I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind with other proteins subsequently, and I am wondering how best to format chemical equations.

I am used to writing chemical equations on a single line like:

$$\ce{[A] + [B] <=>[k_\mathrm{a}][k_\mathrm{d}] [AB]} \tag{1}$$

but formating a reaction where multiple dimers can arise from the same reaction on a single line looks confusing and ugly:

$$\ce{[AB]_1 <=>[k_\mathrm{d1}][k_\mathrm{a1}] [A] + [B] <=>[k_\mathrm{a2}][k_\mathrm{d2}] [AB]_2} \tag{2}$$

Worse than that, its not clear how one would write an equation where a third configuration could emerge from the reaction.

What is the best way to format equations like this?

  • $\begingroup$ FYI: I switched the constants' places in (2), assuming $a$ and $d$ stand for association and dissociation, respectively: $$\ce{[AB]_1 <=>[\color{red}{k_\mathrm{d1}}][\color{red}{k_\mathrm{a1}}] [A] + ...}$$ If this is wrong, feel free to adjust accordingly or roll back. $\endgroup$
    – andselisk
    Sep 22 '17 at 14:27
  • 1
    $\begingroup$ Use vertical space for 3. Fundamentally, there is a limitation in how many you can represent. Probably will need to do something more general: $$\ce{[A] + [B] <=>[k_{\mathrm{a}i}][k_{\mathrm{d}i}] [AB]_{i}}$$ for $1 \leq i \leq n$ $\endgroup$
    – Zhe
    Sep 22 '17 at 14:45

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