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Smooth Transitions

Tip #1: Make the background black. It makes the images appear more vivid

Tip #2: 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 The Structure of PI3K:

Although no with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. In this model, the headgroup of PIP2 is between the . This puts the 5-phosphate of PIP2 near Lys 973 and the . The and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed , deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3.

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

(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

Tip #3: 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.

Tip #4: When switching 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

Tip #5: Eliminate the Scene transition when comparing different binding interactions for similar ligands

Example from the page PI3K Activation, Inhibition, & Medical Implications:

LY294002, a competitive inhibitor of ATP binding in the PI3K kinase domain, was first discovered by scientists at Eli Lilly. Quercetin, Myricetin & Staurosporine are natural compounds which broadly inhibit protein kinases. Understanding how ATP binds to the ATP binding site of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to (1e8x), (1e7u), (1e7v), (1e8w), (1e8z), (1e90).

Tip #6: Whenever possible, try to illustrate points using same .pdb file to avoid "choppy" scene transitions. If unavoidable, include "reorienting" scenes which provide a view of the entire protein.

Tip #7: Use Captions to highlight overall scene and Labels to identify specific residues, etc. Use these often!

Example from the page VirE1-VirE2:

In , the two folded domains of . tightly around the single alpha-helix of VirE1. Both and hydrophobic interactions with VirE1 cement the two domains of VirE2 into a “locked” conformation where the flexible extended linker joining these two independent VirE2 domains does not constrain their relative orientation. Most of the interactions are electrostatic, involving between residues R168, K248, H315, R367 and K471 from VirE2 and N34, D40, E42, E45, E47 and N48 from VirE1. The to its strong electronegative surface resembling that of ssDNA. VirE2 can bind alternatively to VirE1 or to ssDNA. The acidic nature common to both substrates suggests that they bind via electrostatic interactions to a common region of VirE2.