Today a developer by the name of EXETrimAll has released a working Eboot patch that allows the downloaded user to play the PS3 Title Prototype 2. Feel free to check out the release notes and the download link below.
Release Notes:
Prototype 2 [BLES01532] FIX 3.41/3.55 - Prototype.2.BLES01532.EXEtrimALL