PACKMOL: a package for building initial configurations for molecular dynamics simulations

Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer

Molecular dynamics simulations were used to examine the partitioning behaviour of the local anaesthetic benzocaine and the anti-epileptic phenytoin into lipid bilayers, a factor that is critical to their mode of action. Free energy methods are used to quantify the thermodynamics of drug movement between water and octanol as well as for permeation across a POPC membrane. Both drugs are shown to favourably partition into the lipid bilayer from water and are likely to accumulate just inside the lipid headgroups where they may alter bilayer properties or interact with target proteins. Phenytoin experiences a large barrier to cross the centre of the bilayer due to less favourable energetic interactions in this less dense region of the bilayer. Remarkably, in our simulations both drugs are able to pull water into the bilayer, creating water chains that extend back to bulk, and which may modify the local bilayer properties. We find that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations.

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 < 0) and become more attractive with increasing temperature (ΔB2/ΔT < 0) in the temperature range 300 K ≤ T ≤ 360 K. Thus, these hydrophobic interactions are attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.

Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane

The transfer of a lysine amino acid analogue across phospholipid membrane models was investigated using molecular-dynamics simulations. The evolution of the protonation state of this small peptide as a function of its position inside the membrane was studied by determining the local pKa by means of free-energy calculations. Permeability and mean-first-passage time were evaluated and showed that the transfer occurs on the submillisecond time scale. Comparative studies were conducted to evaluate changes in the pKa arising from differences in the phospholipid chemical structure. We compared, hence, the effect of an ether vs an ester linkage of the lipid headgroup as well as linear vs branched lipid tails. The study reveals that protonated lysine residues can be buried further inside an ether lipid membrane than an ester lipid membrane, while branched lipids are found to stabilize less the charged form compared to their unbranched lipid chain counterparts.

Surface composition/organization of ionic liquids with Au nanoparticles revealed by high-sensitivity low-energy ion scattering

High-sensitivity low-energy ion scattering (HS-LEIS) analysis was used to elucidate the outermost layer of both functionalized and non-functionalized imidazolium ionic liquids (ILs). The IL outermost layer is composed of all atoms of both cations and anions. The HS-LEIS analyses also allow for quantitative measurement of the thickness of IL overlayers on Au nanoparticles prepared by sputter deposition, which was shown to be a monolayer of ions, as predicted by density functional theory calculations.

Aspergillus niger β-glucosidase has a cellulase-like tadpole molecular shape: insights into glycoside hydrolase family 3 (GH3) β-glucosidase structure and function

Aspergillus niger is known to secrete large amounts of β-glucosidases, which have a variety of biotechnological and industrial applications. Here, we purified an A. niger β-glucosidase (AnBgl1) and conducted its biochemical and biophysical analyses. Purified enzyme with an apparent molecular mass of 116 kDa forms monomers in solution as judged by native gel electrophoresis and has a pI value of 4.55, as found for most of the fungi of β-glucosidases. Surprisingly, the small angle x-ray experiments reveal that AnBgl1 has a tadpole-like structure, with the N-terminal catalytic domain and C-terminal fibronectin III-like domain (FnIII) connected by the long linker peptide (∼100 amino acid residues) in an extended conformation. This molecular organization resembles the one adopted by other cellulases (such as cellobiohydrolases, for example) that frequently contain a catalytic domain linked to the cellulose-binding module that mediates their binding to insoluble and polymeric cellulose. The reasons why AnBgl1, which acts on the small soluble substrates, has a tadpole molecular shape are not entirely clear. However, our enzyme pulldown assays with different polymeric substrates suggest that AnBgl1 has little or no capacity to bind to and to adsorb cellulose, xylan, and starch, but it has high affinity to lignin. Molecular dynamics simulations suggested that clusters of residues located in the C-terminal FnIII domain interact strongly with lignin fragments. The simulations showed that numerous arginine residues scattered throughout the FnIII surface play an important role in the interaction with lignin by means of cation-π stacking with the lignin aromatic rings. These results indicate that the C-terminal FnIII domain could be operational for immobilization of the enzyme on the cell wall and for the prevention of unproductive binding of cellulase to the biomass lignin.

