Asymmetry and Rippling in Mixed Surfactant Bilayers from All-Atom and Coarse-Grained Simulations: Interdigitation and Per Chain Entropy

Interface Water Assists in Dimethyl Sulfoxide Crossing and Poration in Model Bilayer

Understanding the mechanism of transport and pore formation by a commonly used cryoprotectant, dimethyl sulfoxide (DMSO), across cell membranes is fundamentally crucial for drug delivery and cryopreservation. To shed light on the mechanism and thermodynamics of pore formation and crossing behavior of DMSO, extensive all-atom molecular dynamics simulations of 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) bilayers are performed at various concentrations of DMSO at a temperature above the physiological temperature. Our results unveil that DMSO partially depletes water from the interface and positions itself between lipid heads without full dehydration. This induces a larger area per headgroup, increased disorder, and enhanced fluidity without any disintegration even at the highest DMSO concentration studied. The enhanced disorder fosters local fluctuations at the interface that nucleate dynamic and transient pores. The potential of mean force (PMF) of DMSO crossing is derived from two types of biased simulations: a single DMSO pulling using the umbrella sampling technique and a cylindrical pore formation using the recently developed chain reaction coordinate method. In both cases, DMSO crossing encounters a barrier attributed to unfavorable polar nonpolar interactions between DMSO and lipid tails. As the DMSO concentration increases, the barrier height reduces along with the faster lateral and perpendicular diffusion of DMSO suggesting favorable permeation. Our findings suggest that the energy required for pore formation decreases when water assists in the formation of DMSO pores. Although DMSO displaces water from the interface toward the far interface region without complete dehydration, the presence of interface water diminishes pore formation free energy. The existence of interface water leads to the formation of a two-dimensional percolated water-DMSO structure at the interface, which is absent otherwise. Overall, these insights into the mechanism of DMSO crossing and pore formation in the bilayer will contribute to understanding cryoprotectant behavior under supercooled conditions in the future.

Aspirin-Induced Ordering and Faster Dynamics of a Cationic Bilayer for Drug Encapsulation

The lipid dynamics and phase play decisive roles in drug encapsulation and delivery to the intracellular target. Thus, understanding the dynamic and structural alterations of membranes induced by drugs is essential for targeted delivery. To this end, united-atom molecular dynamics simulations of a model bilayer, dioctadecyldimethylammonium bromide (DODAB), are performed in the absence and presence of the usual nonsteroidal anti-inflammatory drug (NSAID), aspirin, at 298, 310, and 345 K. At 298 and 310 K, the bilayers are in the interdigitated two-dimensional square phases, which become rugged in the presence of aspirin, as evident from height fluctuations. At 345 K, the bilayer is in the fluid phase in both the absence and presence of aspirin. Aspirin is preferentially located near the oppositely charged headgroup and creates void space, which leads to an increase in the interdigitation and order parameters. Although the center of mass of lipids experiences structural arrest, they reach the diffusive regime faster and have higher lateral diffusion constants in the presence of aspirin. Results are found to be consistent with recent quasi-elastic neutron scattering studies that reveal that aspirin acts as a plasticizer and enhances lateral diffusion of lipids in both ordered and fluid phases. Different relaxation time scales of the bonds along the alkyl tails of DODAB due to the multitude of lipid motions become faster upon the addition of aspirin. Our results show that aspirin insertion is most favorable at physiological temperature. Thus, the ordered, more stable, and faster DODAB bilayer can be a potential drug carrier for the protected encapsulation of aspirin, followed by targeted and controlled drug release with antibacterial activity in the future.

