Although I can detect the protein (above 200), leaving it for longer in the transfer (plus 2h), I think I am losing my endogenous protein, as its detection is not getting good. How can I solve it?
I use a step gel: bottom part at 12% and upper part at 6%. You need to be careful when you set up the transfer: handling the gel is somehow tricky but is perfectly doable.
Even when you blot for extended times to increase the transfer of the big protein, it is highly unlikely that you will lose the 37 kDa protein. I would do an 8% gel and stop worrying. Everything below 7,5% is highly fragile and will easily be torn.