Self-aggregation of trehalose in the mixed solvents of 1,3-dimethylimidazolium ionic liquid and water

Abstract

Conformational variations of solvated trehaloses in binary mixtures of 1,3-dialkylimidazolium ([dmim]Cl) ionic liquids and trehalose as well as ternary mixtures of trehalose, [dmim]Cl and water have been studied by molecular dynamics (MD) simulations with and without polarisable force fields. The interaction energy between anion Cl^? and water is stronger than that between water itself in the [dmim]Cl-water mixtures. Isolated water clusters were found in the binary [dmim]Cl-water mixtures with 60.0 and 75.0% mole fraction of water, but a continuous water network appears when the concentration of the mixture increases to 99.9%. In the case of binary mixtures of trehalose and [dmim]Cl, both non-polarisable and polarisable models demonstrated that the pyranose rings of trehalose displayed chair conformations. MD simulations with polarisation model could sample larger conformation space than that with non-polarisable model. A self-aggregation behaviour of trehalose was found in the ternary trehalose-[dmim]Cl-water mixtures, which can be rationalised by the stronger non-bonded interaction energy between trehalose molecules and anion Cl^? than that between trehalose molecules and water.     

Molecular dynamics simulation of proteins under high pressure: Structure,function and thermodynamics

BackgroundMolecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations.Scope of reviewFirst, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure.Major conclusionsRecent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening.General significanceMD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.     

Molecular Dynamics Simulations of Conformational Behavior of Linear RGD Peptidomimetics and Cyclic Prodrugs in Aqueous and Octane Solutions

Abstract

Conformations available to a class of cyclic prodrugs and corresponding linear RGD peptidomimetics were explored using 1 ns length molecular dynamics simulations performed with the program CHARMM. Water and octane, modeled explicitly, were used as solvents to mimic the change of the environment experienced by the solutes upon partition from water to membrane in the trans-cellular transport process. In water, the linear peptidomimetics tended to populate extended-like structures, characterized by strong favorable interactions with solvent and low intrinsic stability. In these extended conformations the charged termini are able to assume large distances, above 15 Å for the longest systems. These linear peptidomimetics have been found to exhibit the highest potency in experimental studies, in accord with the trends experimentally observed for RGD peptides. In contrast, in octane compact conformers of the linear peptidomimetics were favored, with all charged groups aggregated and shielded from solvent, exhibiting high intrinsic stability and weak solute-solvent interactions. Our calculations predict a large unfavorable energy change for transferring the linear systems from water to octane, in agreement with experimental findings that these compounds are not transported via the trans-cellular pathway. The cyclic pro- drugs did not exhibit major structural differences between the simulations in water and octane, adopting turn-like conformations in both solvents. The limited response of the cyclic structures to changes in the environment leads to energies of transfer from water to octane that are also unfavorable, but much less so than for the linear molecules. This effect is in accord with the observed enhanced passive trans-cellular transport of the cyclic prodrugs.     

Molecular Dynamics Study on Protein and it's Water Structure at High Pressure

Abstract

We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two types of solvated proteins-‘denaturation-unfavorable’ protein (insulin) and ‘denaturation-favorable protein’ (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A is mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the water cluster, we have observed that for ribonuclease A, 5-membered ring structure is more favorable than 6-membered ring at higher pressure. However, for insulin, the ratio of 5 to 6-ring is constant over the pressure ranges for which we have performed MD simulation. This indicates that the water structure around insulin does not change under high pressure.     

Molecular dynamics simulation of DPPC bilayer in DMSO

We performed molecular dynamics simulations on dipalmitoylphosphatidylcholine (DPPC)/dimethylsulfoxide (DMSO) system that has the same lipid:solvent weight ratio as in our previous simulation done on DPPC/water. We did not observe a large change in the size of DPPC membrane when the solvent was changed from water to DMSO. Also, we did not observe that a large number of DMSO molecules is permeating into the membrane, as it was suggested to explain the observed change in the bilayer repeat period. We found that the surface potential reverses its sign when water is replaced by DMSO. Based on the results from our simulations, we propose that the repulsion force acting between membranes is reduced when DMSO is added to solvent water and therefore membrane surfaces approach closer to each other and the extra solvent is removed into excess solution.     

