 50 mM ANTS and 12.5 mM DPX followed by extrusion and then gel filtration chromatography using Sephadex G-200 to exchange the external ANTS/DPX solution for buffer. In leakage experiments, 0.5 mM vesicles were mixed with peptide from 0.5 to 10 mM to give peptide to lipid ratios ranging from 1:50 to 1:1000. The increase in ANTS fluorescence after 1 hr incubation with peptide reports on vesicle leakage. A complete leakage control was achieved by the addition of 10 mM of the lytic bee venom peptide melittin.

Infectivity Inhibition Reversibility Assay
Similar to the FFU reduction assays, approximately 200 FFU of dengue virus 2 were incubated with 0 or 10 mM DN59 in a total volume of 100 ml serum-free DMEM for 1 hr at room temperature. Immediately before infecting LLC-MK2 cell monolayers, the virus/peptide mixtures were diluted with serum-free DMEM to 1 ml, reducing the concentration of DN59 to 1 mM.

Cell Toxicity Assays
Cytotoxicity of DN59 was measured by mitochondrial reductase activity using the TACSTM MTT cell proliferation assay (R&D Systems Inc., Minneapolis. MN). DN59 in serum-free DMEM was added to LLC-MK2, BHK, or C6/36 cells for 1 hr at 37uC, the solution was removed and the cells incubated at 37uC in complete medium with 5% CO2 for 24 hrs.

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