# Formating chemical equations for proteins binding in hugely complex configurations

In a previous question I asked about a simple case, I'm now trying to write equations for proteins that bind multivalently. In the simplest case proteins $A_1$ and $A_2$ can bind to up to two $L$ proteins. This gives a massive chemical equation:
` where $(AL_1AL_2)_r$ is a tetramer where $A_1$ and $A_2$ are both bound to both of the $A$ proteins in a ringlike structure. But this diagram misses out one possible state, $A_1LA_2$ which is connected in this way:

I can't see a way of joining this extra state to the above chemical equation without arrows crossing each other.

What is the best way of formatting these kinds of complex protein reaction equations?

• Anyway, this is a question for TeX.SE. Or maybe even for math.SE (these things look mighty reminiscent of so-called commutative diagrams), just remove everything chemical before asking it there. Feb 9 '18 at 13:18
• Agreed that it is a maths problem first, then a TeX one. Frankly, if the diagram is going to be too complex to layout, then it will be too complex to read. Several different diagrams (as you show here) will be more understandable, Feb 9 '18 at 14:34
• How would you divide it in to several different diagrams? Feb 9 '18 at 15:20
• @IvanNeretin i've corrected it Feb 9 '18 at 15:26
• This isn't a Tex problem, I can use xypics fine to generate the above, what I'm interested in is how protein chemists format these kinds of equations (even if it means splitting them up). My external examiner has insisted on chemical equations for every system I investigate in my thesis, so I have to include no matter how ugly it is. There are well studied systems dramatically more complex than this (like microtubules ), so clearly there must be a standard notation used by protein chemists. Feb 9 '18 at 15:44

For each potential binding reaction you have a different dimension. That is, for $L$ binding to $A_1$ on site 1, you go horizontally. For $L$ binding to $A_2$ on site 1, you go vertically. For $L$ binding to $A_1$ on site 2, you go in the Z dimension, and then for $L$ binding to $A_2$ on site 2, you go in the 4th dimension.