Integral equation theories for predicting water structure around molecules

Water plays a crucial role in the structure and function of proteins and other biological macromolecules; thus, theories of aqueous solvation for these molecules are of great importance. However, water is a complex solvent whose properties are still not completely understood. Statistical mechanical integral equation theories predict the density distribution of water molecules around a solute so that all particles are fully represented and thus potentially both molecular and macroscopic properties are included. Here we discuss how several theoretical tools we have developed have been integrated into an integral equation theory designed for globular macromolecular solutes such as proteins. Our approach predicts the three-dimensional spatial and orientational distribution of water molecules around a solute. Beginning with a three-dimensional Ornstein-Zernike equation, a separation is made between a reference part dependent only on the spatial distribution of solvent and a perturbation part dependent also on the orientational distribution of solvent. The spatial part is treated at a molecular level by a modified hypernetted chain closure whereas the orientational part is treated as a Boltzmann prefactor using a quasi-continuum theory we developed for solvation of simple ions. A potential energy function for water molecules is also needed and the sticky dipole models of water, such as our recently developed soft-sticky dipole (SSD) model, are ideal for the proposed separation. Moreover, SSD water is as good as or better than three point models typically used for simulations of biological macromolecules in structural, dielectric and dynamics properties and yet is seven times faster in Monte Carlo and four times faster in molecular dynamics simulations. Since our integral equation theory accurately predicts results from Monte Carlo simulations for solvation of a variety of test cases from a single water or ion to ice-like clusters and ion pairs, the application of this theory to biological macromolecules is promising.     

Role of membrane organization and membrane domains in endocytic lipid trafficking

Lipid compositions vary greatly among organelles, and specific sorting mechanisms are required to establish and maintain these distinct compositions. In this review, we discuss how the biophysical properties of the membrane bilayer and the chemistry of individual lipid molecules play a role in the intracellular trafficking of the lipids themselves, as well as influencing the trafficking of transmembrane proteins. The large diversity of lipid head groups and acyl chains lead to a variety of weak interactions, such as ionic and hydrogen bonding at the lipid/water interfacial region, hydrophobic interactions, and van-der-Waals interactions based on packing density. In simple model bilayers, these weak interactions can lead to large-scale phase separations, but in more complex mixtures, which mimic cell membranes, such phase separations are not observed. Nevertheless, there is growing evidence that domains (i.e., localized regions with non-random lipid compositions) exist in biological membranes, and it is likely that the formation of these domains are based on interactions similar to those that lead to phase separations in model systems. Sorting of lipids appears to be based in part on the inclusion or exclusion of certain types of lipids in vesicles or tubules as they bud from membrane organelles.     

Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks

Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.     

Towards mimicking natural protein channels with aligned carbon nanotube membranes for active drug delivery

AimsCarbon nanotube (CNT) membranes offer an exciting opportunity to mimic natural protein channels due to 1) a mechanism of dramatically enhanced fluid flow 2) ability to place ‘gatekeeper’ chemistry at the entrance to pores 3) the ability for biochemical reactions to occur on gatekeeper molecules and 4) an ability to chemically functionalize each side of the membrane independently.Main methodsAligned CNT membranes were fabricated and CNT pore entrances modified with gatekeeper chemistry. Pressure driven fluid flow and diffusion experiments were performed to study the mechanisms of transport through CNTs.Key findingsThe transport mechanism through CNT membranes is primarily 1) ionic diffusion near bulk expectation 2) gas flow enhanced 1–2 orders of magnitude primarily due to specular reflection 3) fluid flow 4–5 orders of magnitude faster than conventional materials due to a nearly ideal slip-boundary interface. The transport can be modulated by ‘gatekeeper’ chemistry at the pore entrance using steric hindrance, electrostatic attraction/repulsion, or biochemical state. The conformation of charged tethered molecules can be modulated by applied bias setting the stage for programmable drug release devices.SignificanceThe membrane structure is mechanically far more robust than lipid bilayer films, allowing for large-scale chemical separations, delivery or sensing based on the principles of protein channels. The performance of protein channels is several orders of magnitude faster than conventional membrane materials. The fundamental requirements of mimicking protein channels are present in the CNT membrane system.     

