Now I'm using store method to save my data. But since some time this operation takes 2-3 seconds, and I'm afraid will grow even more. Data can't be split to parts to save separately.

Two ideas spring to mind:

• Change your design so that you can split stuff up so you can save/load stuff incrementally (e.g. have the definitive version of your structure on disk and only load what you need to change).
• Instead of storing the whole data structure, store the changes you make to it. Then you can recover it by replaying the changes.

Without knowing more details of your particular application it's hard to come up with specific advice :-)