Estimation of the polarity of the protein interior by optical spectroscopy

Crystallographic studies of myoglobin have shown that the haem pocket is lined with nonpolar amino-acid residues. In order to estimate the true polarity of the interior of proteins, certain studies have used bound fluorophores, the spectroscopic properties of which reflect the polarity of their environment. These studies have most often used 1-amino-8-naphthalene sulphonate (ANS) as a probe, but a more suitable probe, in principle, is 6-propionyl 2-(N,N-dimethyl)aminonaphthalene (PRODAN). We have synthesized a molecule with the advantageous spectroscopic properties of PRODAN but with a higher affinity for apomyogloblin: 2'-(N,N-dimethyl)amino-6-naphthopyl-4-trans-cyclohexanoic acid (DANCA), and report here its use to determine the polarity of the myoglobin haem pocket. Our results show that the pocket is actually a polar environment, and the polarity can be accounted for by peptide amide dipoles.