Paper Citing NAMD - Abstract
Coskuner, Orkid; Bergeron, Denis E.; Rincon, Luis; Hudgens, Jeffrey W.; Gonzalez, Carlos A.
Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe-III
JOURNAL OF PHYSICAL CHEMISTRY A, 112:2940-2947, APR 3 2008
Car-Parrinello molecular dynamics (CPMD) simulations, DFT chemical reactivity index calculations, and mass spectrometric measurements are combined in an integrated effort to elucidate the details of the coordination of a transition-metal ion to a carbohydrate. The impact of the interaction with the Fe-III ion on the glycosidic linkage conformation of methyl-CL-D-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that Fe-III interacts with specific hydroxyl oxygen atoms of the carbohydrate, affecting the ground state carbohydrate conformation. These conformational details are discussed in terms of a set of supporting experiments involving electrospray ionization mass spectrometry, and CPMD simulations clearly indicate that the specific conformational preference is due to intramolecular hydrogen bonding. Classical MD simulations proved insensitive to these important chemical properties. Thus, we demonstrate the importance of chemical reactivity calculations and CPMD simulations in predicting the active sites of biological molecules toward metal cations.
