pSPICA Force Field Extended for Proteins and Peptides.

Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to investigate biological processes involving proteins and lipids. CG force fields (FFs) in these MD studies often use implicit or nonpolar water models to reduce computational costs. CG-MD using water models cannot properly describe electrostatic screening effects owing to the hydration of ionic segments and thus cannot appropriately describe molecular events involving water channels and pores through lipid membranes. To overcome this issue, we developed a protein model in the pSPICA FF, in which a polar CG water model showing the proper dielectric response was adopted. The developed CG model greatly improved the transfer free energy profiles of charged side chain analogues across the lipid membrane. Application studies on melittin-induced membrane pores and mechanosensitive channels in lipid membranes demonstrated that CG-MDs using the pSPICA FF correctly reproduced the structure and stability of the pores and channels. Furthermore, the adsorption behavior of the highly charged nona-arginine peptides on lipid membranes changed with salt concentration, indicating the pSPICA FF is also useful for simulating protein adsorption on membrane surfaces.

Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure.

Lipid droplets (LDs) are intracellular organelles responsible for lipid storage, and they emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly triglycerides (TG), between the two leaflets of the ER membrane. LD biogenesis takes place at ER sites that are marked by the protein seipin, which subsequently recruits additional proteins to catalyze LD formation. Deletion of seipin, however, does not abolish LD biogenesis, and its precise role in controlling LD assembly remains unclear. Here, we use molecular dynamics simulations to investigate the molecular mechanism through which seipin promotes LD formation. We find that seipin clusters TG, as well as its precursor diacylglycerol, inside its unconventional ring-like oligomeric structure and that both its luminal and transmembrane regions contribute to this process. This mechanism is abolished upon mutations of polar residues involved in protein-TG interactions into hydrophobic residues. Our results suggest that seipin remodels the membrane of specific ER sites to prime them for LD biogenesis.

Complex Energy Landscapes of Self-Assembled Vesicles.

The field of supramolecular chemistry has witnessed tremendous progress in bringing the system away from equilibrium for traditionally inaccessible structures and functions. Vesicular assemblies with complex energy landscapes and pathways, which are reminiscent of diverse cellular vesicles like exosomes, remain exceedingly rare. Here, relying on the activation of oligo(ethylene glycol) (OEG) interdigitation and the encoded conformational freedom in monodisperse Janus dendrimers, we reveal a rich landscape and a pathway selection of distinct vesicles. The interdigitation can be selectively switched on and off using temperature ramps, and the critical temperatures can be further determined by molecular design. Our findings suggest that synthetic vesicles, with different energy states and unexpected transition pathways, emulate dynamic cellular vesicles in nature. We anticipate that vesicles with an activated OEG corona conformation will open new routes for nanomedicine and advanced materials.

Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes.

The principles for the selection of the stereochemistry of phospholipids of biological membranes remain unclear and continue to be debated. Therefore, any new experiments on this topic may help progress in this field. To address this question, three libraries of constitutional isomeric glycerol-amphiphilic Janus dendrimers (JDs) with nonsymmetric homochiral, racemic, and symmetric achiral branching points were synthesized by an orthogonal-modular-convergent methodology. These JDs amplify self-assembly, and therefore, monodisperse vesicles known as dendrimersomes (DSs) with predictable dimensions programmed by JD concentration were assembled by rapid injection of their ethanol solution into water. DSs of homochiral JD enantiomers, racemic, including mixtures of different enantiomers, and achiral exhibited similar DS size-concentration dependence. However, the number of bilayers of DSs assembled from homochiral, achiral, and racemic JDs determined by cryo-TEM were different. Statistical analysis of the number of bilayers and coarse-grained molecular dynamics simulations demonstrated that homochiral JDs formed predominantly unilamellar DSs. Symmetric achiral JDs assembled only unilamellar DSs while racemic JDs favored multilamellar DSs. Since cell membranes are unilamellar, these results indicate a new rationale for nonsymmetric homochiral vs racemic selection. Simultaneously, these experiments imply that the symmetric achiral lipids forming more stable membrane, probably had been the preferable assemblies of prebiotic cell membranes.

Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa Cells, and E. coli.

Herein, trimethyl-ß-cyclodextrin (TMe-ß-CDx) and γ-cyclodextrin (γ-CDx) could dissolve a tetraphenylethylene derivative (TPE-OH4 ) in water through high-speed vibration milling. The fluorescence intensity of the TMe-ß-CDx-TPE-OH4 complex was much higher than that of the γ-CDx-TPE-OH4 complex, as the rotation of the central C=C double bond of TPE-OH4 after photoactivation was inhibited in a smaller TMe-ß-CDx cavity in comparison with the γ-CDx cavity. In contrast, the fluorescence intensity of the γ-CDx-TPE-OH4 complex was very weak; nevertheless, it increased after the addition of liposomes due to the transfer of TPE-OH4 from the γ-CDx cavity to the lipid membrane as a "turn-on" phenomenon. Furthermore, to apply temperature sensor, it was demonstrated that the fluorescence intensity in the liposomes depended on the phase-transition temperature. By using the fluorescence turn-on phenomenon, TPE-OH4 could detect the presence of HeLa cells and E. coli by fluorescence.

HER-2-Targeted Boron Neutron Capture Therapy with Carborane-integrated Immunoliposomes Prepared via an Exchanging Reaction.

Boron neutron capture therapy (BNCT) is a promising modality for cancer treatment because of its minimal invasiveness. To maximize the therapeutic benefits of BNCT, the development of efficient platforms for the delivery of boron agents is indispensable. Here, carborane-integrated immunoliposomes were prepared via an exchanging reaction to achieve HER-2-targeted BNCT. The conjugation of an anti-HER-2 antibody to carborane-integrated liposomes successfully endowed these liposomes with targeting properties toward HER-2-overexpressing human ovarian cancer cells (SK-OV3); the resulting BNCT activity toward SK-OV3 cells obtained using the current immunoliposomal system was 14-fold that of the l-BPA/fructose complex, which is a clinically available boron agent. Moreover, the growth of spheroids treated with this system followed by thermal neutron irradiation was significantly suppressed compared with treatment with the l-BPA/fructose complex.

Liquid Structures and Ion Dynamics of Ionic Liquids Viewed from Intermolecular Interactions.

The elucidation of the factors determining liquid structures and transport properties of ionic liquids is important for the design and development of ionic liquid electrolytes. This personal account introduces the importance of computational methods for studying ionic liquids. Molecular dynamics simulations provide detailed information on liquid structures of ionic liquid such as the structures of solvated cation complexes in equimolar mixtures of glymes and Li[TFSA] and the effects of the charges of electrode on liquid structure near the electrode. Ab initio calculations reveal that the magnitude of the attraction between ions and conformational flexibility ions play important roles in determining transport properties of ionic liquids. First principle molecular dynamics simulations elucidate why solvated cation complex is stable in the equimolar mixtures, although the Li+ -[TFSA]- interaction is greater than Li+ -glyme interaction.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study.

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a ß-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH3, -CH3, and -CF3. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH3 and -CF3 SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH3 avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.

Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: plausible reaction path during discharge of lithium-sulfur battery.

The elucidation of elemental redox reactions of sulfur is important for improving the performance of lithium-sulfur batteries. The energies of stable structures of Sn, Sn˙-, Sn2-, [LiSn]- and Li2Sn (n = 1-8) were calculated at the CCSD(T)/cc-pVTZ//MP3/cc-pVDZ level. The heats of reduction reactions of S8 and Li2Sn with Li in the solid phase were estimated from the calculated energies and sublimation energies. The estimated heats of the redox reactions show that there are several redox reactions with nearly identical heats of reaction, suggesting that several reactions can proceed simultaneously at the same discharge voltage, although the discharging process was often explained by stepwise reduction reactions. The reduction reaction for the formation of Li2Sn (n = 2-6 and 8) from S8 normalized as a one electron reaction is more exothermic than that for the formation of Li2S directly from S8, while the reduction reactions for the formation of Li2S from Li2Sn are slightly less exothermic than that for the formation of Li2S directly from S8. If the reduction reactions with large exotherm occur first, these results suggest that the reduction reactions forming Li2Sn (n = 2-6 and 8) from S8 occur first, then Li2S is formed, and therefore, a two-step discharge-curve is observed.

