Effect of polymer grafting on the bilayer gel to liquid-crystalline transition

A generic force field for simulating native protein structures using dissipative particle dynamics

A coarse-grained force field for molecular dynamics simulations of the native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by mapping the bonds and angles for 20 amino acids onto target distributions obtained from fully atomistic simulations in explicit solvent. A dual-basin potential is introduced for stabilizing backbone angles, to cover a wide spectrum of protein secondary structures. The backbone dihedral potential enables folding of the protein from an unfolded initial state to the folded native structure. The proposed force field is validated by evaluating the structural properties of several model peptides and proteins including the SARS-CoV-2 fusion peptide, consisting of α-helices, β-sheets, loops and turns. Detailed comparisons with fully atomistic simulations are carried out to assess the ability of the proposed force field to stabilize the different secondary structures present in proteins. The compact conformations of the native states were evident from the radius of gyration and the high intensity peaks of the root mean square deviation histograms, which were found to be within 0.4 nm. The Ramachandran-like energy landscape on the phase space of backbone angles (θ) and dihedrals (ϕ) effectively captured the conformational phase space of α-helices at ∼(ϕ = 50°,θ = 90°) and β-strands at ∼(ϕ = ±180°,θ = 90-120°). Furthermore, the residue-residue native contacts were also well reproduced by the proposed DPD model. The applicability of the model to multidomain complexes was assessed using lysozyme and a large α-helical bacterial pore-forming toxin, cytolysin A. Our study illustrates that the proposed force field is generic, and can potentially be extended for efficient in silico investigations of membrane bound polypeptides and proteins using DPD simulations.

Phase Behavior of Pure PSPC and PEGylated Multicomponent Lipid and Their Interaction with Paclitaxel: An All-Atom MD Study

Exploring structural behavior of pure 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) and multicomponent PSPC and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(poly(ethylene glycol))-2000] (DSPE-PEG₂₀₀₀) membranes and their interaction with pharmaceutically important drugs carry huge importance in drug delivery. Using all-atom molecular dynamics (MD) simulations, we investigated the phase behavior of pure and PEGylated membranes at the temperature range of 280-360 K. We observe a gel-to-liquid crystalline phase transition for pure PSPC between 320 and 330 K, and in the case of multicomponent membranes, at 320 K, a coexistence of order-disorder phases is observed, which gradually transform to a complete liquid crystalline to gel phase between 320 and 310 K. We further studied the interaction of Paclitaxel with pure PSPC and PEGylated bilayers and elucidated the interaction behavior of Paclitaxel at the bilayer interfaces. Understanding of structural and interaction behaviors of the PEGylated bilayers with Paclitaxel will help to explore Paclitaxel-based drug applications in the future.

Assessing Barriers for Antimicrobial Penetration in Complex Asymmetric Bacterial Membranes: A Case Study with Thymol

The bacterial cell envelope is a complex multilayered structure evolved to protect bacteria in hostile environments. An understanding of the molecular basis for the interaction and transport of antibacterial therapeutics with the bacterial cell envelope will enable the development of drug molecules to combat bacterial infections and suppress the emergence of drug-resistant strains. Here we report the successful creation of an in vitro supported lipid bilayer (SLB) platform of the outer membrane (OM) of E. coli, an archetypical Gram-negative bacterium, containing the full smooth lipopolysaccharide (S-LPS) architecture of the membrane. Using this platform, we performed fluorescence correlation spectroscopy (FCS) in combination with molecular dynamics (MD) simulations to measure lipid diffusivities and provide molecular insights into the transport of natural antimicrobial agent thymol. Lipid diffusivities measured on symmetric supported lipid bilayers made up of inner membrane lipids show a distinct increase in the presence of thymol as also corroborated by MD simulations. However, lipid diffusivities in the asymmetric OM consisting of only S-LPS are invariant upon exposure to thymol. Increasing the phospholipid content in the LPS-containing outer leaflet improved the penetration toward thymol as reflected in slightly higher relative diffusivity changes in the inner leaflet when compared with the outer leaflet. Free-energy computations reveal the presence of a barrier (∼6 kT) only in the core-saccharide region of the OM for the translocation of thymol while the external O-antigen part is easily traversed. In contrast, thymol spontaneously inserts into the inner membrane. In addition to providing leaflet-resolved penetration barriers in bacterial membranes, we also assess the ability of small molecules to penetrate various membrane components. With rising bacterial resistance, our study opens up the possibility of screening potential antimicrobial drug candidates using these realistic model platforms for Gram-negative bacteria.

