Biomedical subjects

John E Enderby

Publications and source records attributed to John E Enderby.

4 recordsLinked to original sources

PubMed2006

Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose.

The techniques of neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulations have been used to examine the rotational conformation of the exocyclic hydroxymethyl group of D-glucopyranose. First order H/D NDIS experiments were performed on the H6 position in 3m aqueous glucose solutions where the average coherent scattering length of the exchangeable hydrogen atoms was zero (i.e., all correlations between exchangeable hydrogen atoms and other atoms cancel and thus are not present in the scattering data). This H6 experimental result suggests that no single conformation for the C4-C5-C6-O6 dihedral reproduces the observed scattering data well, but that a mixture of the gg and gt conformations, which has been suggested by NMR experiments, gives a reasonable agreement between the MD and experimental data.

Computer Simulation↗

PubMed2006

Determination of a hydroxyl conformation in aqueous xylose using neutron scattering and molecular dynamics.

Recently, it was shown using structural neutron diffraction with isotopic substitutions (NDIS) measurements, combined with molecular dynamics simulations, that in an aqueous solution of D-xylose the hydroxyl group on the C4 position does not significantly occupy the position trans to the H4 atom. Here, a similar combination of NDIS and MD studies is described which uses D-xylose deuterated at the C5 position to further characterize this hydroxyl conformation as being trans to the C5 atom, as predicted by constrained MD simulations, confirming the previous study.

Chemistry, Physical↗

PubMed2005

Neutron diffraction and computer simulation studies of D-xylose.

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to examine the pentose D-xylose in aqueous solution. By specifically labeling D-xylose molecules with a deuterium atom at the nonexchangeable hydrogen position on C4, it was possible to extract information about the atomic structuring around just that specific position. The MD simulations were found to give satisfactory agreement with the experimental NDIS results and could be used to help interpret the scattering data in terms of the solvent structuring as well as the intramolecular hydroxyl conformations. Although the experiment is challenging and on the limit of modern instrumentation, it is possible by careful analysis, in conjunction with MD studies, to show that the conformation trans to H4 at 180 degrees is strongly disfavored, in excellent agreement with the MD results. This is the first attempt to use NDIS experiments to determine the rotameric conformation of a hydroxyl group.

Carbohydrate Conformation↗

PubMed2004

The structure of aqueous guanidinium chloride solutions.

The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described. The simulations and experiments were carried out at a concentration of 3 m at room temperature, allowing for an examination of any propensity for ion association in a realistic solution environment. The simulations satisfactorily reproduced the principal features of the neutron scattering and indicate a bimodal hydration of the guanidinium ions, with the N-H groups making well-ordered hydrogen bonds in the molecular plane, but with the planar faces relatively deficient in interactions with water. The most striking feature of these solutions is the rich ion-ion ordering observed around the guanidinium ion in the simulations. The marked tendency of the guanidinium ions to stack parallel to their water-deficient surfaces indicates that the efficiency of this ion as a denaturant is due to its ability to simultaneously interact favorably with both water and hydrophobic side chains of proteins.

Cations↗