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Douglas J Tobias

Publications and source records attributed to Douglas J Tobias.

18 recordsLinked to original sources
PubMed2006

Investigation of finite system-size effects in molecular dynamics simulations of lipid bilayers.

In the absence of external stress, the surface tension of a lipid membrane vanishes at equilibrium, and the membrane exhibits long wavelength undulations that can be described as elastic (as opposed to tension-dominated) deformations. These long wavelength fluctuations are generally suppressed in molecular dynamics simulations of membranes, which have typically been carried out on membrane patches with areas <100 nm2 that are replicated by periodic boundary conditions. As a result, finite system-size effects in molecular dynamics simulations of lipid bilayers have been subject to much discussion in the membrane simulation community for several years, and it has been argued that it is necessary to simulate small membrane patches under tension to properly model the tension-free state of macroscopic membranes. Recent hardware and software advances have made it possible to simulate larger, all-atom systems allowing us to directly address the question of whether the relatively small size of current membrane simulations affects their physical characteristics compared to real macroscopic bilayer systems. In this work, system-size effects on the structure of a DOPC bilayer at 5.4 H2O/lipid are investigated by performing molecular dynamics simulations at constant temperature and isotropic pressure (i.e., vanishing surface tension) of small and large single bilayer patches (72 and 288 lipids, respectively), as well as an explicitly multilamellar system consisting of a stack of five 72-lipid bilayers, all replicated in three dimensions by using periodic boundary conditions. The simulation results are compared to X-ray and neutron diffraction data by using a model-free, reciprocal space approach developed recently in our laboratories. Our analysis demonstrates that finite-size effects are negligible in simulations of DOPC bilayers at low hydration, and suggests that refinements are needed in the simulation force fields.

Computer Simulation↗
PubMed2006

Inertial suppression of protein dynamics in a binary glycerol-trehalose glass.

The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using similar binary glass samples. In this study, we use molecular dynamics (MD) simulations to investigate the dynamics of a hydrated protein encased in glycerol, unary trehalose and binary glycerol-trehalose glasses. We have found that we are able to reproduce the rigidification of the glycerol-trehalose glassy matrix and that there is a direct correlation between bulk glass dynamics and the extent of atomic fluctuation of protein atoms. The detailed microscopic picture that emerges is that protein dynamics are suppressed mainly by inertia of the bulk glass and to a lesser extent specific interactions at the protein-solvent interface. Thus, the inertia of the glassy matrix may be an influential factor in the determination of pharmaceutically relevant formulations.

Glass↗
PubMed2006

Self-induced docking site of a deeply embedded peripheral membrane protein.

As a first step toward understanding the principles of the targeting of C2 domains to membranes, we have carried out a molecular dynamics simulation of the C2 domain of cytosolic phospholipase A2 (cPLA2-C2) in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer at constant pressure and temperature (NPT, 300 K and 1 atm). Using the high-resolution crystal structure of cPLA2-C2 as a starting point, we embedded two copies of the C2 domain into a pre-equilibrated membrane at the depth and orientation previously defined by electron paramagnetic resonance (EPR). Noting that in the membrane-bound state the three calcium binding loops are complexed to two calcium ions, we initially restrained the calcium ions at the membrane depth determined by EPR. But the depth and orientation of the domains remained within EPR experimental errors when the restraints were later removed. We find that the thermally disordered, chemically heterogeneous interfacial zones of phosphatidylcholine bilayers allow local lipid remodeling to produce a nearly perfect match to the shape and polarity of the C2 domain, thereby enabling the C2 domain to assemble and optimize its own lipid docking site. The result is a cuplike docking site with a hydrophobic bottom and hydrophilic rim. Contrary to expectations, we did not find direct interactions between the protein-bound calcium ions and lipid headgroups, which were sterically excluded from the calcium binding cleft. Rather, the lipid phosphate groups provided outer-sphere calcium coordination through intervening water molecules. These results show that the combined use of high-resolution protein structures, EPR measurements, and molecular dynamics simulations provides a general approach for analyzing the molecular interactions between membrane-docked proteins and lipid bilayers.

Binding Sites↗
PubMed2006

A voltage-sensor water pore.

