title: Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe(III).
abstract: 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 FeIII ion on the glycosidic linkage conformation of methyl-alpha-d-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that FeIII 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.
authors.affiliation: Computational Chemistry Group, Physical and Chemical Properties Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8380, Gaithersburg, Maryland 20899, USA. orkid.coskuner@nist.gov
authors.forename: Orkid
authors.initials: O
authors.lastname: Coskuner
authors.forename: Denis E
authors.initials: DE
authors.lastname: Bergeron
authors.forename: Luis
authors.initials: L
authors.lastname: Rincon
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Hudgens
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Gonzalez
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D005290:Ferric Compounds / Q000737:chemistry*; D006027:Glycosides / Q000737:chemistry; D006860:Hydrogen Bonding; D008766:Methylmannosides / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: D005290:Ferric Compounds; D006027:Glycosides; D008766:Methylmannosides; C008466:methylmannoside