Establishing an Electrostatics Paradigm for Membrane Electroporation in the Framework of Dissipative Particle Dynamics

With an exclusive aim to looking into a mechanism of membrane electroporation on mesoscopic length and time scales, we report the dissipative particle dynamics (DPD) simulation results for systems with and without electrolytes. A polarizable DPD model of water is employed for accurate modeling of long-range electrostatics near the water-lipid interfaces. A great deal of discussion on field induced change in dipole moments of water and lipids together with the special variation of electric field is made in order to understand the dielectrophoretic movement of water, initiating a pore formation via an intrusion through the bilayer core. The presence of salt alters the dipolar arrangement of lipids and water, and thereby it reduces the external field required to create a pore in the membrane. The species fluxes through the pore, distributions for bead density, electrostatic potential, stresses across the membrane, etc. are used to answer some of the key questions pertaining to mechanism of electroporation. The findings are compared with the molecular dynamics simulation results found in the literature, and the comparison successfully establishes an electrostatics paradigm for biomembrane studies using DPD simulations.

Amphiphilic copolymers change the nature of the ordered-to-disordered phase transition of lipid membranes from discontinuous to continuous

The phase behaviour as a function of temperature is explored for pure phospholipid (DPPC) and hybrid lipid-polymer (DPPC/Pluronic L64) bilayers with the aid of atomistic MD simulations. The range of the fixed-temperature simulations includes temperatures below and above the known melting temperature (Tm) for DPPC membranes. For the pure lipid bilayer, the main phase transition is discontinuous, as verified by the abrupt changes observed in the membrane structure, elasticity and the lipid diffusivity near the critical temperature Tm, which lies in the region 298.15-303.15 K. A pre-transition step is detected at 298.15 K which has been identified as the ripple phase (Pβ'), where ordered and disordered lipids coexist, causing thickness fluctuations. In the ordered gel phase, the positional ordering as assessed by the lipid radial distribution functions is long-range and some degree of hexagonal packing is measured. The hybrid bilayers on the other hand, transform from a more ordered to a disordered phase in a continuous manner, without finite jumps in their properties. No signs of the ripple phase are identified and the ordered phase exhibits very limited hexagonal packing and some positional ordering that decays fast. The effect of the inserted polymers in the two phases is reversed; at low temperatures, they render the membrane thinner, less cohesive and less ordered compared to the pure one, with the lipids assuming faster diffusion rates, whereas at high temperatures, the polymer interaction with the lipids acts reducing their diffusivity, but also increasing the lipid tail ordering and the membrane stiffness. The ability of the amphiphilic L64 copolymers to change the nature of the main phase transition of lipid membranes and their properties both in the ordered and the disordered phase is of vital importance for the prediction of both the efficacy of hybrid lipid/polymer nanoparticles as drug delivery vehicles as well as their potential adverse implications during interactions with healthy cell membranes.

A Polymer Plugging Gel for the Fractured Strata and Its Application

Well leakage of fractured strata is a tricky problem while drilling. This unwieldy problem is usually caused by the poor formation of the cementing degree, the staggered-mesh of the fracture, and the low bearing capacity of the formation, which can also lead to a narrow and even unsafe window of drilling fluid density. For fractured strata, the normal plugging material has the disadvantages of unsuitable size and low strength, resulting in unsuccessful first time plugging and an increase in cost. Therefore, we developed a polymer plugging gel for the fractured strata, named XNGJ-3. XNGJ-3 is mainly made of an acrylamide monomer and is accompanied by the reactive monomers of carboxyl and hydroxyl as ingredients. XNGJ-3 has a low viscosity before gelling. At 80 °C it becomes gelled, and the gelling time was controlled within the required time of the practical application. These conditions are beneficial for making the plugging material enter the crossing fracture smoothly and occlude the fracture. XNGJ-3 also has a good deformability and can avoid being damaged during the process of fracture closure. The well leakage simulated experiment revealed that the bearing capacity of this material can reach 21 MPa and the inverse bearing capacity can reach 20 MPa. These strengths are more than twice that of common polymer plugging gels. Finally, three leaked wells in the fractured strata of the Sichuan Basin were used to verify the plugging effect of XNGJ-3. Compared with other common plugging materials, XNGJ-3 has the advantages of having a higher success rate of first time plugging, a lower economic cost, a shorter work time, and so forth, which indicate that this plugging material has a good engineering application value in dealing with well leakage of fractured strata.