Parameterization and Application of an Implicit Solvent Model for Macromolecules

Abstract

As the field of theoretical biophysics begins to recognize systems of longer timescales and larger magnitude, rapid approaches for investigating these systems are required. One promising simplification of the typical system of a solute surrounded by water is the use of implicit solvation models. The generalized Born implicit solvent offers a rapid approach for computing the electrostatic effects of bulk solvent without the explicit representation of water molecules. This report describes the parameterization of a generalized Born (GB) model for protein and nucleic acid structures. As a demonstration of the usefulness of this approach, the GB model is applied toward the discrimination of misfolded and properly folded protein structures. This study attempts to illustrate the potential of the GB model for molecular dynamics simulations over longer timescales as well as for screening large structural databases.     

On the Implementation of Friedman Boundary Conditions in Liquid Water Simulations

Abstract

We have applied the image approximation to the reaction field as suggested by H.L. Friedman [Mol. Phys., 29, 1533 (1975)] by investigating appropriate cavity sizes and system parameters for use in molecular simulations. The energy of and the structure around a central simple point charge (SPC) water molecule in a dielectric cavity was found to be in good agreement with the properties of a liquid sample. To confine the water molecules within the cavity, we introduced a short-range repulsion between a real charge and its image as the Lennard-Jones repulsive potential between oxygen atoms of the SPC potential. For a system of 65 water molecules a cavity radius of 10.45 Å is appropriate; this radius is altered to 12.00 Å for a cavity surrounding 113 molecules. The effect of the boundary is restricted to the outer-most water layer which is in contact with the dielectric continuum.     

Transitions between Closed and Open Conformations of TolC: The Effects of Ions in Simulations

Bacteria, such as Escherichia coli, use multidrug efflux pumps to export toxic substrates through their cell membranes. Upon formation of an efflux pump, the aperture of its outer membrane protein TolC opens and thereby enables the extrusion of substrate molecules. The specialty of TolC is its ability to dock to different transporters, making it a highly versatile export protein. Within this study, the transition between two conformations of TolC that are both available as crystal structures was investigated using all-atom molecular dynamics simulations. To create a partially open conformation from a closed one, the stability of the periplasmic aperture was weakened by a double point mutation at the constricting ring, which removes some salt bridges and hydrogen bonds. These mutants, which showed partial opening in previous experiments, did not spontaneously open during a 20-ns equilibration at physiological values of the KCl solution. Detailed analysis of the constricting ring revealed that the cations of the solvent were able to constitute ionic bonds in place of the removed salt bridges, which inhibited the opening of the aperture in simulations. To remove the ions from these binding positions within the available simulation time, an extra force was applied onto the ions. To keep the effect of this additional force rather flexible, it was applied in form of an artificial external electric field perpendicular to the membrane. Depending on the field direction and the ion concentration, these simulations led to a partial opening. In experiments, this energy barrier for the ions can be overcome by thermal fluctuations on a longer timescale.     

Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters

BackgroundThe availability of high-resolution X-ray structures has shown that proteins contain numerous water molecules, but their role is still not fully understood. Protonated and deprotonated water species are often involved in biochemical reactions. However protons are exceedingly difficult to detect directly because they are electron-poor species.MethodsThe oxygen‑oxygen distance of the crystallographic water molecules was analyzed in a large high-resolution data set. Moreover, a detailed analysis was carried out on the protein-bound water in the available structures of carbonic anhydrase II and cytochrome c oxidase, chosen as protein models in which protonated and deprotonated water species play a significant role.ResultsThe analysis shows an excess of water-water distances below the expected value for hydrogen bond. In the cavities and on the surface of the considered model proteins, clusters of water molecules are found, whose structure suggests the presence of chemical species deriving from self-ionization of water.ConclusionsThe presence of a small maximum below the hydrogen bond threshold in the oxygen‑oxygen distance distribution of crystallographic water molecules, along with the location of many of these water clusters, suggest the presence of Zundel-like structures in, or near, the proteins. Particularly significant is the presence of such structures in protein regions which have been identified as proton antennae or channels.General significanceThis work shows the possibilities, still unexplored, offered by this type of analysis in detecting in structures obtained by X-ray diffraction the presence of aqueous protons or hydroxide ions, which are chemical species as important as elusive.     

