Currently I'm not using prototype because I remember that a day I've read an article where it was stated that Prototype is not supported in IE 7 and down below, but I can't find that article again but by the way it would be good to know how it is supported overall.
JScript (Microsoft's interpretation of Javascript) has supported the prototype property since version 2.0 (MSDN). The first version of Internet Explorer that supported JScript 2.0 was IE 3 (MSDN).
I'd say you're safe with IE7!
Edit: perhaps you're thinking about modifying the prototypes of host objects, such as Node. This is indeed not supported by IE >=7, and is a bad idea anyway. A good article on this is at perfectionkills.com.