Thylakoid Composition Facilitates Chlorophyll a Dimerization through Stronger Interlipid Interactions

Plant thylakoid membrane serves as a crucial matrix for the aggregation of chlororophyll a (CLA) pigments, essential for light harvesting. To understand the role of lipid compositions in the stability of CLA aggregates, dimerization of chlorophyll a molecules (CLA) is studied in the presence of the thylakoid and the bilayers comprising either the least or the highest unsaturated lipids by using coarse-grained molecular dynamics simulations. The thylakoid membrane enhances the stability of the CLA dimer compared with other membranes due to very strong lipid-lipid interactions. The thylakoid exhibits a distinct distribution of lipids around the CLA dimer. Less unsaturated lipids reside in close proximity to the dimer, promoting increased order and efficient packing. Conversely, higher unsaturated lipids are depleted from the dimer, imparting flexibility to the membrane. The combination of tight packing near the dimer and membrane flexibility away from the dimer enhances the stability of the dimer in the thylakoid membrane. Our results suggest that lipid mixing, rather than lipid unsaturation, plays a critical role in facilitating CLA dimerization by modulating the membrane microenvironment through stronger lipid-lipid interactions. These insights will be useful in understanding how lipid compositions affect efficient light absorption and energy transfer during photosynthesis in the future.

Quantifying dynamical heterogeneity length scales of interface water across model membrane phase transitions

All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes reveal a drastic growth in the heterogeneity length scales of interface water (IW) across fluid to ripple to gel phase transitions. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatiotemporal scales of the IW and membranes at various phases under physiological and supercooled conditions.

Wetting Properties of Clathrate Hydrates in the Presence of Polycyclic Aromatic Compounds: Evidence of Ion-Specific Effects

Polycyclic aromatic hydrocarbons (PAHs) have attracted remarkable multidisciplinary attention due to their intriguing π-π stacking configurations, showing enormous opportunity for their use in a variety of advanced applications. To secure progress, detailed knowledge on PAHs' interfacial properties is required. Employing molecular dynamics, we probe the wetting properties of brine droplets (KCl, NaCl, and CaCl₂) on sII methane-ethane hydrate surfaces immersed in various oil solvents. Our simulations show synergistic effects due to the presence of PAHs compounded by ion-specific effects. Our analysis reveals phenomenological correlations between the wetting properties and a combination of the binding free-energy difference and entropy changes upon oil solvation for PAHs at oil/brine and oil/hydrate interfaces. The detailed thermodynamic analysis conducted upon the interactions between PAHs and various interfaces identifies molecular-level mechanisms responsible for wettability alterations, which could be applicable for advancing applications in optics, microfluidics, biotechnology, medicine, as well as hydrate management.

Simulation study of domain formation in a model bacterial membrane

Recent experimental studies revealed that functional membrane microdomains (FMMs) are formed in prokaryotic cells which are structurally and functionally similar to the lipid rafts formed in eukaryotic cells. In this study, we employ coarse-grained molecular dynamics simulations to investigate the mechanism of domain formation and its physiochemical properties in a model methicillin-resistant staphylococcus aureus (MRSA) cell membrane. We find that domains are formed through lateral segregation of staphyloxanthin (STX), a carotenoid which shields the bacteria from the host's immune because of its antioxidant nature. Simulation results suggest that membrane integrity increases with the size of the domain, which is assessed by computing bond order parameter of the lipid tails, membrane expansion modulus and water permeability across the membrane. Various membrane domain proteins such as flotillin-like protein floA and penicillin binding protein (PBP2a) preferentially bind with the STX and accumulate in the membrane domain which is consistent with the recent experimental results.

Insights into the Phase Diagram of Pluronic L64 Using Coarse-Grained Molecular Dynamics Simulations

We investigate the concentration-dependent phase diagram of pluronic L64 in aqueous media at 300 and 320 K using coarse-grained (CG) molecular dynamics (MD) simulations. The CG model is derived by adapting the Martini model for nonbonded interactions along with the Boltzmann inversion (BI) of bonded interactions from all-atom (AA) simulations. Our derived CG model successfully captures the experimentally observed micellar-, hexagonal-, lamellar-, and polymer-rich solution phase. The end-to-end distance reveals the conformational change from an open-chain structure in the micellar phase to a folded-chain structure in the lamellar phase, increasing the orientational order. An increase in temperature leads to expulsion of water molecules from the L64 moiety, suggesting an increase in L64 hydrophobicity. Thermodynamic analysis using the two-phase thermodynamics (2PT) method suggests the entropy of the system decreases with increasing L64 concentration and the decrease in free energy (F) with temperature is mainly driven by the entropic factor (-TS). Further, the increase in aggregation number at lower concentrations and self-assembly at very high concentrations is energetically driven, whereas the change from the micellar phase to the lamellar phase with increasing L64 concentration is entropically driven. Our model provides molecular insights into L64 phases which can be further explored to design functionality-based suprastructures for drug delivery and tissue engineering applications.

