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Smooth Transitions

Tip #1: When developing a series of scenes illustrating related parts of a protein, use the “transition options” to create smooth transitions void of peculiar zoom-outs, etc.

Example from the page HMG-CoA Reductase:

The HMG binding pocket is the site of catalysis in HMGR. is a critical structural element of this binding site. Residues and are positioned in the active site as is . It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from . It is then believed that the close proximity of increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.

Compared with:

The HMG binding pocket is the site of catalysis in HMGR. is a critical structural element of this binding site. Residues and are positioned in the active site as is . Etc…

Tip #2: It is best to establish a color scheme for all domains of interest and to stick with this color scheme throughout the analysis

Example from the page The Structure of PI3K

Compared with:

Tip #3: When Transitioning focus to a new domain, it is best to zoom out and orient the reader to the new domain of interest

Example from the page The Structure of PI3K:

(residues 340-345) is anchored into Helix α11K of the (residues 1017-1024) nSH2 interacts with the through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong ^[1]

Tip #4: Providing a wide view scene of an area of interest before zooming in provides context

Example from the page The Structure of PI3K

This loop in which contains the hotspots (residues 542-546) is located precisely where The salt bridge formed between like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3.