Sandbox 1k4r: Difference between revisions
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<StructureSection load='1ok8' size='500' side='right' caption='Dengue virus inside cell (PDB entry [[1ok8]])' scene=''> | <StructureSection load='1ok8' size='500' side='right' caption='Dengue virus inside cell (PDB entry [[1ok8]])' scene=''> | ||
'''Dengue Virus inside Cell'''[[1ok8]] | '''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 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. | 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 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 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 <scene name='56/565763/Trimer/3'>fusion loop</scene>, 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 | 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 | ||
</StructureSection> | </StructureSection> | ||
<StructureSection load='2j7w' size='500' side='right' caption='NS5 polymerase (PDB entry [[2j7w]])' scene=''> | <StructureSection load='2j7w' size='500' side='right' caption='NS5 polymerase (PDB entry [[2j7w]])' scene=''> | ||
'''Dengue NS5 Protein'''[[2j7w]] | '''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. The NS5 protein also contains guanylyltransferase activities, which, along with methyltransferase, help protect the viral genome and create efficient protein translation. | 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. 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, and the NS5 protein is most prominent in the Dengue-2-serotype, helping it with its pathogenesis. | There are four serotypes of the Dengue virus, and the NS5 protein is most prominent in the Dengue-2-serotype, helping it with its pathogenesis. | ||
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<scene name='56/565763/Active_site_gtp/4'>GTP in the binding site</scene> is what allows the Dengue-2-methyltransferase to complete its functions; these functions include translation, transcription and replication processes.</StructureSection> | <scene name='56/565763/Active_site_gtp/4'>GTP in the binding site</scene> is what allows the Dengue-2-methyltransferase to complete its functions; these functions include translation, transcription and replication processes.</StructureSection> | ||
<StructureSection load='2vbc' size='500' side='right' caption='Structure of protease and helicase (PDB entry [[2vbc]])' scene=''>'''Dengue NS3/NS2B Protein'''[[2vbc]] | <StructureSection load='2vbc' size='500' side='right' caption='Structure of protease and helicase (PDB entry [[2vbc]])' scene=''>'''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 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 <scene name='56/565763/Ns2b/3'>(His-51, Asp-75 and Ser-135)</scene>, is found between these two β-barrels, and its activity is dependent on the presence of the <scene name='56/565763/Ns2b/7'>NS2B</scene>. 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.</StructureSection> | The catalytic triad <scene name='56/565763/Ns2b/3'>(His-51, Asp-75 and Ser-135)</scene>, is found between these two β-barrels, and its activity is dependent on the presence of the <scene name='56/565763/Ns2b/7'>NS2B</scene>. 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.</StructureSection> | ||