Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations

The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry

The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only the P1 space group is supported for periodic boundary conditions (PBC) and thus reflection and/or rotational crystal symmetries are not supported. In this work, we outline the development and implementation of the Extended Eighth-Shell (EES) method that allows rotational symmetry by using an extended import region compared to the ES method. It simulates only the asymmetric unit and communicates coordinates and forces with images that correspond to P2₁ PBC. The P2₁ PBC has application in lipid bilayer simulations as it can be used to allow lipids to switch leaftlets, thus rapidly balancing the chemical potential difference between the two layers. Our results show that the EES method scales efficiently over large number of processes and can be used for simulations with P2₁ symmetry in an orthorhombic crystal.

Application of the fuzzy-oil-drop model to membrane protein simulation

The analysis of structural properties and biological activity of membrane proteins requires long lasting simulation of molecular dynamics. The large number of atoms present in protein molecule, membrane (phospholipids), and water environment makes the simulation of large scale. The implementation of simplified model representing the natural environment for membrane proteins is presented and compared with the vacuum simulation and simulation in the presence of water molecules and membrane phospholipids presented explicite. The comparative structural analysis and computational times for these three models makes the simplified model promising.

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments

Order parameters from deuterium NMR are often used to validate or calibrate molecular dynamics simulations. This paper gives a short overview of the literature in which experimental order parameters from (2)H NMR are compared to those calculated from MD simulations. The different ways in which order parameters from experiment are used to calibrate and validate simulations are reviewed. In the second part of this review, a case study of cholesterol in a DMPC bilayer is presented. It is concluded that the agreement between experimental data and simulation is favorable in the hydrophobic region of the membrane, for both the phospholipids and cholesterol. In the interfacial region the agreement is less satisfactory, probably because of the high polarity of this region which makes the correct computation of the electrostatics more complex.

Zinc is a voltage-dependent blocker of native and heterologously expressed epithelial Na+ channels

Zn(2+) (1-1,000 microM) applied to the apical side of polarized A6 epithelia inhibits Na(+) transport, as reflected in short-circuit current and conductance measurements. The Menten equilibrium constant for Zn(2+) inhibition was 45 microM. Varying the apical Na(+) concentration, we determined the equilibrium constant of the short-circuit current saturation (34.9 mM) and showed that Zn(2+) inhibition is non-competitive. A similar effect was observed in Xenopus oocytes expressing alphabetagammarENaC (alpha-, beta-, and gamma-subunits of the rat epithelial Na(+) channel) in the concentration range of 1-10 microM Zn(2+), while at 100 microM Zn(2+) exerted a stimulatory effect. The analysis of the voltage dependence of the steady-state conductance revealed that the inhibitory effect of Zn(2+) was due mainly to a direct pore block and not to a change in surface potential. The equivalent gating charge of ENaC, emerging from these data, was 0.79 elementary charges, and was not influenced by Zn(2+). The stimulatory effect of high Zn(2+) concentrations could be reproduced by intra-oocyte injection of Zn(2+) (approximately 10 microM), which had no direct effect on the amiloride-sensitive conductance, but switched the effect of extracellular Zn(2+) from inhibition to activation.

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions

We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.

Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL channel

The crystal structure of the Mycobacterium tuberculosis homolog of the bacterial mechanosensitive channel of large conductance (Tb-MscL) provides a unique opportunity to consider mechanosensitive signal transduction at the atomic level. Molecular dynamics simulations of the Tb-MscL channel embedded in an explicit lipid bilayer and of its C-terminal helical bundle alone in aqueous solvent were performed. C-terminal calculations imply that although the helix bundle structure is relatively unstable at physiological pH, it may have been stabilized under low pH conditions such as those used in the crystallization of the channel. Specific mutations to the C-terminal region, which cause a similar conservation of the crystal structure conformation, have also been identified. Full channel simulations were performed for the wild-type channel and two experimentally characterized gain-of-function mutants, V21A and Q51E. The wild-type Tb-MscL trajectory gives insight into regions of relative structural stability and instability in the channel structure. Channel mutations led to observable changes in the trajectories, such as an alteration of intersubunit interactions in the Q51E mutant. In addition, interesting patterns of protein-lipid interactions, such as hydrogen bonding, arose in the simulations. These and other observations from the simulations are relevant to previous and ongoing experimental studies focusing on characterization of the channel.