Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipid Bilayers: A Comparative Study of Water Models

Evaluating Polarizable Biomembrane Simulations against Experiments

Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.

Extension of the CAVS model to the simulation of helical peptides in a membrane environment

Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.

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.

Interfacial Water Structure at Zwitterionic Membrane/Water Interface: The Importance of Interactions between Water and Lipid Carbonyl Groups

In this work, atomistic molecular dynamics (MD) simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer were carried out to investigate the effect of water models on membrane dipole potential, which is primarily associated with the preferential orientation of molecular dipoles at the membrane-water interface. We discovered that the overestimation of the dipole potential by the TIPS3P water model can be effectively reduced by the TIP4P water model. On the one hand, the TIP4P water model decreases the negative contribution of lipid to the dipole potential through influencing the orientation of lipid headgroups. On the other hand, the TIP4P water model reduces the positive contribution of water to the dipole potential by increasing the preference of H-down orientation (the water dipole orients toward the bilayer center). Interestingly, the TIP4P water model affects the orientation of interfacial water molecules more obviously than that of lipid headgroups, leading to the decrease in the dipole potential. Furthermore, the MD results revealed that the water close to the positively charged choline (namely, N-associated water) prefers the H-down orientation while the water around the negatively charged phosphate (namely, P-associated water) favors the H-up orientation, in support of recent experimental and MD studies. However, interfacial water molecules are more strongly influenced by the phosphate groups than by the choline groups, resulting in the net H-up orientation (the water dipole orients toward the bilayer center) in the region of lipid headgroups. In addition, it is intriguing that the preference of H-up orientation decreases when water molecules penetrate more deeply into the lipid bilayer. This is attributed to the counteracting effect of lipid carbonyl groups, and the effect varies with the lipid chains (oleoyl and palmitoyl chains), suggesting the important role of lipid carbonyl groups.

Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Potential and Sterol Flip-Flop Motion in Bilayer Membranes

A variety of experimental and theoretical approaches have been employed to investigate the sterol flip-flop motion in lipid bilayer membranes. However, the sterol effect on the dipole potential of lipid bilayer membranes is less well studied and the influence of dipole potential on sterol flip-flop motion in lipid bilayer membranes is less well understood. In our previous works, we have demonstrated the performance of our coarse-grained (CG) model in the computation of the dipole potential. In this work, five 30 μs CG simulations of dimyristoylphosphatidylcholine (DMPC) bilayers were carried out at different sterol concentrations (in a range from 10 to 50% mole fraction). Then, a comparison was made between the effects of cholesterol (CHOL) and 6-ketocholestanol (6-KC) on the dipole potential of DMPC lipid bilayers as well as the sterol flip-flop motion. Our CG simulations show that the membrane dipole potential is impacted more significantly by 6-KC than by CHOL. This finding is consistent with recent experimental studies. Meanwhile, our work suggests that the sterol-sterol interactions (in particular, electrostatic interactions) should be critical to the formation of sterol-sterol clusters, which would hinder the sterol flip-flop motion inside the lipid bilayers. This is in support of the recent experimental study on the sterol transportation in lipid bilayer membranes.

Improved general-purpose five-point model for water: TIP5P/2018

A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration of Nistor et al. [J. Chem. Phys. 125, 094108 (2006)]. By taking the density and diffusion dependence on temperature as target properties, significant improvements to the behavior of isothermal compressibility were achieved along with improvements to other thermodynamic and rotational properties. While exhibiting a dipole moment close to ab initio values, TIP5P/2018 suffers from a too small quadrupole moment due to the charge assignment procedure and results in an overestimation of the dielectric constant.