Mechanistic investigation of domain specific unfolding of human serum albumin and the effect of sucrose

This study is devoted to understand the unfolding mechanism of a multidomain protein, human serum albumin (HSA), in absence and presence of the sucrose by steady-state and time-resolved fluorescence spectroscopy with domain specific marker molecules and is further being substantiated by molecular dynamics (MD) simulation. In water, the domain III of HSA found to unfold first followed by domains I and II as the concentration of GnHCl is increased in the medium. The sequential unfolding behavior of different domains of HSA remains same in presence of sucrose; however, a higher GnHCl concentration is required for unfolding, suggesting stabilizing effect of sucrose on HSA. Domain I is found to be most stabilized by sucrose. The stabilization of domain II is somewhat similar to domain I, but the effect of sucrose on domain III is found to be very small. MD simulation also predicted a similar behavior of sucrose on HSA. The stabilizing effect of sucrose is explained in terms of the entrapment of water molecules in between HSA surface and sucrose layer as well as direct interaction between HSA and sucrose.

The N-terminal sequence of tyrosine hydroxylase is a conformationally versatile motif that binds 14-3-3 proteins and membranes

Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the synthesis of catecholamine neurotransmitters, and a reduction in TH activity is associated with several neurological diseases. Human TH is regulated, among other mechanisms, by Ser19-phosphorylation-dependent interaction with 14-3-3 proteins. The N-terminal sequence (residues 1-43), which corresponds to an extension to the TH regulatory domain, also interacts with negatively charged membranes. By using X-ray crystallography together with molecular dynamics simulations and structural bioinformatics analysis, we have probed the conformations of the Ser19-phosphorylated N-terminal peptide [THp-(1-43)] bound to 14-3-3γ, free in solution and bound to a phospholipid bilayer, and of the unphosphorylated peptide TH-(1-43) both free and bilayer bound. As seen in the crystal structure of THp-(1-43) complexed with 14-3-3γ, the region surrounding pSer19 adopts an extended conformation in the bound state, whereas THp-(1-43) adopts a bent conformation when free in solution, with higher content of secondary structure and higher number of internal hydrogen bonds. TH-(1-43) in solution presents the highest mobility and least defined structure of all forms studied, and it shows an energetically more favorable interaction with membranes relative to THp-(1-43). Cationic residues, notably Arg15 and Arg16, which are the recognition sites of the kinases phosphorylating at Ser19, are also contributing to the interaction with the membrane. Our results reveal the structural flexibility of this region of TH, in accordance with the functional versatility and conformational adaptation to different partners. Furthermore, this structural information has potential relevance for the development of therapeutics for neurodegenerative disorders, through modulation of TH-partner interactions.

Embedding Aβ42 in heterogeneous membranes depends on cholesterol asymmetries

Using a coarse-grained lipid and peptide model, we show that the free energy stabilization of amyloid-β in heterogeneous lipid membranes is predicted to have a dependence on asymmetric distributions of cholesterol compositions across the membrane leaflets. We find that a highly asymmetric cholesterol distribution that is depleted on the exofacial leaflet but enhanced on the cytofacial leaflet of the model lipid membrane thermodynamically favors membrane retention of a fully embedded Aβ peptide. However, in the case of cholesterol redistribution that increases concentration of cholesterol on the exofacial layer, typical of aging or Alzheimer's disease, the free energy favors peptide extrusion of the highly reactive N-terminus into the extracellular space that may be vulnerable to aggregation, oligomerization, or deleterious oxidative reactivity.

Photochemistry of "end-only" oligo-p-phenylene ethynylenes: complexation with sodium dodecyl sulfate reduces solvent accessibility

Cationic oligo-p-phenylene ethynylenes are very effective light-activated biocides and biosensors but degrade upon exposure to light. In this study, we explore the photochemistry of a class of "end-only" compounds from this series, which have cationic moieties on the ends of the backbone. Product characterization by mass spectrometry reveals that the photoreactivity of these molecules is higher than that of a previously studied oligomer and that the primary products of photolysis result from the addition of water or oxygen across the triple bond. In addition, a product suggesting the addition of peroxide or other reactive oxygen species across the triple bond was observed. To explore avenues by which the photodegradation of these compounds can be mitigated, the effects of complexation with sodium dodecyl sulfate micelles on their photochemistry was explored. Classical molecular dynamics simulations revealed that compounds that were protected from photolysis by SDS buried their phenylene ethynylene backbones into the interior of the micelle, protecting it from contact with water. This work has revealed a molecular basis for the protection of a novel class of light-activated biocides from irradiation that is consistent with the proposed photochemistry of these compounds. This information can be useful for developing photodegradation-resistant biocidal materials and applications for current compounds and leads to new molecular design.