Voltage-sensor (VS) domains cause the pore of voltage-gated ion channels to open and close in response to changes in transmembrane potential. Recent experimental studies suggest that VS domains are independent structural units. This independence is revealed dramatically by a voltage-dependent proton-selective channel (Hv), which has a sequence homologous to the VS domains of voltage-gated potassium channels (Kv). Here we show by means of molecular dynamics simulations that the isolated open-state VS domain of the KvAP channel in a lipid membrane has a configuration consistent with a water channel, which we propose as a common feature underlying the conductance of protons, and perhaps other cations, through VS domains.

Animals↗
PubMed2006

Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations.

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level.

Birefringence↗
PubMed2006

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study.

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.

Computer Simulation↗
PubMed2006

On NO3--H2O interactions in aqueous solutions and at interfaces.

The constrained molecular-dynamics technique was employed to investigate the transport of a nitrate ion across the water liquid/vapor interface. We developed a nitrate-ion-water polarizable potential that accurately reproduces the solvation properties of the hydrated nitrate ion. The computed free-energy profile for the transfer of the nitrate ion across the air/water interface increases monotonically as the nitrate ion approaches the Gibbs dividing surface from the bulk liquid side. The computed density profiles of 1M KNO(3) salt solution indicate that the nitrate and potassium ions are both found below the aqueous interface. Upon analyzing the results, we conclude that the probability of finding the nitrate anion at the aqueous interface is quite small.

Air↗
PubMed2005

Interface connections of a transmembrane voltage sensor.

Voltage-sensitive ion channels open and close in response to changes in transmembrane (TM) potential caused by the motion of the S4 voltage sensors. These sensors are alpha-helices that include four or more positively charged amino acids, most commonly arginine. The so-called paddle model, based on the high-resolution structure of the KvAP K+ channel [Jiang, et al. (2003) Nature 423, 33-41], posits that the S4 sensors move within the membrane bilayer in response to TM voltage changes. Direct exposure of S4 sensors to lipid is contrary to the classical expectation that the dielectric contrast between the membrane hydrocarbon core and water presents an insurmountable energetic penalty to burial of electric charges. Nevertheless, recent experiments have shown that a helix with the sequence of KvAP S4 can be inserted across the endoplasmic reticulum membrane. To reconcile this result with the classical energetics argument, we have carried out a molecular dynamics simulation of an isolated TM S4 helix in a lipid bilayer. The simulation reveals a stabilizing hydrogen-bonded network of water and lipid phosphates around the arginines that reduces the effective thickness of the bilayer hydrocarbon core to approximately 10 A in the vicinity of the helix. It suggests that bilayer phospholipids can adapt locally to strongly perturbing protein elements, causing the phospholipids to become a structural extension of the protein.

Hydrogen Bonding↗
PubMed2005

Molecular dynamics simulations of atmospheric oxidants at the air-water interface: solvation and accommodation of OH and O3.

A comparative study of OH, O3, and H2O equilibrium aqueous solvation and gas-phase accommodation on liquid water at 300 K is performed using a combination of ab initio calculations and molecular dynamics simulations. Polarizable force fields are developed for the interaction potential of OH and O3 with water. The free energy profiles for transfer of OH and O3 from the gas phase to the bulk liquid exhibit a pronounced minimum at the surface, but no barrier to solvation in the bulk liquid. The calculated surface excess of each oxidant is comparable to calculated and experimental values for short chain, aliphatic alcohols. Driving forces for the surface activity are discussed in terms of the radial distribution functions and dipole orientation distributions for each molecule in the bulk liquid and at the surface. Simulations of OH, O3, and H2O impinging on liquid water with a thermal impact velocity are used to calculate thermal accommodation (S) and mass accommodation (alpha) coefficients. The values of S for OH, O3, and H2O are 0.95, 0.90, and 0.99, respectively. The approaching molecules are accelerated toward the liquid surface when they are approximately 5 angstroms above it. The molecules that reach thermal equilibrium with the surface do so within 2 ps of striking the surface, while those that do not scatter into the gas phase with excess translational kinetic energy in the direction perpendicular to the surface. The time constants for absorption and desorption range from approximately 35 to 140 ps, and the values of alpha for OH, O3, and H2O are 0.83, 0.047, and 0.99, respectively. The results are consistent with previous formulations of gas-phase accommodation from simulations, in which the process occurs by rapid thermal and structural equilibration followed by diffusion on the free energy profile. The implications of these results with respect to atmospheric chemistry are discussed.

Air↗
PubMed2005

Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: spectroscopic and molecular dynamics studies.

