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MD and NMR studies of alpha-bungarotoxin surface accessibility.

Venditti V, Bernini A, De Simone A, Spiga O, Prischi F, Niccolai N

Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via A. Fiorentina 1, 53100 Siena, Italy.

Protein surface accessibility represents a dimension of structural biology which has not been discussed in details so far, in spite of its fundamental role in controlling the molecular recognition process. In the present report the surface accessibility of alpha-bungarotoxin, a small and well characterized protein, has been investigated by analyzing its interaction with solvent and paramagnetic molecules in an integrated way. The presence of strong hydration sites, identified by a combined analysis of MD simulation and NMR results, seems to prevent the access of Gd(III)DTPA-BMA to the protein surface. On the contrary, the limited hydration of the alpha-bungarotoxin active site favors frequent encounters between the paramagnetic probe and the protein in the latter region. All the data obtained here for alpha-bungarotoxin suggest that shape and stability of the solvation shell control its surface accessibility and, hence, intermolecular interactions in a way which could be common to many other proteins.

Published 20 March 2007 in Biochem Biophys Res Commun, 356(1): 114-7.
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