title: MD and NMR studies of alpha-bungarotoxin surface accessibility.
abstract: 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.
authors.affiliation: Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via A. Fiorentina 1, 53100 Siena, Italy.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Venditti
authors.forename: Andrea
authors.initials: A
authors.lastname: Bernini
authors.forename: Alfonso
authors.initials: A
authors.lastname: De Simone
authors.forename: Ottavia
authors.initials: O
authors.lastname: Spiga
authors.forename: Filippo
authors.initials: F
authors.lastname: Prischi
authors.forename: Neri
authors.initials: N
authors.lastname: Niccolai
mesh_terms: D002038:Bungarotoxins / Q000737:chemistry*; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D008968:Molecular Conformation; D013499:Surface Properties
chemical_list: D002038:Bungarotoxins