Biomedical subjects

Marie-Pierre Gaigeot

Publications and source records attributed to Marie-Pierre Gaigeot.

4 recordsLinked to original sources

PubMed2006

A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).

We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.

Cations, Divalent↗

PubMed2006

Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides.

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.

Cobalt↗

PubMed2006

Differentiation of the fucoidan sulfated L-fucose isomers constituents by CE-ESIMS and molecular modeling.

Alpha-L-fucose, the monosaccharide component of fucoidan, is found in the polysaccharide mainly as its sulfated form where sulfate groups are in position 2 and/or 4 and/or 3. The correlation between biological activities and structure of fucoidan requires the determination of the sulfation pattern of the fucose residues. Therefore, it is of importance to discriminate between the isobaric sulfated fucose isomers. For this purpose, the three isomers 2-O-, 3-O-, and 4-O-sulfated fucose have been analyzed using electrospray ion trap mass spectrometry and capillary electrophoresis. The results reported herein show that it is possible to differentiate between these three positional isomers of sulfated fucose based on their fragmentation pattern upon MS/MS experiments. 3-O-Sulfated fucose was characterized by the loss of the hydrogenosulfate anion HSO4- as the main fragmentation product, while the two other isomers 2-O-, and 4-O-sulfated fucose exhibited cross-ring fragmentation yielding to distinctive (0,2)X and (0,2)A daughter ion, respectively. A computational study of the conformation of the sulfated fucose isomers was carried out providing an understanding of the fragmentation pattern with respect to the position of the sulfate group.

Carbohydrate Sequence↗

PubMed2004

Density-functional theory-based molecular simulation study of liquid methanol.

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.

Journal Article↗