title: Molecular structures and solvation of free monomeric and dimeric ferriheme in aqueous solution: insights from molecular dynamics simulations and extended X-ray absorption fine structure spectroscopy.
abstract: CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.
authors.affiliation: Scientific Computing Research Unit, †Department of Chemistry, University of Cape Town , Private Bag, Rondebosch 7701, South Africa.
authors.forename: David
authors.initials: D
authors.lastname: Kuter
authors.forename: Victor
authors.initials: V
authors.lastname: Streltsov
authors.forename: Natalia
authors.initials: N
authors.lastname: Davydova
authors.forename: Gerhard A
authors.initials: GA
authors.lastname: Venter
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Naidoo
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Egan
mesh_terms: D019281:Dimerization; D006427:Hemin / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D012995:Solubility; D012996:Solutions; D014867:Water / Q000737:chemistry; D056928:X-Ray Absorption Spectroscopy
chemical_list: D012996:Solutions; D014867:Water; D006427:Hemin