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