I\'m using protocol buffer as a wire data-format in a client-server architecture. Domain objects (java beans) will go through following life-cycle.
I have no experience with protocol buffers, but I would not recommend implementing your domain objects tailored to a specific serialization/transfer framework. You might regret that in the future.
The domain objects and logic of a software application should be as independent as possible from specific implementation issues (in your case serialization/transfer), because you want your domain to be easy to understand and be reusable/maintainable in the future.
If you want to define your domain objects independent of serialization/transfer, you have two options:
The disadvantages of option 1 are that your domain is defined two times (which is undesirable with respect to modifications) and the copying of information (which produces error-prone and non maintainable code).
The disadvantages of option 2 are that you lose schema evolution (although ProtoStuff apparently supports it) and the complete (potentially large) object graph is serialized and transferred. Although you could prune the object graph (manually or with JGT) before serialization/transfer.