The ugly, bad, and good stories of large-scale biomolecular simulations

Molecular modeling of large biomolecular assemblies exemplifies a disruptive area holding both promises and contentions. Propelled by peta and exascale computing, several simulation methodologies have now matured into user-friendly tools that are successfully employed for modeling viruses, membranous nano-constructs, and key pieces of the genetic machinery. We present three unifying biophysical themes that emanate from some of the most recent multi-million atom simulation endeavors. Despite connecting molecular changes with phenotypic outcomes, the quality measures of these simulations remain questionable. We discuss the existing and upcoming strategies for constructing representative ensembles of large systems, how new computing technologies will boost this area, and make a point that integrative modeling guided by experimental data is the future of biomolecular computations.

Correlating Antiagglomerant Performance with Gas Hydrate Cohesion

Although inhibiting hydrate formation in hydrocarbon-water systems is paramount in preventing pipe blockage in hydrocarbon transport systems, the molecular mechanisms responsible for antiagglomerant (AA) performance are not completely understood. To better understand why macroscopic performance is affected by apparently small changes in the AA molecular structure, we perform molecular dynamics simulations. We quantify the cohesion energy between two gas hydrate nanoparticles dispersed in liquid hydrocarbons in the presence of different AAs, and we achieve excellent agreement against experimental data obtained at high pressure using the micromechanical force apparatus. This suggests that the proposed simulation approach could provide a screening method for predicting, in silico, the performance of new molecules designed to manage hydrates in flow assurance. Our results suggest that entropy and free energy of solvation of AAs, combined in some cases with the molecular orientation at hydrate-oil interfaces, are descriptors that could be used to predict performance, should the results presented here be reproduced for other systems as well. These insights could help speed up the design of new AAs and guide future experiments.

Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes

Phospholipids, which are an integral component of cell membranes, exhibit a rich variety of lamellar phases modulated by temperature and composition. Molecular dynamics (MD) simulations have greatly enhanced our understanding of phospholipid membranes by capturing experimentally observed phases and phase transitions at molecular resolution. However, the ripple (P_β') membrane phase, observed as an intermediate phase below the main gel-to-liquid crystalline transition with some lipids, has been challenging to capture with MD simulations, both at all-atom and coarse-grained (CG) resolutions. Here, with an aggregate ∼2.5 μs all-atom and ∼122 μs CGMD simulations, we systematically assess the ability of six CG MARTINI 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid and water force-field (FF) variants, parametrized to capture the DPPC gel and fluid phases, for their ability to capture the P_β' phase, and compared observations with those from an all-atom FF. Upon cooling from the fluid phase to below the phase transition temperature with smaller (380-lipid) and larger (>2200-lipid) MARTINI and all-atom (CHARMM36 FF) DPPC lipid bilayers, we observed that smaller bilayers with both all-atom and MARTINI FFs sampled interdigitated P_β' and ripple-like states, respectively. However, while all-atom simulations of the larger DPPC membranes exhibited the formation of the P_β' phase, MARTINI membranes did not sample interdigitated ripple-like states at larger system sizes. We then demonstrated that the ripple-like states in smaller MARTINI membranes were kinetically trapped structures caused by finite size effects rather than being representative of true P_β' phases. We showed that a MARTINI FF variant that could capture the tilted L_β' gel phase, a prerequisite for stabilizing the P_β' phase, was unable to capture the rippled phase upon cooling. Our study reveals that the current MARTINI FFs (including MARTINI3) may require specific reparametrization of the interaction potentials to stabilize lipid interdigitation, a characteristic of the ripple phase.