Design sequence

Calvin-Benson cycle

How plants capture carbon: thirteen steps, a solved structure for each, and every one of them improved at the same time.

01 · Proteome

Signal spreads across a map of how Arabidopsis proteins interact.All natural Arabidopsis proteins

A six-part sequence built from real computational objects, in a plant rather than a patient. It begins with Synthyra’s predicted Arabidopsis thaliana protein-interaction map of 27,448 proteins, in which a signal propagates along predicted edges. The map resolves to ribulose-1,5-bisphosphate carboxylase/oxygenase, the large subunit rbcL (UniProt O03042, node 15,822), whose experimentally determined structure from PDB entry 5IU0 at 1.50 angstrom is shown as a space-filling molecular surface moving along its elastic-network normal modes, with the RuBisCO small subunit from the same crystal in its crystallographic pose. A ring of thirteen stations then rises: the thirteen reactions of the Calvin-Benson group of AraCore version 2.1, in the order the carbon travels, each drawn as the C-alpha trace of a deposited structure for that enzyme. The sequence adds a SwissBioPics plant-cell diagram carrying the same network, a rail of eight registered herbicides linked to the proteins they are predicted to bind, and AraCore version 2.1, a published curated model of plant primary metabolism with 585 reactions and 415 metabolites, drawn as a metabolite-by-reaction incidence map. One candidate column and nine constraint rows are added while the published model is held fixed. All readouts are modeled and relative.

Sources and licenses

Every object below is a real computational artifact. Readouts are modeled.

Interaction map: Synthyra Atlas-PPI predicted Arabidopsis thaliana interactome, 27,448 proteins of reference proteome UP000006548. Edges are model predictions. The layer under the cell is the 110,000 highest-scoring of 291,460 edges, none below 0.96.
Cell diagram: SwissBioPics plant cell, SIB Swiss Institute of Bioinformatics, CC BY 4.0. Redrawn as single-weight line art.
Protein structure: PDB 5IU0 at 1.50 angstrom, chain A residues 13 to 475: the RuBisCO large subunit rbcL, from Arabidopsis. Public domain (CC0). Valegard, Hasse and Andersson, Acta Crystallogr D Struct Biol, 2018.
Motion: Anisotropic network model normal modes over C-alpha atoms within 13 angstrom, first six non-trivial modes.
The cycle ring: The thirteen reactions of the Calvin-Benson group of AraCore v2.1, in carbon order, as eleven EC numbers and eleven PDB entries. Each station is the C-alpha trace of the best-resolution green-plant X-ray entry for that EC number, preferring Arabidopsis. Filled markers are the four AraCore names itself.
Metabolic model: AraCore v2.1, Arnold and Nikoloski 2014, github.com/pwendering/ArabidopsisCoreModel, MIT licence. Ten subsystems shown, currency metabolites hidden, rows and columns reordered. No reaction added or removed.
Registered herbicides: Glyphosate, atrazine, glufosinate, mesotrione, chlorsulfuron, paraquat, metolachlor and 2,4-D, screened proteome-wide with Atlas-PLI; five are on the rail. The screen ranks the published target first for mesotrione (HPPD) and second for chlorsulfuron (ALS).
Outcome rows: Fatty acid biosynthesis (GO:0006633, 49 proteins), the precursor pool downstream of the cycle. Response to oxidative stress (GO:0006979, 41), what running it harder costs the host. Photorespiration (GO:0009853, 23), the carbon spent undoing RuBisCO’s oxygenase reaction.

Nothing in this sequence is an illustration. Every readout is a prediction, and it shows direction rather than an absolute number. What each object is and where it came from are in the disclosure above.