I am writing an article about Rubisco affinity to its substrates CO2 and O2.
Rubisco is an enzyme with quite complicated working mechanism. Firstly, it covalently bounds to the RuBP, forming RuBP enediolate. I believe that i can simulate this docking with AutoDock flexible side chain method, but I'm not entirely sure, because binding mechanism is, in a way, complex.
Then, enediolate of the RuBP binds with either carbon dioxide or oxygen. This process is too quite complex. The best way would be, if i could dock CO2 or O2 covalently to the enediolate in AutoDock. However, if it is not possible there is a way to calculate it's binding energy by DFT calculations. It is described in this article: https://pubs.acs.org/doi/full/10.1021/ja011362p (accesible on sci-hub).
Mechanism of Rubisco is well described here: https://www.ebi.ac.uk/thornton-srv/m-csa/entry/797/.
So to sum this up - I plan to dock RuBP to Rubisco using AutoDock flexible side chain method, then i plan to calculate DFT of CO2/O2 addition OR dock CO2/O2 covalently.
So, here are my questions:
Is there an easy tutorial to AutoDock flexible side chain method? Will this method be useful in this case (docking RuBP)?
Will it be possible to covalently dock CO2 and O2 if it has so complicated binding mechsnism?
and if it is not possible, what is the best free and easy-to-use program to calculate DFT?