Synthetic biology outside the cell: linking computational tools to cell-free systems

As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

Conformational, dynamical. and tensional study of tethered bilayer lipid membranes in coarse-grained molecular simulations

Tethered bilayer lipid membranes (tBLMs) have attracted great interest recently due to their crucial roles in elucidating fundamental membrane characteristics and the implications in biochemical sensors and pharmaceutical drug carriers. Nevertheless, they have not yet been investigated computationally on the molecular scale. Here, we study tBLMs consisting of DOPCs (1,2-dioleoyl-sn-glycero-3-phosphocholine) as free lipids and pegylated DOPCs (on phosphate group) as tethers in water by a variation of the MARTINI model. By varying grafting densities and tether lengths, distinct conformational changes from planar to undulated bilayers are observed. Lateral diffusivities and lateral pressure profiles show that the dynamical and tensional states are specific to the system configurations. These results suggest that the conformations, fluidity, and elasticity of the tBLMs can be tuned and manipulated to conform to various requirements in theoretical investigations and technological applications.

Pressure and surface tension control self-assembled structures in mixtures of Pegylated and non-pegylated lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies.

Phospholipase A(2)-susceptible liposomes of anticancer double lipid-prodrugs

A novel approach to anticancer drug delivery is presented based on lipid-like liposome-forming anticancer prodrugs that are susceptible to secretory phospholipase A(2) (sPLA(2)) that is overexpressed in several cancer types. The approach provides a selective unloading of anticancer drugs at the target tissues, as well as circumvents the necessity for "conventional" drug loading. In our attempts to improve the performance of the liposomes in vivo, several PEGylated and non-PEGylated liposomal formulations composed of a retinoid prodrug premixed with the sPLA(2)-hydrolyzable DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) were prepared. Besides favorably modifying the physicochemical properties of the liposomes, the incorporation of DPPC and PEG-lipids in the liposomes should substantially enhance the enzymatic activity, as concluded from literature. In addition, one can reap benefits from the presumed permeability enhancing effect of the liberated fatty acids and lysolipids. The size distribution of the prepared liposomes as well as their phase behavior, enzymatic hydrolysis, and cytotoxicity, in the presence and absence of sPLA(2), were determined. The liposomes were around 100nm in diameter and in the gel/fluid coexistence region at 37°C. The enzymatic hydrolysis of the prodrug was pronouncedly accelerated upon the premixing with DPPC, and the hydrolysis was further enhanced by PEGylation. Interestingly, the faster hydrolysis of the prodrug and the released fatty acids and lysolipids from DPPC did not improve the cytotoxicity of the mixture; the effect of combining the prodrug with DPPC was additive and not synergistic. The data presented here question the significance of the permeability enhancing effects claimed for fatty acids and lysolipids at the target cell membrane, and whether these effects can be achieved using physiologically achievable concentrations of fatty acids and lysolipids.

Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.

Investigations on the melting and bending modulus of polymer grafted bilayers using dissipative particle dynamics

Understanding the influence of polymer grafted bilayers on the physicomechanical properties of lipid membranes is important while developing liposomal based drug delivery systems. The melting characteristics and bending moduli of polymer grafted bilayers are investigated using dissipative particle dynamics simulations as a function of the amount of grafted polymer and lipid tail length. Simulations are carried out using a modified Andersen barostat, whereby the membrane is maintained in a tensionless state. For lipids made up of four to six tail beads, the transition from the low temperature L(β) phase to the L(α) phase is lowered only above a grafting fraction of G(f)=0.12 for polymers made up of 20 beads. Below G(f)=0.12 small changes are observed only for the HT(4) bilayer. The bending modulus of the bilayers is obtained as a function of G(f) from a Fourier analysis of the height fluctuations. Using the theory developed by Marsh et al. [Biochim. Biophys. Acta 1615, 33 (2003)] for polymer grafted membranes, the contributions to the bending modulus due to changes arising from the grafted polymer and bilayer thinning are partitioned. The contributions to the changes in κ from bilayer thinning were found to lie within 11% for the lipids with four to six tail beads, increasing to 15% for the lipids containing nine tail beads. The changes in the area stretch modulus were also assessed and were found to have a small influence on the overall contribution from membrane thinning. The increase in the area per head group of the lipids was found to be consistent with the scalings predicted by self-consistent mean field results.