Investigations of the air-liquid interface of aqueous salt solutions containing ammonium (NH(4)(+)) and sulfate (SO(4)(2-)) ions were carried out using molecular dynamics simulations and vibrational sum frequency generation spectroscopy. The molecular dynamics simulations show that the predominant effect of SO(4)(2-) ions, which are strongly repelled from the surface, is to increase the thickness of the interfacial region. The vibrational spectra reported are in the O-H stretching region of liquid water. Isotropic Raman and ATR-FTIR (attenuated total reflection Fourier transform infrared) spectroscopies were used to study the effect of ammonium and sulfate ions on the bulk structure of water, whereas surface sum frequency generation spectroscopy was used to study the effect of these ions on the interfacial structure of water. Analysis of the interfacial and bulk vibrational spectra reveal that aqueous solutions containing SO(4)(2-) perturb the interfacial water structure differently than the bulk and, consistent with the molecular dynamics simulations, reveal an increase in the thickness of the interfacial region.

Journal Article↗
PubMed2005

Unified molecular picture of the surfaces of aqueous acid, base, and salt solutions.

The molecular structure of the interfacial regions of aqueous electrolytes is poorly understood, despite its crucial importance in many biological, technological, and atmospheric processes. A long-term controversy pertains between the standard picture of an ion-free surface layer and the strongly ion specific behavior indicating in many cases significant propensities of simple inorganic ions for the interface. Here, we present a unified and consistent view of the structure of the air/solution interface of aqueous electrolytes containing monovalent inorganic ions. Molecular dynamics calculations show that in salt solutions and bases the positively charged ions, such as alkali cations, are repelled from the interface, whereas the anions, such as halides or hydroxide, exhibit a varying surface propensity, correlated primarily with the ion polarizability and size. The behavior of acids is different due to a significant propensity of hydronium cations for the air/solution interface. Therefore, both cations and anions exhibit enhanced concentrations at the surface and, consequently, these acids (unlike bases and salts) reduce the surface tension of water. The results of the simulations are supported by surface selective nonlinear vibrational spectroscopy, which reveals among other things that the hydronium cations are present at the air/solution interface. The ion specific propensities for the air/solution interface have important implications for a whole range of heterogeneous physical and chemical processes, including atmospheric chemistry of aerosols, corrosion processes, and bubble coalescence.

Acids↗
PubMed2005

Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations.

We report the sum frequency generation (SFG) spectra of aqueous sodium iodide interfaces computed with the methodology outlined by Morita and Hynes (J. Phys. Chem. B 2002, 106, 673), which is based on molecular dynamics simulations. The calculated spectra are in qualitative agreement with experiment. Our simulations show that the addition of sodium iodide to water leads to an increase in SFG intensity in the region of 3400 cm(-1), which is correlated with an increase in ordering of hydrogen-bonded water molecules. Depth-resolved orientational distribution functions suggest that the ion double layer orders water molecules that are approximately one water layer below the Gibbs dividing surface. We attribute the increase in SFG intensity to these ordered subsurface water molecules that are present in the aqueous sodium iodide/air interfaces but are absent in the neat water/air interface.

Air↗
PubMed2004

Hydroxyl radical at the air-water interface.

Interaction of the hydroxyl radical with the liquid water surface was studied using classical molecular dynamics computer simulations. From a series of scattering trajectories, the thermal and mass accommodation coefficients of OH on liquid water at 300 K were determined to be 0.95 and 0.83, respectively. The calculated free energy profile for transfer of OH across the air-water interface at 300 K exhibits a minimum in the interfacial region, with the free energy of adsorbtion (DeltaGa) being about 1 kcal/mol more negative than the hydration free energy (DeltaGs). The propensity of the hydroxyl radical for the air-water interface manifests itself in partitioning of OH radicals between the bulk water and the surface. The enhancement of the surface concentration of OH relative to its concentration in the aqueous phase suggests that important OH chemistry may be occurring in the interfacial layer of water droplets, aqueous aerosol particles, and thin water films adsorbed on solid surfaces. This has profound consequences for modeling heterogeneous atmospheric chemical processes.

Air↗
PubMed2004

Methyl group dynamics as a probe of the protein dynamical transition.

