Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations

Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes.

Conformational analysis of lipid molecules by self-organizing maps

The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.

Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints

The authors introduce a coarse-grained (CG) model for a lipid membrane comprised of phospholipids and cholesterol at different molar concentrations, which allows them to study systems that are approximately 100 nm in linear size. The systems are studied in the fluid phase above the main transition temperature. The effective interactions for the CG model are extracted from atomic-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique, an approach similar to the one the authors used earlier to construct another CG bilayer model [T. Murtola et al., J. Chem. Phys. 121, 9156 (2004)]. Here, the authors improve their original CG model by employing a more accurate description of the molecular structure for the phospholipid molecules. Further, they include a thermodynamic constraint in the IMC procedure to yield area compressibilities in line with experimental data. The more realistic description of the molecular structure of phospholipids and a more accurate representation of the interaction between cholesterols and phospholipid tails are shown to improve the behavior of the model significantly. In particular, the new model predicts the formation of denser transient regions in a pure phospholipid system, a finding that the authors have verified through large scale atomistic simulations. They also find that the model predicts the formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the original model and the experimental phase diagram. However, the domains observed here are much more distinct compared to the previous model. Finally, the authors also explore the limitations of the model, discussing its advantages and disadvantages.

Coarse-grained model for phospholipid/cholesterol bilayer

We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach.

Transient ordered domains in single-component phospholipid bilayers

We report evidence of dense, ordered nanodomains in single-component fluid lipid bilayers. Our atomic-scale molecular dynamics simulations suggest that the area available to a lipid acyl chain exhibits large fluctuations, resulting in denser and sparser domains. The sizes of the dense domains can be up to approximately 10 nm, and their lifetimes are of the order of approximately 10 ns. In addition, our simulations suggest that domains of lipids with highly ordered acyl chains form predominantly within the dense regions, their sizes ranging from a few chains up to a few nanometers, and with lifetimes between approximately 10 ps-10 ns. These observations shed light on the origin of experimentally observed fluctuations, as well as on the mechanisms of phase transitions in lipid membranes.

Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity

We have studied the effects of cholesterol and steroid-based antibiotic fusidic acid (FA) on the behavior of lipid bilayers using a variety of experimental techniques together with atomic-scale molecular dynamics simulations. Capillary electrophoretic measurements showed that FA was incorporated into fluid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranes. Differential scanning calorimetry in turn showed that FA only slightly altered the thermodynamic properties of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers, whereas cholesterol abolished all endotherms when the mole fraction of cholesterol (X(chol)) was >0.20. Fluorescence spectroscopy was then used to further characterize the influence of these two steroids on DPPC large unilamellar vesicles. In the case of FA, our result strongly suggested that FA was organized into lateral microdomains with increased water penetration into the membrane. For cholesterol/DPPC mixtures, fluorescence spectroscopy results were compatible with the formation of the liquid-ordered phase. A comparison of FA and cholesterol-induced effects on DPPC bilayers through atomistic molecular dynamics simulations showed that both FA and cholesterol tend to order neighboring lipid chains. However, the ordering effect of FA was slightly weaker than that of cholesterol, and especially for deprotonated FA the difference was significant. Summarizing, our results show that FA is readily incorporated into the lipid bilayer where it is likely to be enriched into lateral microdomains. These domains could facilitate the association of elongation factor-G into lipid rafts in living bacteria, enhancing markedly the antibiotic efficacy of FA.

Response to comment by Almeida et al.: free area theories for lipid bilayers--predictive or not?

Free area theories for lateral diffusion in lipid bilayers are reviewed and discussed. It has been suggested by Almeida et al. that free area theories yield quantitative predictions for lateral diffusion coefficients of lipids. We investigate the plausibility of this suggestion by first sketching what is to be expected of a quantitative theory with predictive power, and subsequently examining whether existing free area theories comply with these expectations. Our conclusion is that current free area theories for lipid bilayers are not quantitative theories with predictive power. They involve a number of adjustable parameters, all of which are not estimated independently, but derived from fitting the theory to the very data whose behavior the theory is supposed to predict. Further, the interpretation and behavior of some of the parameters are ambiguous. The best example is the so-called activation barrier, whose qualitative behavior with the cholesterol concentration in a DMPC bilayer varies depending on the experimental method used to generate the input data and the exact assumptions made to formulate the theory. Independent determination of the activation barrier from numerical simulations or experiments appears to be very difficult.