Transport Properties of Water and Sodium Dodecyl Sulfate

In this work, results from atomistic molecular dynamics studies investigating the effect of surfactant concentration on the transport properties of bulk surfactant aqueous solutions, focusing on the anionic surfactant sodium dodecyl sulfate (SDS), are reported. The surfactant self-diffusion and the thermal conductivity of bulk aqueous SDS solutions were computed at a range of concentrations at room and boiling temperatures. Additionally, MP2f (Akin-Ojo et al., 2008, “Developing Ab Initio Quality Force Fields From Condensed Phase Quantum-Mechanics/Molecular-Mechanics Calculations Through the Adaptive Force Matching Method,” J. Phys. Chem., 129, p. 064108), one of a new generation water potentials is assessed for its suitability in reproducing the transport and thermal properties of bulk water. The thermal conductivity of MP2f water model was found to be: 0.64 W/(m⋅K) at 298 K and 0.66 W/(m⋅K) at 373 K, in much better agreement with the experimental values compared to both the rigid and the flexible TIP3P water model.

Characterizing the membrane-bound state of cytochrome P450 3A4: structure, depth of insertion, and orientation

Cytochrome P450 3A4 (CYP3A4) is the most abundant membrane-associated isoform of the P450 family in humans and is responsible for biotransformation of more than 50% of drugs metabolized in the body. Despite the large number of crystallographic structures available for CYP3A4, no structural information for its membrane-bound state at an atomic level is available. In order to characterize binding, depth of insertion, membrane orientation, and lipid interactions of CYP3A4, we have employed a combined experimental and simulation approach in this study. Taking advantage of a novel membrane representation, highly mobile membrane mimetic (HMMM), with enhanced lipid mobility and dynamics, we have been able to capture spontaneous binding and insertion of the globular domain of the enzyme into the membrane in multiple independent, unbiased simulations. Despite different initial orientations and positions of the protein in solution, all the simulations converged into the same membrane-bound configuration with regard to both the depth of membrane insertion and the orientation of the enzyme on the surface of the membrane. In tandem, linear dichroism measurements performed on CYP3A4 bound to Nanodisc membranes were used to characterize the orientation of the enzyme in its membrane-bound form experimentally. The heme tilt angles measured experimentally are in close agreement with those calculated for the membrane-bound structures resulted from the simulations, thereby verifying the validity of the developed model. Membrane binding of the globular domain in CYP3A4, which appears to be independent of the presence of the transmembrane helix of the full-length enzyme, significantly reshapes the protein at the membrane interface, causing conformational changes relevant to access tunnels leading to the active site of the enzyme.

Coarse-grained molecular dynamics simulations of photoswitchable assembly and disassembly

The supramolecular self-assembly and disassembly that are responsive to external stimuli are of critical importance to the design and synthesis of functional supramolecular materials. In this work, we performed a coarse-grained molecular dynamics study of photo-controlled assembly and disassembly on a timescale of ten microseconds. The spontaneous assembly of cis-AzoC10, trans-AzoC10, and cis-AzoC10/α-CD into micelle-like aggregates, and the disassembly of trans-AzoC10/α-CD starting from a pre-assembled micelle were directly simulated. Our results of simulations have revealed a significant size and shape dependence of aggregates on the molecular structure and concentrations of monomers. As demonstrated, with careful design, coarse-grained molecular dynamics simulations are useful in the study of controlled assembly and disassembly to bridge the gap between atomistic simulations and experiments.

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations

The association of hemagglutinin (HA) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A. Lipid rafts are thought to be small, fluctuating patches of membrane enriched in saturated phospholipids, sphingolipids, cholesterol and certain types of protein. However, raft-associating transmembrane (TM) proteins generally partition into Ld domains in model membranes, which are enriched in unsaturated lipids and depleted in saturated lipids and cholesterol. The reason for this apparent disparity in behavior is unclear, but model membranes differ from the plasma membrane in a number of ways. In particular, the higher protein concentration in the plasma membrane may influence the partitioning of membrane proteins for rafts. To investigate the effect of high local protein concentration, we have conducted coarse-grained molecular dynamics (CG MD) simulations of HA clusters in domain-forming bilayers. During the simulations, we observed a continuous increase in the proportion of raft-type lipids (saturated phospholipids and cholesterol) within the area of membrane spanned by the protein cluster. Lateral diffusion of unsaturated lipids was significantly attenuated within the cluster, while saturated lipids were relatively unaffected. On this basis, we suggest a possible explanation for the change in lipid distribution, namely that steric crowding by the slow-diffusing proteins increases the chemical potential for unsaturated lipids within the cluster region. We therefore suggest that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids. This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes.

