VP40... The Dimer State
(based on 4LDB.pdb)
The model shown at startup shows a spacefilled model of the VP40 dimer in cpk.
This model shows the polar(red) and nonpolar(yellow) nature of the VP40 Dimer.
This model highlights the two domains, the N-terminal domain in cyan and the C-terminal domain in pink.
This backbone model of the VP40 Dimer highlights key amino acid chains in the N and C terminal domains utilized for structure, and key amino acids utilized in hexamerization and oligomerization of the hexamers and octamers. The amino acids shown in orange are important towards the oligomerization of monomers, or the building blocks for hexamers and octamers in further VP40 formations. Blue highlights the NTD responsible for binding the actual monomers to form the dimer, and eventually the hexamer or octamer as a result. Hexamerization is the formation from dimer to hexamer, and is shown in the purple amino acids that are responsible for binding into the lengthy hexameric form. Green amino acid chains are parts of the CTD, and are responsible for interacting with other VP40 proteins to oligomerize or to continue through with their processes.

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The Hexamer State
(based on 4LDD.pdb)
The model shown at startup shows the spacefilled version of the all important matrix protein VP40 in its hexamer state.
The hexamer chains are colored differently.
The hexamer chains in backbone notation
The polar locations of the hexamer chain are shown in red, while the hydrophobic residues are in blue.

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Octamer
(based on 4LDM.pdb)
The model shown at startup shows the spacefilled GP2 trimer in the fusion-active conformation VP40 octamer structure colored in cpk.
The polar residues of the octamer are shown in red; the hydrophobic residues are shown in blue.
Polar residues in red and hydrophobic residues are shown in blue in this backbone model. The hydrogen bonds present are also indicated in orange.
The octamer complex showing the monomers in different colors.
VP40 as an octamer shown in spacefill is key to the transcription and regulation of viral RNA. Shown in blue, key amino acids are responsible for the formation of the ring-shaped octamer which allows it to transcript and regulate RNA. Critical aminos in green are present in each form of VP40, and are important for the structure of each formation. Finally, amino acids shown in red are responsible for interactions between separate NTD in monomers allowing them to bind together into separate formations. Blue: Used to create the formation of the Octamer. Green: Amino acids responsible for formation of the octamer with monomers. Red: The NTD interacting with each other to place together the monomers to form the octamer.

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