tovarich, Are you trying to couple to a peptide (meaning something that might be 10-20 amino acids long), or are you trying to couple to a protein? Can you practice your coupling reaction with a commercially available NHS-ester? You would obviously need some sort of assay to decide whether or not coupling had occurred.
discodermolide, When I suggested reacting my protein with an electrophilic reagent and using DMSO with a solvent, my advisor threatened me with bodily harm. Maybe if I had suggested DMF, it would have been OK with him. More seriously, I know that a few proteins tolerate some organic solvents, but to the best of my knowledge, it is very situation-dependent.