[show abstract][hide abstract] ABSTRACT: Free volume pockets inside a cell membrane play a prominent role in a variety of dynamic processes such as the permeability of small molecules across membranes and the diffusion of, e.g., lipids, drugs, and electron carriers in the plane of the membrane. Nonetheless, by now the chances for characterizing free volume voids in a nonperturbative manner through experiments have been very limited. Here we use lipid membranes as an example to show how positron annihilation spectroscopy (PALS) together with atomistic simulations can be employed to gauge changes in free volume pockets in biological macromolecular complexes. The measurements show that PALS is a viable technique to probe free volume in biomolecular systems. As examples, we consider the gel-to-fluid transition and the role of increasing cholesterol concentration in a lipid membrane. Further applications proposed in this work for PALS are likely to provide a great deal of insight into the understanding of the role of free volume in the dynamics of biomolecular complexes.
The Journal of Physical Chemistry B 02/2009; 113(7):1810-2. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
Proteins Structure Function and Bioinformatics 07/2008; 71(4):1995-2011. · 3.34 Impact Factor
[show abstract][hide abstract] ABSTRACT: There is no comprehensive model for the dynamics of cellular membranes. Even mechanisms of basic dynamic processes, such as lateral diffusion of lipids, are poorly understood. Our atomic-scale molecular dynamics simulations support a novel, concerted mechanism for lipid diffusion. We find that a lipid and its nearest neighbors move in unison, forming loosely defined clusters. What is more, the motions of lipids are correlated over tens of nanometers: the lateral displacements of lipids in a given monolayer produce striking two-dimensional flow patterns. These flow patterns should have wide implications, affecting, for example, the formation of membrane domains, protein functionality, and action of lipases and drugs on membranes.
Journal of the American Chemical Society 02/2008; 130(1):44-5. · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
The Journal of Chemical Physics 03/2007; 126(7):075101. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
The Journal of Chemical Physics 03/2007; 126(5):054707. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes—we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle–mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: 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.
The Journal of Chemical Physics 04/2005; 122(9):094904. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
The Journal of Chemical Physics 01/2005; 121(24):12676-89. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: Free volume pockets or voids are crucial for a variety of dynamic processes in lipid membranes. Voids facilitate the diffusion of lipid molecules in the plane of the membrane and are highly relevant for the permeation of small solutes across the membrane. We employ atomic-scale molecular dynamics simulations to study the free volume and packing properties of different lipid membrane systems, focusing on lipids commonly found in lipid rafts. We find that the free volume properties of membranes comprised of saturated (DMPC, DPPC) and diunsaturated (PLPC) phosphatidylcholine (PC) molecules have many common features, while bilayers consisting of palmitoylsphingomyelin (PSM) are distinctly different. PSM has a significantly smaller average close-packed cross-sectional area than the PCs. The free volume fraction is significantly larger in the center of a PSM bilayer than in the center of a DPPC bilayer. The opposite is true for the acyl chain and head group regions: here DPPC has a higher free volume fraction. A detailed analysis of the size, shape and orientation of voids in DPPC and PSM shows that the properties of voids are quite different in bilayers consisting of DPPC and PSM. Compared to DPPC, the number density of voids of all sizes is reduced in the head group and acyl chain regions of PSM. In the bilayer center the situation is reversed. Also the shapes and orientations of voids differ, especially in the acyl chain region. Together with recent work on DPPC/cholesterol mixtures,15, 20 this article summarizes the central role of free volume in comprehending the structural properties of membrane domains rich in cholesterol and sphingomyelin.
Journal of Computational and Theoretical Nanoscience 01/2005; 2:401. · 0.67 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
The Journal of Chemical Physics 12/2004; 121(18):9156-65. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: 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.
The European Physical Journal E 04/2004; 13(3):267-75. · 1.82 Impact Factor
[show abstract][hide abstract] ABSTRACT: We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular dynamics simulations and study various dynamic properties of individual lipids in a membrane, including the velocity autocorrelation function, the lateral and rotational diffusion coefficients, and the autocorrelation function for the area per molecule. We compare the results based on the Particle-Mesh Ewald (PME) and reaction field (RF) techniques with those obtained by an approach where the electrostatic interactions are truncated at rcut = 1.8, 2.0, and 2.5 nm. We find that the overall performance of PME is very good; its results are consistent with the expected behavior. The RF method performs rather well, too, despite certain inherent problems and the fact that its results differ from those obtained by PME. Nevertheless, the largest differences are found for the truncation methods, for which all examined truncation methods lead to results distinctly different from those obtained by PME. The lateral diffusion coefficients obtained by PME and truncation at 1.8 nm, for example, differ by a factor of 10, while the PME results are consistent with experimental values. The observed deviations can be interpreted in terms of artificial ordering due to truncation and highlight the important role of electrostatic interactions in the dynamics of systems composed of lipids and other biologically relevant molecules such as proteins and DNA.
The Journal of Physical Chemistry B 01/2004; 108:4485. · 3.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: 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.