Summary The outer membrane (OM) of Gram-negative bacteria is replete with a host of β-barrel outer membrane proteins (OMPs). Despite serving a variety of essential functions, including immune response evasion, the exact mechanism of OMP folding and membrane insertion remains largely unclear. The β-barrel assembly machinery (BAM) complex is required for OMP biogenesis. Crystal structures and molecular dynamics (MD) simulations of the central and essential component, BamA, suggest a mechanism involving lateral opening of its barrel domain. MD simulations reported here reveal an additional feature of BamA: a substrate exit pore positioned above the lateral opening site. Disulfide crosslinks that prevent lateral opening and exit pore formation result in a loss of BamA function, which can be fully rescued by the reductant TCEP. These data provide strong evidence that lateral opening and exit pore formation are required for BamA function.

The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to ∼3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen-mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane-containing systems. Here, we compare the results of simulations of a variety of membranes and membrane–protein systems run using a 2 fs time step and a 4 fs time step with HMR. For pure membrane systems, we find almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing show very little dependence on HMR and the time step. We also tested a 9 Å cutoff as compared to the standard CHARMM cutoff of 12 Å, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 Å cutoff is not.

BtuB is a TonB-dependent transporter that permits the high-affinity binding and transport of cobalamin (CBL), or vitamin B 12 , across the asymmetric outer membrane (OM) of Gram-negative bacteria. It has been shown that Ca 2þ binding is necessary for high-affinity binding of CBL to BtuB, and earlier simulations suggested that calcium ions serve to stabilize key substrate-binding extracellular loops. However, those simulations did not account for the lipopolysaccharides in the OM. To illuminate the roles of both Ca 2þ and lipopolysaccharides in protein functionality, we performed simulations of apo and Ca 2þ -loaded BtuB in symmetric and asymmetric bilayers. The simulations reveal that the oligosaccharides of LPS stabilize the extracellular loops to some degree, apparently obviating the need for Ca 2þ . However, it is shown that Ca 2þ ions stabilize a key substrate-binding loop to an even greater degree, as well as reposition specific CBL-binding residues, bringing them closer to the organization found in the CBL-bound structure. These results indicate the importance of including realistic membrane models when simulating outer-membrane proteins.

Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Enhanced microwave absorption in columnar structured magnetic materials J. Appl. Phys. 112, 083908 (2012) Terahertz emission from cubic semiconductor induced by a transient anisotropic photocurrent J. Appl. Phys. 112, 073115 (2012) Resonant plasmonic effects in periodic graphene antidot arrays Appl. Phys. Lett. 101, 151119 (2012) Room temperature terahertz polariton emitter Appl. Phys. Lett. 101, 141118 (2012) Optical parameters of ZnTe determined using continuous-wave terahertz radiation A three-dimensional finite element model of an experimental near-field scanning microwave microscope (NSMM) has been developed and compared to experiment on non conducting samples. The microwave reflection coefficient S 11 is calculated as a function of frequency with no adjustable parameters. There is qualitative agreement with experiment in that the resonant frequency can show a sizable increase with sample dielectric constant; a result that is not obtained with a two-dimensional model. The most realistic model shows a semi-quantitative agreement with experiment. The effect of different sample thicknesses and varying tip sample distances is investigated numerically and shown to effect NSMM performance in a way consistent with experiment. Visualization of the electric field indicates that the field is primarily determined by the shape of the coupling hooks. V C 2012 American Institute of Physics.