Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data

Nanoscale lipid domains determine the dynamic molecular portraits of mixed DOPC/DOPS bilayers in a fluid phase: A computational insight

Lateral heterogeneity, or mosaicity, is a fundamental property inherent to cell membranes that is crucial for their functioning. While microscopic inhomogeneities (e.g. rafts) are easily detected experimentally, lipid domains with nanoscale dimensions (nanoclusters of nanodomains, NDs) resist reliable characterization by instrumental methods. In such a case, important insight can be gained via computer modeling. Here, NDs composed of lipid's head groups in the mixed zwitterionic dioleoylphosphatidylcholine (DOPC) and negatively charged dioleoylphosphatidylserine (DOPS) bilayers were studied by molecular dynamics. A new algorithm has been developed to identify NDs. Unlike most similar methods, it implicitly considers the heterogeneous distribution of lipid head atomic density and does not require subjectively chosen parameters. In DOPS-rich membranes, lipids form more compact and stable NDs due to strong interlipid interactions. In DOPC-rich systems, NDs arise due to the "packing" effect of weakly bound lipid heads. The clustering picture is related to the physical properties of the bilayer surface: DOPS-rich systems show more pronounced surface heterogeneity of hydrophilic/hydrophobic regions compared to DOPC-rich ones. The results obtained are important for the effective quantitative characterization of the "dynamic molecular portrait" of a membrane surface - its "fingerprint" characterizing dynamical distribution of its physicochemical properties.

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.

Automated collective variable discovery for MFSD2A transporter from molecular dynamics simulations

Biomolecules often exhibit complex free energy landscapes in which long-lived metastable states are separated by large energy barriers. Overcoming these barriers to robustly sample transitions between the metastable states with classical molecular dynamics (MD) simulations presents a challenge. To circumvent this issue, collective variable (CV)-based enhanced sampling MD approaches are often employed. Traditional CV selection relies on intuition and prior knowledge of the system. This approach introduces bias, which can lead to incomplete mechanistic insights. Thus, automated CV detection is desired to gain a deeper understanding of the system/process. Analysis of MD data with various machine-learning algorithms, such as principal component analysis (PCA), support vector machine, and linear discriminant analysis (LDA) based approaches have been implemented for automated CV detection. However, their performance has not been systematically evaluated on structurally and mechanistically complex biological systems. Here, we applied these methods to MD simulations of the MFSD2A (Major Facilitator Superfamily Domain 2A) lysolipid transporter in multiple functionally relevant metastable states with the goal of identifying optimal CVs that would structurally discriminate these states. Specific emphasis was on the automated detection and interpretive power of LDA-based CVs. We found that LDA methods, which included a novel gradient descent-based multiclass harmonic variant, termed GDHLDA, we developed here, outperform PCA in class separation, exhibiting remarkable consistency in extracting CVs critical for distinguishing metastable states. Furthermore, the identified CVs included features previously associated with conformational transitions in MFSD2A. Specifically, conformational shifts in transmembrane helix 7 and in residue Y294 on this helix emerged as critical features discriminating the metastable states in MFSD2A. This highlights the effectiveness of LDA-based approaches in automatically extracting from MD trajectories CVs of functional relevance that can be used to drive biased MD simulations to efficiently sample conformational transitions in the molecular system.

nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

Activation of the influenza B M2 proton channel (BM2)

Influenza B viruses have co-circulated during most seasonal flu epidemics and can cause significant human morbidity and mortality due to their rapid mutation, emerging drug resistance, and severe impact on vulnerable populations. The influenza B M2 proton channel (BM2) plays an essential role in viral replication, but the mechanisms behind its symmetric proton conductance and the involvement of a second histidine (His27) cluster remain unclear. Here we perform the membrane-enabled continuous constant-pH molecular dynamics simulations on wildtype BM2 and a key H27A mutant to explore its pH-dependent conformational switch. Simulations capture the activation as the first histidine (His19) protonates and reveal the transition at lower pH values compared to AM2 is a result of electrostatic repulsions between His19 and pre-protonated His27. Crucially, we provide an atomic-level understanding of the symmetric proton conduction by identifying pre-activating channel hydration in the C-terminal portion. This research advances our understanding of the function of BM2 function and lays the groundwork for further chemically reactive modeling of the explicit proton transport process as well as possible anti-flu drug design efforts.