Dynamics and scaling of polymers in a dilute solution: Analytical treatment in two and higher dimensions

We consider the dynamical scaling of a single polymer chain in good solvent. In the case of two-dimensional systems, Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)] have suggested that the dynamical scaling for a dilute polymer solution breaks down. Using scaling arguments and analytical calculations based on the Zimm model, we show that the dynamical scaling of a dilute two-dimensional polymer system holds when the relevant dynamical quantities are properly extracted from finite systems. Most important, the polymer diffusion coefficient in two dimensions scales logarithmically with system size, in excellent agreement with our extensive computer simulations. This scaling is the reason for the failure of the previous attempts to resolve the dynamical scaling of dilute two-dimensional polymer systems. In three and higher dimensions our analytic calculations are in agreement with previous results in the literature.

Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers

We employ 100-ns molecular dynamics simulations to study the influence of cholesterol on structural and dynamic properties of dipalmitoylphosphatidylcholine bilayers in the fluid phase. The effects of the cholesterol content on the bilayer structure are considered by varying the cholesterol concentration between 0 and 50%. We concentrate on the free area in the membrane and investigate quantities that are likely to be affected by changes in the free area and free volume properties. It is found that cholesterol has a strong impact on the free area properties of the bilayer. The changes in the amount of free area are shown to be intimately related to alterations in molecular packing, ordering of phospholipid tails, and behavior of compressibility moduli. Also the behavior of the lateral diffusion of both dipalmitoylphosphatidylcholine and cholesterol molecules with an increasing amount of cholesterol can in part be understood in terms of free area. Summarizing, our results highlight the central role of free area in comprehending the structural and dynamic properties of membranes containing cholesterol.

Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions

We study many-particle diffusion in 2D colloidal suspensions with full hydrodynamic interactions through a novel mesoscopic simulation technique. We focus on the behaviour of the effective scaled tracer and collective-diffusion coefficients DT(rho)/D0 and DC(rho)/D0 respectively, where D0 is the single-particle diffusion coefficient, as a function of the density of the colloids rho. At low Schmidt numbers Sc - 1, we find that hydrodynamics has essentially no effect on the behaviour of DT (rho)/D0. At larger Sc, DT (rho)/D0 seems to be enhanced at all densities, although the differences compared to the case without hydrodynamics are rather minor. The collective-diffusion coefficient, on the other hand, is much more strongly coupled to hydrodynamical conservation laws and is distinctly different from the purely dissipative case without hydrodynamic interactions.

Impact of cholesterol on voids in phospholipid membranes

Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role. Cholesterol has been suggested to change the structure and function of membranes by altering their free volume properties. We study the effect of cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC) bilayers by means of atomistic molecular dynamics simulations. We find that an increasing cholesterol concentration reduces the total amount of free volume in a bilayer. The effect of cholesterol on individual voids is most prominent in the region where the steroid ring structures of cholesterol molecules are located. Here a growing cholesterol content reduces the number of voids, completely removing voids of the size of a cholesterol molecule. The voids also become more elongated. The broad orientational distribution of voids observed in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a distribution where orientation along the bilayer normal is favored. Our results suggest that instead of being uniformly distributed to the whole bilayer, these effects are localized to the close vicinity of cholesterol molecules.

Dynamics and scaling of two-dimensional polymers in a dilute solution

The breakdown of dynamical scaling for a dilute polymer solution in two dimensions has been suggested by Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)]. However, we show here through extensive computer simulations that dynamical scaling holds when the relevant dynamical quantities are properly extracted from finite systems. To verify dynamical scaling, we present results based on mesoscopic simulations in two dimensions for a polymer chain in a good solvent with full hydrodynamic interactions. We also present analytical arguments for the size dependence of the diffusion coefficient and find excellent agreement with the present large-scale simulations.

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.