THE INFLUENCE OF ELECTROLYTES ON THE ELECTRIFICATION AND THE RATE OF DIFFUSION OF WATER THROUGH COLLODION MEMBRANES

1. When pure water is separated by a collodion membrane from a watery solution of an electrolyte the rate of diffusion of water is influenced not only by the forces of gas pressure but also by electrical forces. 2. Water is in this case attracted by the solute as if the molecules of water were charged electrically, the sign of the charge of the water particles as well as the strength of the attractive force finding expression in the following two rules, (a) Solutions of neutral salts possessing a univalent or bivalent cation influence the rate of diffusion of water through a collodion membrane, as if the water particles were charged positively and were attracted by the anion and repelled by the cation of the electrolyte; the attractive and repulsive action increasing with the number of charges of the ion and diminishing inversely with a quantity which we will designate arbitrarily as the "radius" of the ion. The same rule applies to solutions of alkalies. (b) Solutions of neutral or acid salts possessing a trivalent or tetravalent cation influence the rate of diffusion of water through a collodion membrane as if the particles of water were charged negatively and were attracted by the cation and repelled by the anion of the electrolyte. Solutions of acids obey the same rule, the high electrostatic effect of the hydrogen ion being probably due to its small "ionic radius." 3. The correctness of the assumption made in these rules concerning the sign of the charge of the water particles is proved by experiments on electrical osmose. 4. A method is given by which the strength of the attractive electric force of electrolytes on the molecules of water can be roughly estimated and the results of these measurements are in agreement with the two rules. 5. The electric attraction of water caused by the electrolyte increases with an increase in the concentration of the electrolyte, but at low concentrations more rapidly than at high concentrations. A tentative explanation for this phenomenon is offered. 6. The rate of diffusion of an electrolyte from a solution to pure solvent through a collodion membrane seems to obey largely the kinetic theory inasmuch as the number of molecules of solute diffusing through the unit of area of the membrane in unit time is (as long as the concentration is not too low) approximately proportional to the concentration of the electrolyte and is the same for the same concentrations of LiCl, NaCl, MgCl₂, and CaCl₂.     

Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from <Emphasis Type="Italic">Streptococcus pneumoniae</Emphasis>

Protein crystallization is in part driven by the changes in the entropy of the system, but opinions differ as to whether the solute (protein) or solvent (water) molecules make more of a contribution to the overall entropic change. Methylation of lysine residues in proteins has been used to enhance protein crystallization. We investigated using molecular dynamics simulations with explicit solvent molecules, the behavior of several native proteins and their methylated counterparts chosen from an earlier large-scale study. Methylated lysines are capable of making a variety of interactions including H-bonds with protein residues and solvent. We demonstrate that methylation on the lysine slightly increases its side chain conformational entropy by about 3.5 J mol⁻¹ K⁻¹. Analysis of the radial and spatial distributions of the water molecules around the methylated lysine surface in oxidoreductase from Streptococcus pneumoniae revealed a larger sphere of water molecules with low entropy, as compared with solvent associated with unmethylated lysine. If methylated lysine were to make interactions at the protein–protein interface, the low-entropy water molecules associated with methylated lysines would be released, resulting in a gain of entropy. We show that this gain more than compensates for the loss of protein entropy. Therefore, we propose that lysine methylation favors the formation of crystals through solvent entropic gain.     

Solvent Interactions and Protein Dynamics in Spin-labeled T4 Lysozyme

Abstract

Aspects of T4 lysozyme dynamics and solvent interaction are investigated using atomically detailed Molecular Dynamics (MD) simulations. Two spin-labeled mutants of T4 lysozyme are analyzed (T4L-N40C and T4L-K48C), which have been found from electronic paramagnetic resonance (EPR) experiments to exhibit different mobilities at the site of spin probe attachment (N- and C-terminus of helix B, respectively). Similarities and differences in solvent distribution and diffusion around the spin label, as well as around exposed and buried residues within the protein, are discussed. The purpose is to capture possible strong interactions between the spin label (ring) and solvent molecules, which may affect EPR lineshapes. The effect of backbone motions on the water density profiles is also investigated. The focus is on the domain closure associated with the T4 lysozyme hinge-bending motion, which is analyzed by Essential Dynamics (ED). The N-terminus of helix B is found to be a “hinge” residue, which explains the high degree of flexibility and motional freedom at this site.     