The cell membrane is composed of a wide variety of lipids and proteins. Until recently, these were thought to be mixed evenly, but we now have evidence of the existence of “lipid rafts” — small, slow-moving areas of membrane in which certain types of lipid and protein accumulate. Rafts have many important biological functions in healthy cells, but also play a role in the assembly of influenza virus. For example, after the viral protein hemagglutinin is made inside the host cell, it accumulates in rafts. Exiting virus particles then take these portions of cell membrane with them as they leave the host cell. However, the mechanism by which proteins associate with lipid rafts is unclear. Here, we have used computers to simulate lipid membranes containing hemagglutinin. The simulations allow us to look in detail at the motions and interactions of individual proteins and lipids. We found that clusters of proteins altered the properties of nearby lipids, leading to accumulation of raft-type lipids. It therefore appears that aggregation of hemagglutinin may be enough to drive its association with rafts. This helps us to better understand both the influenza assembly process and the properties of lipid rafts.

Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools

The use of model membranes is currently part of the daily workflow for many biochemical and biophysical disciplines. These membranes are used to analyze the behavior of small substances, to simulate transport processes, to study the structure of macromolecules or for illustrative purposes. But, how can these membrane structures be generated? This mini review discusses a number of ways to obtain these structures. First, the problem will be formulated as the Membrane Packing Problem. It will be shown that the theoretical problem of placing proteins and lipids onto a membrane area differ significantly. Thus, two sub-problems will be defined and discussed. Then, different - partly historical - membrane modeling methods will be introduced. And finally, membrane modeling tools will be evaluated which are able to semi-automatically generate these model membranes and thus, drastically accelerate and simplify the membrane generation process. The mini review concludes with advice about which tool is appropriate for which application case.

Effect of counterions on the shape, hydration, and degree of order at the interface of cationic micelles: the triflate case

Specific ion effects in surfactant solutions affect the properties of micelles. Dodecyltrimethylammonium chloride (DTAC), bromide (DTAB), and methanesulfonate (DTAMs) micelles are typically spherical, but some organic anions can induce shape or phase transitions in DTA(+) micelles. Above a defined concentration, sodium triflate (NaTf) induces a phase separation in dodecyltrimethylammonium triflate (DTATf) micelles, a phenomenon rarely observed in cationic micelles. This unexpected behavior of the DTATf/NaTf system suggests that DTATf aggregates have unusual properties. The structural properties of DTATf micelles were analyzed by time-resolved fluorescence quenching, small-angle X-ray scattering, nuclear magnetic resonance, and electron paramagnetic resonance and compared with those of DTAC, DTAB, and DTAMs micelles. Compared to the other micelle types, the DTATf micelles had a higher average number of monomers per aggregate, an uncommon disk-like shape, smaller interfacial hydration, and restricted monomer chain mobility. Molecular dynamic simulations supported these observations. Even small water-soluble salts can profoundly affect micellar properties; our data demonstrate that the -CF3 group in Tf(-) was directly responsible for the observed shape changes by decreasing interfacial hydration and increasing the degree of order of the surfactant chains in the DTATf micelles.

Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment

The nonadiabatic photodynamics of the all-trans-2,4-pentadiene-iminium cation (protonated Schiff base 3, PSB3) and the all-trans-3-methyl-2,4-pentadiene-iminium cation (MePSB3) were investigated in the gas phase and in polar (aqueous) and nonpolar (n-hexane) solutions by means of surface hopping using a multireference configuration-interaction (MRCI) quantum mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for radiationless deactivation to the ground state, and structural and electronic parameters are compared. A strong influence of the polar solvent on the location of the crossing seam, in particular in the bond length alternation (BLA) coordinate, is found. Additionally, inclusion of the polar solvent changes the orientation of the intersection cone from sloped in the gas phase to peaked, thus enhancing considerably its efficiency for deactivation of the molecular system to the ground state. These factors cause, especially for MePSB3, a substantial decrease in the lifetime of the excited state despite the steric inhibition by the solvent.