how were you planning to use a control?
In your experiment, are you allowed to put more than one protein per well?
It appears that space is constrained to three 384-well plates, but not time. Can we assume, you have time to incubate more than one plate?
In the o.p., lets make an assumption that only a small dose is necessary, to test positive for lethality (e.g. 1 ul) of wine. The line "You need to determine the answer after 24 hours"
is to be interpreted that, you need to find out the answer at the conclusion of 24 hours.
So time is a constraint. You only have time to run one experiment.