All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution.

Immature hepatitis B virus (HBV) captures nucleotides in its capsid for reverse transcription. The nucleotides and nucleotide analog drugs, which are triphosphorylated and negatively charged in the cell, approach the capsid via diffusion and are absorbed into it. In this study, we performed a long-time molecular dynamics calculation of the entire HBV capsid containing pregenome RNA to investigate the interactions between the capsid and negatively charged substances. Electric field analysis demonstrated that negatively charged substances can approach the HBV capsid by thermal motion, avoiding spikes. The substances then migrate all over the floor of the HBV capsid. Finally, they find pores through which they can pass through the HBV capsid shell. Free energy profiles were calculated along these pores for small ions to understand their permeability through the pores. Anions (Cl-) showed higher free energy barriers than cations (Na+ and K+) through all pores, and the permeation rate of Cl- was eight times slower than that of K+ or Na+. Furthermore, the ions were more stable in the capsid than in the bulk water. Thus, the HBV capsid exerts ion selectivity for uptake and provides an environment for ions, such as nucleotides and nucleotide analog drugs, to be stabilized within the capsid.

Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine.

Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryotic and eubacterial origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaeal membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study, we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in a membrane using 2H nuclear magnetic resonance (NMR) measurements of the synthetic lipid with a high stereochemical purity and molecular dynamics (MD) simulations. Deuterium-labeled 3',3'-CD3,D-DPhPC (2) and 7',7'-CD3,D-DPhPC (3) showed the characteristic quadrupole splitting width in the 2H NMR spectra, which corresponded to the bent orientation reported for the archaeal lipid PGP-Me [Yamagami, M., et al. (2019) Biochemistry 58, 3869-3879]. However, MD simulations, which reproduced the 2H NMR results well, unveiled the unknown features of DPhPC in the membrane; DPhPC has a chain-specific average orientation, where two bent orientations with upward and downward methyl groups occur at positions C3 and C7 of the sn-1 and sn-2 chains of DPhPC, respectively. These MD and NMR results reveal that these two bent orientations define the average orientation of DPhPC for the shallow part of the acyl chains, which is considered to be an important factor in the stability of DPhPC membranes.

Molecular simulation of the shape deformation of a polymersome.

Vesicles composed of diblock copolymers, or polymersomes, have proven to possess numerous applications ranging from drug delivery to catalytically driven nano-motors. The shape of a polymersome can be responsive to external stimuli, such as light or solvent. Molecular dynamics simulations reveal that the shape change upon the contraction of the inner volume of a polymersome vesicle occurs in two separate regimes-a stretching regime and a bending regime. The barrier is shown to be dependent on the solvent environment. These results suggest that tailoring the bending modulus of polymer membranes can be used as a design methodology to engineer new stimuli-responsive vesicles.

Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation.

In molecular dynamics (MD) calculations of the free energies of ions and ionic molecules, we often encounter net charged molecular systems where the electrical neutrality condition is broken. This charge causes a problem in the evaluation of long-range Coulombic interactions under periodic boundary conditions. A standard remedy for this problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of Coulombic interactions for such systems including background charge using the fast multipole method (FMM). Furthermore, an efficient scheme is developed to evaluate solute-solvent interaction energies using the FMM, reducing the computational burden for the far-field part. We calculate the hydration free energies of Mg2+, Na+, and Cl- ions dissolved in a neutral solvent using the new expression. The calculated free energies show good agreement with the results obtained using the well-established particle mesh Ewald method. This demonstrates the validity of the proposed expression. This work should make a contribution to highly parallelized MD calculations for large-scale charged systems (particularly, those with over million particles).

Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission.

A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated-fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare submicron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.

Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup.

Sphingomyelin (SM) and cholesterol (Cho) are the important lipids for the formation of biologically functional membrane domains, lipid rafts. However, the interaction between Cho and the headgroup of SM remains unclear. In this study, we performed solid-state NMR experiments to reveal the Cho effects on the headgroup conformation using 2H-labeled stearoyl-SM (SSM). Deuterated SSMs at the Cα, Cß, and Cγ positions of a choline moiety were separately prepared and subjected to NMR measurements to determine the quadrupolar splitting of 2H signals in hydrated SSM unitary and SSM/Cho (1:1) bilayers. Using 2H NMR and 13C-31P REDOR data, the conformation and orientation of the choline moiety were deduced and compared with those derived from molecular dynamics simulations. In SSM unitary bilayers, three torsional angles in the phosphocholine moiety, P-O-Cα-Cß, were found to be consecutive +gauche(g)/+g/+g or -g/-g/-g. The orientation and conformation of the SSM headgroup were consistent with the results of our molecular dynamics simulations and the previous results on phosphatidylcholines. The quadrupolar coupling at the α methylene group slightly increased in the presence of Cho, and those at the Cß and Cγ decreased more significantly, thus suggesting that Cho reduced the gauche conformation at the Cα-Cß torsion. The conformational ensemble in the presence of Cho may enhance the so-called umbrella effect of the SSM headgroup, resulting in the stabilization of Cho near the SM molecules by concealing the hydrophobic Cho core from interfacial water. We also examined the effect of the chiral centers at the sphingosine chain to the headgroup conformation by determining the enantiomeric excess between the diastereomeric +g/+g/+g and -g/-g/-g conformers using (S)-Cα-deuterated and (R)-Cα-deuterated SSMs. Their 2H NMR measurements showed that the chiral centers induced the slight diastereomeric excess in the SM headgroup conformation.

Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes.

The average conformation of the methyl-branched chains of archaeal lipid phosphatidyl glycerophosphate methyl ester (PGP-Me) was examined in a hydrated bilayer membrane based on the 2H nuclear magnetic resonance (NMR) of enantioselectively 2H-labeled compounds that were totally synthesized for the first time in this study. The NMR results in combination with molecular dynamics simulations revealed that the PGP-Me chain appeared to exhibit behavior different from that of typical membrane lipids such as dimyristoylphosphatidylcholine (DMPC). The C-C bonds of the PGP-Me chain adopt alternative parallel and tilted orientations to the membrane normal as opposed to a DMPC chain where all of the C-C bonds tilt in the same way on average. This characteristic orientation causes the intertwining of PGP-Me chains, which plays an important role in the excellent thermal and high-salinity stabilities of archaeal lipid bilayers and membrane proteins.

The Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly.

Amphotericin B (AmB) is a polyene macrolide antibiotic clinically used as an antifungal drug. Its preferential complexation with ergosterol (Erg), the major sterol of fungal membranes, leads to the formation of a barrel-stave-like ion channel across a lipid bilayer. To gain a better understanding of the mechanism of action, the mode of lipid bilayer spanning provides essential information. However, because of the lack of methodologies to observe it directly, it has not been revealed for the Erg-containing channel assembly for many years. In this study, we disclosed that the AmB-Erg complex spans a lipid bilayer with a single-molecule length, using solid-state nuclear magnetic resonance (NMR) experiments. Paramagnetic relaxation enhancement by Mn2+ residing near the surface of lipid bilayers induced the depth-dependent decay of 13C NMR signals for individual carbon atoms of AmB. We found that both terminal segments, the 41-COOH group and C38-C40 methyl groups, come close to the lipid bilayer surfaces, suggesting that the AmB-Erg complex spans a palmitoyloleoylphosphatidylcholine (POPC) bilayer with a single-molecule length. Molecular dynamics simulation experiments further confirmed the stabilization of the AmB-Erg complex as a single-length spanning complex. These results provide experimental evidence of the single-length complex incorporated in the membrane by making thinner a POPC-Erg bilayer that mimics fungal membranes.

