Mutating a protein without mutating the gene?
I assume that you mean changing the amino acid sequence in a single protein in an organism to one that no longer reflects the sequence predicted from the DNA sequence.  In that case, I would suggest using ADAR (Double-stranded RNA-specific adenosine deaminase) or similar enzymes.  ADAR deaminates adenosine to inosine, which is read by the ribosome as a guanine.  I know that it's activity is regulated, but I'm not sure how you could redirect it (perhaps with an antisense RNA that yields a double-stranded binding stretch in the target RNA.