Hydrated proteins undergo a dynamical transition around 200 K from glasslike to liquidlike motion. Molecular dynamics simulations have been used to study the temperature dependence of the dynamics of ribonuclease A in the hydrated crystal, a model dehydrated powder, and aqueous solution. Changes in the dynamics accompanying the transition throughout the protein have been quantified in terms of the mean-squared fluctuations (MSFs) of methyl hydrogen atoms on the 100 ps time scale. In solution at 300 K the MSFs span a broad distribution, consistent with NMR relaxation measurements. The MSF distribution in the hydrated crystal at 300 K is qualitatively similar to the solution result, except for a slight shift to lower values, and dehydration results in a dramatic shift of the MSFs to lower values. As the temperature is lowered, the whole distribution of methyl group fluctuations in the hydrated crystal shifts to lower values. Most of the methyl groups in the hydrated protein display a nonlinear temperature dependence with a dynamical transition at approximately 200 K, but most methyl groups do not undergo a transition in the dehydrated protein. We conclude that the dynamical transition occurs throughout most of the protein and that solvent is required for the transition.

Computer Simulation↗
PubMed2004

Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach.

A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the same way as experimental data by determining the structure factors of the system and, via Fourier reconstruction, the overall transbilayer scattering-density profiles. Multi-nanosecond molecular dynamics simulations of a dioleoylphosphatidylcholine bilayer at 66% RH (5.4 waters/lipid) were performed in the constant pressure and temperature ensemble using the united-atom GROMACS and the all-atom CHARMM22/27 force fields with the GROMACS and NAMD software packages, respectively. The quality of the simulated bilayer structures was evaluated by comparing simulation with experimental results for bilayer thickness, area/lipid, individual molecular-component distributions, continuous and discrete structure factors, and overall scattering-density profiles. Neither the GROMACS nor the CHARMM22/27 simulations reproduced experimental data within experimental error. The widths of the simulated terminal methyl distributions showed a particularly strong disagreement with the experimentally observed distributions. A comparison of the older CHARMM22 with the newer CHARMM27 force fields shows that significant progress is being made in the development of atomic force fields for describing lipid bilayer systems empirically.

Computer Simulation↗
PubMed2003

Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer.

Pulmonary surfactant is a complex mixture of lipids and proteins that lines the air/liquid interface of the alveolar hypophase and confers mechanical stability to the alveoli during the breathing process. The desire to formulate synthetic mixtures for low-cost prophylactic and therapeutic applications has motivated the study of the specific roles and interactions of the different components. All-atom molecular dynamics simulations were carried out on a model system composed of a monolayer of palmitic acid (PA) and a surfactant protein B peptide, SP-B(1-25). A detailed structural characterization as a function of the lipid monolayer specific area revealed that the peptide remains inserted in the monolayer up to values of specific area corresponding to an untilted condensed phase of the the pure palmitic acid monolayer. The system remains stable by altering the conformational order of both the anionic lipid monolayer and the peptide secondary structure. Two elements appear to be key for the constitution of this phase: an electrostatic interaction between the cationic peptide residues with the anionic headgroups, and an exclusion of the aromatic residues on the hydrophobic end of the peptide from the hydrophilic and aqueous regions.

Biomimetics↗
PubMedDate not supplied

Molecular dynamics simulations of aqueous pullulan oligomers.

Molecular dynamics (MD) simulations have been used to model small-angle X-ray scattering (SAXS) data on aqueous solutions of four oligomeric segments of the glucan pullulan: the trimer G(3) (comprising one polymer repeating unit), the hexamer (G(3))(2), the nonamer (G(3))(3), and the dodecamer (G(3))(4). The AMBER force field was used in conjunction with the GB/SA continuum solvation model to calculate both the mean global dimensions of the oligomers from the limiting small angle scattering behavior and the shorter range structural information implicit in the Debye scattering function at larger scattering angles. This same force field and solvation treatment were employed earlier by Liu et al. (Macromolecules 1999, 32, 8611-8620) with apparent success in a rotational isomeric state (RIS) treatment of the same experimental data. The present work discloses that, despite numerical success in modeling the SAXS data, the RIS treatment, which includes only the interactions within dimeric segments of the polymer chain, fails to account accurately for excluded volume effects at the range of 3-12 sugar residues in the polymer backbone. It is suggested that MD simulations using continuum solvation models can be used to circumvent errors inherent in the computationally efficient RIS treatments of polymer nano- and picosecond dynamics while at the same time avoiding the heavy computational requirements of all-atom methods.

Carbohydrate Conformation↗