A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers.

We study here the permeability of the hydrophobic O2 molecule through a model DPPC bilayer at 323K and 350K, and of the trace amine p-tyramine through PC bilayers at 310K. The tyramine results are compared to previous experimental work at 298K. Nonequilibrium work methods were used in conjunction to simultaneously obtain both the potential of mean force (PMF) and the position dependent transmembrane diffusion coefficient, D(z), from the simulations.

Structural basis for autoinhibition of CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in phosphatidylcholine synthesis, by its membrane-binding amphipathic helix.

CTP:phosphocholine cytidylyltransferase (CCT) interconverts between an inactive soluble and active membrane-bound form in response to changes in membrane lipid composition. Activation involves disruption of an inhibitory interaction between the αE helices at the base of the active site and an autoinhibitory (AI) segment in the regulatory M domain and membrane insertion of the M domain as an amphipathic helix. We show that in the CCT soluble form the AI segment functions to suppress kcat and elevate the Km for CTP.

Identification of human microRNA-like sequences embedded within the protein-encoding genes of the human immunodeficiency virus.

Background: MicroRNAs (miRNAs) are highly conserved, short (18-22 nts), non-coding RNA molecules that regulate gene expression by binding to the 3' untranslated regions (3'UTRs) of mRNAs. While numerous cellular microRNAs have been associated with the progression of various diseases including cancer, miRNAs associated with retroviruses have not been well characterized. Herein we report identification of microRNA-like sequences in coding regions of several HIV-1 genomes.

Calculating diffusion and permeability coefficients with the oscillating forward-reverse method.

The forward-reverse or FR method is an efficient bidirectional work method for determining the potential of mean force w(z) and also supposedly gives in principle the position-dependent diffusion coefficient D(z). Results from a variation called the OFR (oscillating FR) method suggest inconsistencies in the D(z) values when calculated as prescribed by the FR method. A new steering protocol has thus been developed and applied to the OFR method for the accurate determination of D(z) and also provides greater convergence for w(z) in molecular dynamics simulations.

Scattering density profile model of POPG bilayers as determined by molecular dynamics simulations and small-angle neutron and X-ray scattering experiments.

We combine molecular dynamics (MD) simulations and experiment, both small-angle neutron (SANS) and small-angle X-ray scattering (SAXS), to determine the precise structure of bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), a lipid commonly encountered in bacterial membranes. Experiment and simulation are used to develop a one-dimensional scattering density profile (SDP) model suitable for the analysis of experimental data. The joint refinement of such data (i.

Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force.

We present a method that enables the use of the forward-reverse (FR) method of Kosztin et al. on a broader range of problems in soft matter physics. Our method, which we call the oscillating forward-reverse (OFR) method, adds an oscillatory steering potential to the constant velocity steering potential of the FR method.