Sandbox 1k4r

Dengue Virus inside Cell (1ok8)

When the virus is in its infectious form the surface is smooth (figure 1), but as it is exposed to the acidic environment of the cell cytoplasm, this causes the proteins to snap into a trimeric spike (or trimer), which allows it to penetrate and fuse with the lysozome membrane of the host cell. In experimental laboratory settings, the extraction or isolation of this trimer model can be done in many different ways. The main, observed, extraction was separated by detergent isolation. The model shows a chloride ion (detergent) liganded by three amide nitrogens from Lys-110. The chloride is believed to dissolve away the liposome on the trimer tip. The tip of the trimer, or , displays three hydrophobic residues, Trp-101, Lys-107, and Phe-108. Due to this dissolution from the chloride molecule, the three-fold –clustered membrane tip does not tightly bind together and thereby does not penetrate very deep into the host cell membrane. The fusion loop is thinking to be held into the membrane by an “aromatic anchor” formed by Trp-101 and Phe-108

Dengue NS5 Protein (2j7w)

The NS5 protein is a 900-residue peptide, which contains a methyltransferase domain. This protein plays an important role in the Dengue virus replication. The protein not only functions as a methyltransferase, but also as a RNA polymerase (which helps replicate its RNA). The NS5 protein also contains guanylyltransferase activities, which, along with methyltransferase, help protect the viral genome and create efficient protein translation. There are four serotypes of the Dengue virus (1-4), and the NS5 protein is most prominent in the Dengue-2-serotype, helping it with its pathogenesis. Dengue-2 NS5 contains an also has an which is considered a "S-adenosyl methionine-dependent methyltransferase fold" structure. The S-adenosyl methionine (SAM) ligand is methylated in the methyltransferase domain, creating S-adenosyl-l-homocysteine ()as a by-product. The SAM and SAH are useful in aiding in the folding of the active site. In the NS5 protein, there is another binding site for GTP. This binding of GTP is done in the N-terminal domain on the protein. The is what allows the Dengue-2-methyltransferase to complete its functions; these functions include translation, transcription and replication processes.

Dengue NS3/NS2B Protein (2vbc)

The NS3 protease is a serine protease that can also function as a RNA helicase and RTPase/NTPase. The enzymatic function of this protease is important for the Dengue virus to replicate. This enzyme of the virus is also a potential target for vaccines and antiviral drugs. The catalytic triad , is found between these two beta barrels, and its activity is dependent on the presence of the cofactor. This cofactor then wraps around the NS3 protease domain and becomes part of the active site. The NS2B cofactor is critical for proteolytic activation of the NS3 protease. The NS3 protease is made up of an extensive network of hydrogen bond and hydrophobic interaction, making it very rigid. NS2B is also important in contributing to substrate binding. This implies that NS2B acts as an enzyme activator as well as being directly involved in substrate binding/interactions.