User:Jonathon Ferrell/Sandbox 1

Test

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Design

The design of this protein occurred in two different phases; the initial design of the alpha bundle helix and then the installation of the cysteine hydrolase functional triad into that bundle.^[3]

α-Barrel Design

The design of the coiled coiled heptamer occurred previously, in which a computational and geometrical framework was created. This framework was inspired by classical α-helical bundles that use a heptad repeat, generally written as abcdefg, with the a and d positions occupied by hydrophobic amino acids. This gives rise to hydrophobic seams which can give rise to aggregation and coiled coils which are generally further stabilized by charged interactions at the g and e positions. However in an α-barrel each helix acts with an independent hydrophobic seam with its neighbor. The resulting possible interactions from this interface can be broken down into three types of which type II is utilized for the CC-Heptamer in which a, d, e, and g are all hydrophobic. They used these principles to create CCBuilder an in silico modeler of α-helical coiled coils and α-barrels. ^[4]

Installation of Cysteine Hydrolase

Function

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.