How do I draw a phosphorylation event?

Add "Show phosphorylation as a small orange P circle attached to the substrate, connected to the kinase by an arrow."

Life ScienceText → ImageMid creditEN

Mechanism Pathway Diagram

Cell-signaling pathway with activation and inhibition, color-coded by molecule class.

When to use this prompt

For biology / pharmacology / molecular biology papers showing intracellular signaling.

The prompt

A cell-signaling pathway diagram showing the interaction between epigenetic regulation and autophagy in a stylised cell.

Layout: left-to-right, three vertical zones — upstream / midstream / downstream.

Upstream (left):
- Energy / nutrient sensors: AMPK (activated by low ATP) and mTOR (activated by amino acids).
- Show AMPK -> activates ULK1 (arrow with arrowhead).
- Show mTOR -| inhibits ULK1 (blunt-ended T-bar).

Midstream (center):
- HDAC enzymes -> deacetylate ATG proteins.
- DNA methylation -| silences BECN1 promoter.
- Show converging arrows on a hub box: "Autophagy initiation".

Downstream (right):
- Autophagosome formation -> fusion with lysosome -> cargo degradation.
- Feedback dashed arrow: "autophagy degrades chromatin modifiers" looping back upstream to the HDAC / DNAm box.

Style:
- Color code by molecule class: kinases purple, transcription factors orange, lipids green, organelles teal.
- Activation arrows have arrowheads; inhibition arrows have blunt T-bars.
- Membrane structures (autophagosome, lysosome) drawn as small recognisable organelle shapes.
- Clean publication style, white background, sans-serif labels, suitable for Cell / Molecular Cell.

Variations

Drug-target overlay

Same pathway, but overlay drug-target stars on the molecules being targeted by a candidate compound (e.g. a star on HDAC and a star on mTOR), with a small drug-name label next to each star.

Tips

Distinguish activation from inhibition with explicit shape names ("arrowhead" vs "T-bar").
Use feedback arrows sparingly — one feedback loop reads well; three creates spaghetti.
Color-code molecule classes consistently across all your figures for instant readability.