It has the same meaning for proteins as in all other contexts. It is a particular spatial arrangement of smaller parts that make up the whole object. Here are 24 different topologies of a human hand and fingers:
If you think of original Rubik's cube, that would be the arrangement of 27 small cubes that make up the whole cube. For proteins, we are talking about the arrangement of secondary structure elements that are connected like beads on a string. For example, how many beta-sheet topologies can be created from N beta strands?
The answer is N! * 2^(N-2), which is 96 for N=4 and 960 for N=5. I should mention that most of them don't occur in nature.