Surface-contaminated nanomaterials may elicit substantially distinct biological responses in vitro and in vivo compared to cleaner phases of the same nanomaterials.
Interesting question, would this irreversible absorption not automatically trigger a conformational change in the newly bound molecule? Probably that is size dependent. Optical methods come to mind again though this might just be me just having a hammer and thus interpreting most problems as roughly nail-shaped.
It is true that unintentional modifications are the ones to look out for in a toxicological context. Nanotoxicology is increasingly aware of the fact that no coating really survives environmental changes very well. Especially in the complex and highly varied biological realm there is nearly always a more attractive binding partner than the planned one.
Landsiedel et al. wrote about this problem in his recent review:
Landsiedel, R., Fabian, E., Ma-Hock, L., Wohlleben, W., Wiench, K., Oesch, F., & van Ravenzwaay, B. (2012). Toxico-/biokinetics of nanomaterials. Archives of toxicology. doi:10.1007/s00204-012-0858-7
The citations therein are also very interesting. One should bear his affiliations in mind though. That said he seems extremely knowledgeable and writes very well. I enjoyed that article very much.