Biomedical subjects

Flemming Y Hansen

Publications and source records attributed to Flemming Y Hansen.

3 recordsLinked to original sources

PubMed2007

Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD.

The nucleotide-induced structural rearrangements in ATP binding cassette (ABC) transporters, leading to substrate translocation, are largely unknown. We have modeled nucleotide binding and release in the vitamin B(12) importer BtuCD using perturbed elastic network calculations and biased molecular dynamics simulations. Both models predict that nucleotide release decreases the tilt between the two transmembrane domains and opens the cytoplasmic gate. Nucleotide binding has the opposite effect. The observed coupling may be relevant for all ABC transporters because of the conservation of nucleotide binding domains and the shared role of ATP in ABC transporters. The rearrangements in the cytoplasmic gate region do not provide enough space for B(12) to diffuse from the transporter pore into the cytoplasm, which could suggest that peristaltic forces are needed to exclude B(12) from the transporter pore.

ATP-Binding Cassette Transporters↗

PubMed2005

Ellipsometric and neutron diffraction study of pentane physisorbed on graphite.

High-resolution ellipsometry and neutron diffraction measurements have been used to investigate the structure, growth, and wetting behavior of fluid pentane (n-C(5)H(12)) films adsorbed on graphite substrates. We present isotherms of the thickness of pentane films adsorbed on the basal-plane surfaces of a pyrolytic graphite substrate as a function of the vapor pressure. These isotherms are measured ellipsometrically for temperatures between 130 and 190 K. We also describe neutron diffraction measurements in the temperature range 11-140 K on a deuterated pentane (n-C(5)D(12)) monolayer adsorbed on an exfoliated graphite substrate. Below a temperature of 99 K, the diffraction patterns are consistent with a rectangular centered structure. Above the pentane triple point at 143.5 K, the ellipsometric measurements indicate layer-by-layer adsorption of at least seven fluid pentane layers, each having the same optical thickness. Analysis of the neutron diffraction pattern of a pentane monolayer at a temperature of 130 K is consistent with small clusters having a rectangular-centered structure and an area per molecule of approximately 37 A(2) in coexistence with a fluid monolayer phase. Assuming values of the polarizability tensor from the literature and that the monolayer fluid has the same areal density as that inferred for the coexisting clusters, we calculate an optical thickness of the fluid pentane layers in reasonable agreement with that measured by ellipsometry. We discuss how these results support the previously proposed "footprint reduction" mechanism of alkane monolayer melting. In the hypercritical regime, we show that the layering behavior is consistent with the two-dimensional Ising model and determine the critical temperatures for layers n = 2-5.

Journal Article↗

PubMed2005

Methodological problems in pressure profile calculations for lipid bilayers.

From molecular dynamics simulations of a dipalmitoyl-phosphatidyl-choline (DPPC) lipid bilayer in the liquid crystalline phase, pressure profiles through the bilayer are calculated by different methods. These profiles allow us to address two central and unresolved problems in pressure profile calculations: The first problem is that the pressure profile is not uniquely defined since the expression for the local pressure involves an arbitrary choice of an integration contour. We have investigated two different choices leading to the Irving-Kirkwood (IK) and Harasima (H) expressions for the local pressure tensor. For these choices we find that the pressure profile is almost independent of the contour used, which indicates that the local pressure is well defined for a DPPC bilayer in the liquid crystalline phase. This may not be the case for other systems and we therefore suggest that both the IK and H profiles are calculated in order to test the uniqueness of the profile. The second problem is how to include electrostatic interactions in pressure profile calculations when the simulations are conducted without truncating the electrostatic potential, i.e., using the Ewald summation technique. Based on the H expression for the local pressure, we present a method for calculating the contribution to the lateral components of the local pressure tensor from electrostatic interactions evaluated by the Ewald summation technique. Pressure profiles calculated with an electrostatic potential truncation (cutoff) from simulations conducted with Ewald summation are shown to depend on the cutoff in a subtle manner which is attributed to the existence of long-ranged charge ordering in the system. However, the pressure profiles calculated with relatively long cutoffs are qualitatively similar to the Ewald profile for the DPPC bilayer studied here.

1,2-Dipalmitoylphosphatidylcholine↗