The datastore uses Protocol-Buffers internally, and there is no way round, as its the only way your application can communicate with the datastore.
(The implementation can be found in the SDK/google/appengine/datastore/entity_pb.py)
If you think, (de)serialization is too slow in your case, you probably have two choices
- Move to a lower DB API. There's another API next to the two well-documented ext.db and ext.ndb APIs at google.appengine.datastore. This hasn't all the fancy model-stuff and provides a simple (and hopefully fast) dictionary-like api. This will keep your datastore-layout compatible with the other two DB APIs.
- Serialize the object yourself, and store it in a dummy entry consisting just of a text-field. But you'll probably need to duplicate data into your base entry, as you cannot filter/sort by data inside your self-serialized text.