Another exciting update. Both the interface and the pathway search engine now support molecules containing simple side chains. Specifically, methyl radicals, including substituted methyl radicals. The user can view this additional feature by beginning with a pentane skeleton and adding a Carbon atom to either the second, third, or fourth Carbon of the pentane chain, thus creating either 3-methylpentane or 2-methylpenate. It should be noted that adding the Carbon to the first or fifth, the terminal Carbons of the skeleton, will cause a change in the recognized primary skeleton, by lengthening it, to hexane. Additionally the user can interact with the atoms of the side chain and add additional attachments. For example, by adding an Oxygen atom to the methyl side chain in 3-methylpentane the user can create 3-(hydroxymethyl)pentane.
Support is also now in place for molecules containing Sulfur atoms and CoEnzyme A. Similar to Phosphate, CoEnzyme A is represented as a single atom for simplicity.
In light of support for molecules with simple side chains, molecules with Sulfur, and molecules with CoEnzyme A, the Tricarboxylic/Citric acid cycle has now been modeled and added to the Biochemical Pathways page. Additionally, the second portion of the Glycolysis reactions has been added. Finally, the intermediate step, the conversion of the pyruvate resulting from Glycolysis to AcetylCoA for entry into the TCA cycle, has also been modeled and added.
In fact, an exciting result of support for parts or all of 4 different biochemical pathways is that we are now able to find a COMPLETE metabolic pathway for Ribulose-5-phosphate, the precursor of the molecule with which plants fixate Carbon Dioxide, all the way to Oxaloacetate, the molecule left over after energy has been captured from the initial Carbon Dioxide molecule via the Calvin cycle, Glycolysis, and the Citric acid cycle. A completely modeled pathway for everything that happens in one of the main pathways of a plant converting Carbon Dioxide to energy!
Standards - Per usual, standard IUPAC naming of molecules containing simple side chain rules apply. Of particular interest is rule P-65.1.2.2.1, concerning molecules with 3 or more carboxylic acid substituents: P-65.1.2.2.1 If an unbranched chain is linked to more than two carboxy groups, all carboxy groups are named from the parent hydride by substitutive use of the suffix ‘carboxylic acid’, preceded by the appropriate numerical prefix ‘tri’, ‘tetra’ etc. and appropriate locants. This is particularly relevant for Citric Acid/Citrate, the product of Acetyl CoA and Oxaloacetate that enters the Tricarboxylic acid cycle. The systematic IUPAC name of Citrate is 2-hydroxypropane-1,2,3-tricarboxylic acid, reflecting a primary chain of propane rather than pentane as the outer Carbons are considered part of the substituents only. This is furthermore relevant for other tricarboxylic acids in the TCA cycle.
Controls - The controls have fundamentally not changed. As mentioned previously, creation of a side chain is possible by first adding a Carbon to a skeleton as an attachment, and then adding attachments to that Carbon. CoEnzymeA functional groups can be created by adding a CoEnzyme A attachment to a Sulfur atom. Of note, restrictions have been placed to NOT allow molecules more complex than those currently supported to be created. For example, ethers, esters, and anhydrides are not YET supported, so an Oxygen atom cannot be bivalent.
Future considerations - Thus far, the creation process has been iterations of 1) building the infrastructure supporting the interface and pathway search engine, 2) adding functionality, supported pathways, and supported molecules 3) refining the infrastructure as better ways of modeling the molecules and pathways as well as interacting with the interface were discovered/imagined. Since adding support for molecules with side chains is a major step, I expect there to be plenty of refinements on the infrastructure in the near future. More excitingly, many new metabolic pathways are now supported and will shortly be added including fatty acid oxidation and some amino acid pathways. I also expect to soon add modeling of the first part of glycolysis, including representation of the ring form of D-glucose in the interface.
