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.

Overlay databank unlocks data-driven analyses of biomolecules for all.

Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.

Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes.

Cells use homeostatic mechanisms to ensure an optimal composition of distinct types of lipids in cellular membranes. The hydrophilic region of biological lipid membranes is mainly composed of several types of phospholipid headgroups that interact with incoming molecules, nanoparticles, and viruses, whereas the hydrophobic region consists of a distribution of acyl chains and sterols affecting membrane fluidity/rigidity related properties and forming an environment for membrane-bound molecules such as transmembrane proteins. A fundamental open question is to what extent the motions of these regions are coupled and, consequently, how strongly the interactions of phospholipid headgroups with other molecules depend on the properties and composition of the membrane hydrophobic core. We combine advanced solid-state nuclear magnetic resonance spectroscopy with high-fidelity molecular dynamics simulations to demonstrate how the rotational dynamics of choline headgroups remain nearly unchanged (slightly faster) with incorporation of cholesterol into a phospholipid membrane, contrasting the well-known extreme slowdown of the other phospholipid segments. Notably, our results suggest a new paradigm in which phospholipid dipole headgroups interact as quasi-freely rotating flexible dipoles at the interface, independent of the properties in the hydrophobic region.

Particle-particle particle-mesh algorithm for electrolytes between charged dielectric interfaces.

Ionic distributions near charged interfaces control processes from colloidal aggregation to solvent flow in nanodevices. Such interfaces are often characterized by a jump in the permittivity, which gives rise to the surface polarization charge. This induced charge may significantly affect the ionic distributions so that efficient methods for modeling spatially varying dielectrics are needed. We formulate a method with O(N⁡log⁡N) scaling for electrolytes between charged planar interfaces with asymmetric dielectric contrasts. Our approach, which builds on earlier work, is based on combining image charges with the particle-particle particle-mesh algorithm and representing uniform surface charges via an electric field. This enables simulations of complex dielectric interactions that outperform most alternative methods in speed and accuracy. To make the method practically useful, we provide guidelines-based upon careful tests-for choosing optimal simulation parameters. Explicit expressions for the electrostatic forces are given to facilitate the implementation of our algorithm in standard molecular dynamics packages.

Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.

Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.

Dielectric Effects on Ion Transport in Polyelectrolyte Brushes.

Surface-grafted polyelectrolytes provide a versatile way to create functionalized interfaces and nanochannels with externally controllable properties. Understanding the behavior of ions within the brush-like assemblies is crucial for the further development of these devices. We demonstrate that the ion transport through the brushes is governed by the interplay of electrostatic ion-polymer binding and steric effects, leading to a mobility that depends nonmonotonically on grafting density. However, the ion-polymer binding can be modulated by the dielectric properties of the substrate. As a result, surface polarization suppresses ion mobility near insulating interfaces and enhances it near conducting interfaces, even causing a shift from nonmonotonic to monotonic variation with grafting density.

Dielectric Modulation of Ion Transport near Interfaces.

Ion mobility and ionic conductance in nanodevices are known to deviate from bulk behavior, a phenomenon often attributed to surface effects. We demonstrate that dielectric mismatch between the electrolyte and the surface can qualitatively alter ionic transport in a counterintuitive manner. Instead of following the polarization-induced modulation of the concentration profile, mobility is enhanced or reduced by changes in the ionic atmosphere near the interface and affected by a polarization force parallel to the surface. In addition to revealing this mechanism, we explore the effect of salt concentration and electrostatic coupling.

Repulsion between oppositely charged rod-shaped macromolecules: Role of overcharging and ionic confinement.

The interaction between two oppositely charged rod-shaped macro-ions in a micro-ion solution is investigated via Monte Carlo simulations of the primitive model. The focus is on the asymmetry in rod and/or ion charge, i.e., conditions where oppositely charged objects can repel one another. For equally and oppositely charged rods with asymmetric z:1 micro-ions, repulsion may be induced by overcharging one of the rods with the z valent ions. For asymmetrically charged rods in a symmetric z:z micro-ion solution, a repulsive interaction-at separation of the order of one ion diameter-can arise via an unbalanced osmotic pressure contribution from the ionic atmosphere in the inter-rod space, and an attractive interaction-at a smaller separation-may occur due to a "squeezing out" of the micro-ions from the space between the rods (with a consequent gain in entropy). The thermodynamics of each mechanism is investigated in terms of rod charge and size and micro-ion valence, size, and concentration. Our findings contribute to the understanding of the complex role of charge asymmetry on the interaction of, for example, oppositely charged polyelectrolytes, functionalized nanotubes, and rod-like biomolecules, e.g., viruses.

Role of Salt and Water in the Plasticization of PDAC/PSS Polyelectrolyte Assemblies.

In this work, we investigate the effect of salt and water on plasticization and thermal properties of hydrated poly(diallyldimethylammonium chloride) (PDAC) and poly(sodium 4-styrenesulfonate) (PSS) assemblies via molecular dynamics simulations and modulated differential scanning calorimetry (MDSC). Commonly, both water and salt are considered to be plasticizers of hydrated polyelectrolyte assemblies. However, the simulation results presented here show that while water has a plasticizing effect, salt can also have an opposite effect on the PE assemblies. On one hand, the presence of salt ions provides additional free volume for chain motion and weakens PDAC-PSS ion pairing due to electrostatic screening, which contributes toward plasticization of the complex. On the other hand, salt ions bind water in their hydration shells, which decreases water mobility and reduces the plasticization by hydration. Our MDSC results connect the findings to macroscopic PE plasticization and the glass-transition-like thermal transition Ttr under controlled PE hydration and salt content. This work identifies and characterizes the dual nature of salt both as plasticizer and hardener of PE assemblies and maps the interconnection of the influence of salt with the degree of hydration in the system. Our findings provide insight into the existing literature data, bear fundamental significance in understanding of hydrated polyelectrolyte assemblies, and suggest a direct means to tailor the mechanical characteristics of PE assemblies via interplay of water and salt.