Microstructures,interactions and dynamics properties studies of N-methyldiethanolamine + guanidinium triflate ionic liquid + water tertiary system at the standard temperature

Molecular dynamics simulations with an all-atom force field have been carried out in order to understand the phase equilibrium behaviour of ternary aqueous mixtures containing guanidinium triflate ionic liquid [gua][OTf] and water mixed with N-methyldiethanolamine (MDEA) in different function composition at the standard temperature of 298.15 K. A very good numerical agreement has been obtained for the prediction of the mixture densities. The analysis of structural and dynamic properties showed that the molecular level of ternary mixtures is slightly affected by the presence of MDEA and [gua][OTf] molar fractions. For MDEA–water interactions in [gua][OTf] media, we found that MDEA prefers to be surrounded by water molecules rather than by MDEA molecules even at a high MDEA molar fraction. While for [gua][OTf]–water interaction in MDEA media, as [gua][OTf] molar fraction increases, water molecules replace counterions in the coordination shell of both ions, thus weakening their interaction. On the other hand, for MDEA–[gua][OTf] interactions in water media, we have found that as the molar fraction of [gua][OTf] increases, a sulfonate group from anion appears to have a stronger association by making hydrogen bonding with MDEA molecules. The chemical process using ionic liquids (ILs) as solvents is commonly limited by their high viscosity. Based on their physical properties such as viscosities, these ternary solvents can be applied in natural gas industry, such as removing carbon dioxide using aqueous MDEA and IL at high pressure.     

Modeling structure and flexibility of <Emphasis Type="Italic">Candida antarctica</Emphasis> lipase B in organic solvents

Background  

The structure and flexibility of Candida antarctica lipase B in water and five different organic solvent models was investigated using multiple molecular dynamics simulations to describe the effect of solvents on structure and dynamics. Interactions of the solvents with the protein and the distribution of water molecules at the protein surface were examined.     

Molecular dynamics simulations of Nafion and sulfonated polyether sulfone membranes. I. Effect of hydration on aqueous phase structure

We measured the water uptakes and proton conductivities of a Nafion membrane and three sulfonated polyether sulfone membranes (SPESs) with different values of ion-exchange capacity (IEC = 0.75, 1.0 and 1.4 meq/g) in relation to relative humidity in order to apply the findings to polymer electrolyte membrane fuel cells. The number of water molecules per sulfonic acid group λ at each humidity level was independent of the relative humidity for all membranes, but the proton conductivities of the SPESs were inferior to that of Nafion for the same λ value. Classical molecular dynamics simulations for the same membranes were carried out using a consistent force field at λ = 3, 6, 9, 12 and 15. The structural properties of water molecules and hydronium ions at a molecular level were estimated from radial distribution functions and cluster size distributions of water. We found that the radial distribution function of S(sulfonic acid)–S(sulfonic acid) of Nafion at λ = 3 indicated a significant correlation between the S–S pair, due to water channels, while the S–S pair of the SPESs showed a poor correlation. The cluster size distribution of water was also calculated in order to estimate the connectivity of the water channel. It is clear that some water is present in the SPESs as small, isolated clusters, especially when the water content is low.     

Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies

Amphotericin B (AmB) is a polyene macrolide antibiotic used to treat systemic fungal infections. The molecular mechanism of AmB action is still only partly characterized. AmB interacts with cell-membrane components and forms membrane channels that eventually lead to cell death. The interaction between AmB and the membrane surface can be regarded as the first (presumably crucial) step on the way to channel formation. In this study molecular dynamics simulations were performed for an AmB–lipid bilayer model in order to characterize the molecular aspects of AmB–membrane interactions. The system studied contained a box of 200 dimyristoylphosphatidylcholine (DMPC) molecules, a single AmB molecule placed on the surface of the lipid bilayer and 8,065 water molecules. Two molecular dynamics simulations (NVT ensemble), each lasting 1 ns, were performed for the model studied. Two different programs, CHARMM and NAMD2, were used in order to test simulation conditions. The analysis of MD trajectories brought interesting information concerning interactions between polar groups of AmB and both DMPC and water molecules. Our studies show that AmB preferentially took a vertical position, perpendicular to the membrane surface, with no propensity to enter the membrane. Our finding may suggest that a single AmB molecule entering the membrane is very unlikely.Figure The figure presents the whole structure of the system simulated—starting point. AmB is presented as a space-filling model, DMPC molecules—green sticks, water molecules—red sticks