%proteinLU is a nested structure that is best traversed using recursive code. If you can't figure out how to achieve what you need when you get to the future, come back with a specific question to get a specific answer.

In the mean time, don't worry about it! By the time you get to writing that code you will have a little more Perl understanding and with a little luck a solution will present itself. It is good to gain understanding from an exercise like this, but avoid spending too much time solving future problems that may not ever present themselves.