Interaction modes between asymmetrically and oppositely charged rods.

The interaction of oppositely and asymmetrically charged rods in salt-a simple model of (bio)macromolecular assembly-is observed via simulation to exhibit two free energy minima, separated by a repulsive barrier. In contrast to similar minima in the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the governing mechanism includes electrostatic attraction at large separation, osmotic repulsion at close range, and depletion attraction near contact. A model accounting for ion condensation and excluded volume is shown to be superior to a mean-field treatment in predicting the effect of charge asymmetry on the free-energy profile.

Ewald Electrostatics for Mixtures of Point and Continuous Line Charges.

Many charged macro- or supramolecular systems, such as DNA, are approximately rod-shaped and, to the lowest order, may be treated as continuous line charges. However, the standard method used to calculate electrostatics in molecular simulation, the Ewald summation, is designed to treat systems of point charges. We extend the Ewald concept to a hybrid system containing both point charges and continuous line charges. We find the calculated force between a point charge and (i) a continuous line charge and (ii) a discrete line charge consisting of uniformly spaced point charges to be numerically equivalent when the separation greatly exceeds the discretization length. At shorter separations, discretization induces deviations in the force and energy, and point charge-point charge correlation effects. Because significant computational savings are also possible, the continuous line charge Ewald method presented here offers the possibility of accurate and efficient electrostatic calculations.

The influence of ionic strength and mixing ratio on the colloidal stability of PDAC/PSS polyelectrolyte complexes.

Polyelectrolyte complexes (PECs) form by mixing polycation and polyanion solutions together, and have been explored for a variety of applications. One challenge for PEC processing and application is that under certain conditions the as-formed PECs aggregate and precipitate out of suspension over the course of minutes to days. This aggregation is governed by several factors such as electrostatic repulsion, van der Waals attractions, and hydrophobic interactions. In this work, we explore the boundary between colloidally stable and unstable complexes as it is influenced by polycation/polyanion mixing ratio and ionic strength. The polymers examined are poly(diallyldimethylammonium chloride) (PDAC) and poly(sodium 4-styrenesulfonate) (PSS). Physical properties such as turbidity, hydrodynamic size, and zeta potential are investigated upon complex formation. We also perform detailed molecular dynamics simulations to examine the structure and effective charge distribution of the PECs at varying mixing ratios and salt concentrations to support the experimental findings. The results suggest that the colloidally stable/unstable boundary possibly marks the screening effects from added salt, resulting in weakly charged complexes that aggregate. At higher salt concentrations, the complexes initially form and then gradually dissolve into solution.

On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields.

The Thole induced point dipole model is combined with three different point charge fitting methods, Merz-Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self-consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4-10%.

Chemistry specificity of DNA-polycation complex salt response: a simulation study of DNA, polylysine and polyethyleneimine.

In this work, the chemistry specific stability determining factors of DNA-polycation complexes are examined by performing all-atom molecular dynamics simulations. To this end, we conduct a systematic variation of polycation line charge through polyethyleneimine (PEI) protonation and polycation chemistry via comparison with poly-l-lysine (PLL). Our simulations show that increasing line charge of the polycation alone does not lead to more salt tolerant complexes. Instead, the effective charge compensation by the polycation correlates with the increased stability of the complex against additional salt. The salt stability of PEI-DNA complexes also links to the proton sponge property of weak polycations, commonly assumed to be behind the effectivity of PEI as a gene delivery vector. Examination of the complexes reveals the mechanism behind this behaviour; more Cl(-) ions are attracted by the protonated complexes but, in contrast to the common depiction of the proton sponge behaviour, the ion influx does not cause swelling of the complex structure itself. However, PEI protonation leads to release of PEI while DNA remains tightly bound to the complex. Jointly, these findings shed light on the stability determining factors of DNA-polycation complexes, raise charge distribution as an important stability determining contributor, and indicate that the effectivity of PEI in gene delivery is likely to result from the freed PEI facilitating gene transfection.

Polyelectrolyte decomplexation via addition of salt: charge correlation driven zipper.

We report the first atomic scale studies of polyelectrolyte decomplexation. The complex between DNA and polylysine is shown to destabilize and spontaneously open in a gradual, reversible zipper-like mechanism driven by an increase in solution salt concentration. Divalent CaCl2 is significantly more effective than monovalent NaCl in destabilizing the complex due to charge correlations and water binding capability. The dissociation occurs accompanied by charge reversal in which charge correlations and ion binding chemistry play a key role. Our results are in agreement with experimental work on complex dissociation but in addition show the underlying microstructural correlations driving the behavior. Comparison of our full atomic level detail and dynamics results with theoretical works describing the PEs as charged, rigid rods reveals that although charge correlation involved theories provide qualitatively similar responses, considering also specific molecular chemistry and molecular level water contributions provides a more complete understanding of PE complex stability and dynamics. The findings may facilitate controlled release in gene delivery and more in general tuning of PE membrane permeability and mechanical characteristics through ionic strength.

Polarizable force fields.

This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.