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers.

A dissociative force field for all-atomistic molecular dynamics calculations has been developed to investigate impact fracture of polymers accompanying dissociation of chemical bonds of polymer main chain. Energy of dimer molecules was evaluated as a function of both bond-length b and bond-angle θ by CASPT2 calculations, whose quality is enough to describe dissociation of chemical bonds. Because we found that the bond dissociation energy D decreases with increasing bond-angle, we employed the Morse-type function VBond (b, θ) = {D - VAngle (θ)}[1 - exp{-α(b - b0 ) - ß(b - b0 )2 }] where a quartic function VAngle (θ) = k1 (θ - θ0 ) + k2 (θ - θ0 )2 + k3 (θ - θ0 )3 + k4 (θ - θ0 )4 . This function reproduced well the CASPT2 potential energy surface in a wide range of b and θ. The parameters have been obtained for four popular glassy polymers, polyethylene, poly(methyl methacrylate), poly(styrene), and polycarbonate. © 2019 Wiley Periodicals, Inc.

Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation.

The lamellar phase produced by surfactants with water exhibits several subphases, such as hydrated crystal (Lc), gel (Lß), tilted gel (Lß'), and liquid crystal (Lα) phases, depending on temperature, pressure, and hydration. The dynamics of the surfactant molecules in these phases are still unclear. In the present study, we investigate the translational and conformational dynamics of sodium linear alkylbenzene sulfonate (LAS) molecules in the Lc, Lß', and Lα phases. In the Lα phase, the lateral diffusion of LAS is as fast as that found for phospholipid bilayers in the Lα phase. The diffusion coefficient was undetectably small for the Lc and Lß' phases. The conformation of LAS in the Lα phase relaxes very rapidly, whereas those in the Lc and Lß' phases relax very slowly. The time scale of the relaxations greatly depends on the segment of the LAS molecule for the latter two phases. The relaxation time for the SO3- head group and benzene ring of LAS was much longer than that for alkyl chains. Conformational pattern analyses of LAS alkyl chains revealed that the high fraction of the gauche conformation for the odd-numbered C-C bonds aligns the chain parallel to the bilayer normal and is the main origin of the different relaxation times for different segments in the chain. In the Lc, Lß', and Lα phases, the orientations of the SO3- group and the benzene ring are locked by the salt bridge among SO3- groups and sodium ions. As a result, the orientational order found for the C-C bonds in the LAS alkyl chains is kept even in the Lα phase.

Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study.

A good understanding of the surface hydrophobicity of fluorinated materials is useful for their application as coating materials. The present study investigates the surface hydrophobicity of perfluoroalkyl acrylate (PFA) thin films using molecular dynamics simulations. Surface hydrophobicity is characterized by examining the contact angle of a water droplet on PFA surfaces and the cavity formation free energy in the vicinity of the surface. It is found that the calculated microscopic contact angles are in good agreement with the experimental results and partially capture the difference in the hydrophobicity of the surface arising from the variation of packing density and side chain length of PFA. The variations of cavity formation free energy in the vicinity of the surface elucidate that the surface hydrophobicity is mainly governed by the packing density rather than the chain length of PFA. The hydrophobicity generally increases with decreasing the packing density to some extent and then turns to decrease as further reducing the packing density. At higher packing density, the surface hydrophobicity slightly decreases with increasing the chain length, while at the lower packing density, the surface hydrophobicity is increased when chain length of PFA is longer than six carbons. Furthermore, we found that the influence of packing density on the surface hydrophobicity is directly related to the variation of the surface roughness and chain flexibility, that is, the surface hydrophobicity increases with increase in the surface roughness, while the chain flexibility plays a secondary role in the enhancement by affecting the stability of water staying near the interface. The study provides a significant insight into the local hydrophobicity and microscopic structure of the PFA surfaces, which would be useful for the application of surface modification.