Linked Life Data

19236000

Source:http://linkedlifedata.com/resource/pubmed/id/19236000

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
11
pubmed:dateCreated
2009-3-13
pubmed:abstractText
We discuss the coordination mechanism of Fe(III) and methyl-alpha-mannopyranoside in aqueous solution using a recently presented integrated approach comprising ab initio electronic structure calculations, molecular dynamics simulations, and mass spectrometric measurements. First principles Car-Parrinello molecular dynamics (CPMD) simulations find that a single Fe(III) ion interacts with specific hydroxyl groups of the saccharide in aqueous solution. Specifically, we find that one Fe(III) ion complexed to methyl-alpha-mannopyranoside also associates with two water molecules. These simulations are in accord with electrospray ionization mass spectrometry measurements involving guided ion beam hydration measurements, which reveal an optimal coordination number of four about the Fe(III) ion. CPMD simulations identified specific intramolecular and intermolecular hydrogen bonding interactions that have an impact on the conformation of the saccharide and on the coordination with Fe(III); in contrast, classical molecular dynamics simulations were insensitive to these effects. This study illustrates the strength of ab initio molecular dynamics simulations, chemical reactivity calculations, and natural partial charge analysis coupled with mass spectrometric measurements in identifying the active sites of biomolecules toward ligands and for studying the complexation and coordination chemistry associated with substrate and ligand interactions relevant to the design of biochemical syntheses, drugs, and biomarkers in medicine.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1520-5215
pubmed:author
pubmed:issnType
Electronic
pubmed:day
19
pubmed:volume
113
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
2491-9
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Identification of active sites of biomolecules II: Saccharide and transition metal ion in aqueous solution.
pubmed: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
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't