Interior pH-sensing residue of human voltage-gated proton channel Hv1 is histidine 168

The molecular mechanisms governing the human voltage-gated proton channel hHv1 remain elusive. Here, we used membrane-enabled hybrid-solvent continuous constant pH molecular dynamics (CpHMD) simulations with pH replica exchange to further evaluate the structural models of hHv1 in the closed (hyperpolarized) and open (depolarized) states recently obtained with MD simulations and explore potential pH-sensing residues. The CpHMD titration at a set of symmetric pH conditions revealed three residues that can gain or lose protons upon channel depolarization. Among them, residue H168 at the intracellular end of the S3 helix switches from the deprotonated to the protonated state and its protonation is correlated with the increased tilting of the S3 helix during the transition from the closed to the open state. Thus, the simulation data suggest H168 as an interior pH sensor, in support of a recent finding based on electrophysiological experiments of Hv1 mutants. We propose that protonation of H168 acts as a key that unlocks the closed channel configuration by increasing the flexibility of the S2-S3 linker, which increases the tilt angle of S3 and enhances the mobility of the S4 helix, thus promoting channel opening. Our work represents an important step toward deciphering the pH-dependent gating mechanism of hHv1.

Salting-out and Competitive Adsorption of Ethanol into Lipid Bilayer Membranes: Conflicting Effects of Salts on Ethanol-Membrane Interactions Studied by Molecular Dynamics Simulations

Small amphiphilic molecules, such as ethanol, disturb the structure of lipid bilayer membranes to increase the membrane permeability, which is important for applications such as drug delivery, disinfection, and fermentation. To investigate how and the extent to which coexisting salts affect membrane disturbance, we performed molecular dynamics (MD) simulations on lipid bilayer membranes composed of zwitterionic lipids in aqueous ethanol solutions containing 0-631 mM NaCl, KCl, and KI salts. The addition of salts at low concentrations induced cationic adsorption on the lipid membrane, which competes with ethanol adsorption, thereby reducing the hydrogen bonds between ethanol and lipid molecules. This competitive adsorption mitigated the membrane disturbance and decreased the permeation of ethanol molecules into the membrane. In contrast, higher salt concentrations enhanced the membrane disturbance and permeability, which was caused by the salting-out of ethanol from the aqueous phase to the lipid bilayer. These conflicting effects appearing at different concentrations were stronger with the chloride salts than with the iodide salt. Among the two chloride salts, NaCl and KCl, the latter showed a greater enhancement in ethanol permeation at high concentrations. This seeming anti-Hofmeister salting-out behavior resulted from greater Na+ adsorption, preventing the ethanol-lipid interactions.

Structural Determinants of Peptide Nanopore Formation

We have evolved the nanopore-forming macrolittin peptides from the bee venom peptide melittin using successive generations of synthetic molecular evolution. Despite their sequence similarity to the broadly membrane permeabilizing cytolytic melittin, the macrolittins have potent membrane selectivity. They form nanopores in synthetic bilayers made from 1-palmitoyl, 2-oleoyl-phosphatidylcholine (POPC) at extremely low peptide concentrations and yet have essentially no cytolytic activity against any cell membrane, even at high concentration. Here, we explore the structural determinants of macrolittin nanopore stability in POPC bilayers using atomistic molecular dynamics simulations and experiments on macrolittins and single-site variants. Simulations of macrolittin nanopores in POPC bilayers show that they are stabilized by an extensive, cooperative hydrogen bond network comprised of the many charged and polar side chains interacting with each other via bridges of water molecules and lipid headgroups. Lipid molecules with unusual conformations participate in the H-bond network and are an integral part of the nanopore structure. To explore the role of this H-bond network on membrane selectivity, we swapped three critical polar residues with the nonpolar residues found in melittin. All variants have potency, membrane selectivity, and cytotoxicity that were intermediate between a cytotoxic melittin variant called MelP5 and the macrolittins. Simulations showed that the variants had less organized H-bond networks of waters and lipids with unusual structures. The membrane-spanning, cooperative H-bond network is a critical determinant of macrolittin nanopore stability and membrane selectivity. The results described here will help guide the future design and optimization of peptide nanopore-based applications.

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.

Molecular mechanisms of Na+-driven bile acid transport in human NTCP

Human Na+ taurocholate co-transporting protein (hNTCP) is a key bile salt transporter to maintain enterohepatic circulation and is responsible for the recognition of hepatitis B and D viruses. Despite landmark cryoelectron microscopy studies revealing open-pore and inward-facing states of hNTCP stabilized by antibodies, the transport mechanism remains largely unknown. To address this knowledge gap, we used molecular dynamics and enhanced sampling metadynamics simulations to elucidate the intrinsic mechanism of hNTCP-mediated taurocholate acid (TCA) transport driven by Na+ binding. We uncovered three TCA-binding modes, including one that closely matched the limited cryoelectron microscopy density observed in the open-pore hNTCP. We also captured several key hNTCP conformations in the substrate transport cycle, particularly including an outward-facing, substrate-bound state. Furthermore, we provided thermodynamic evidence supporting that changes in the Na+-binding state drive the TCA transport by exploiting the amphiphilic nature of the substrate and modulating the protein environment, thereby enabling the TCA molecule to flip through. Understanding these mechanistic details of Na+-driven bile acid transport may aid in the development of hNTCP-targeted therapies for liver diseases.

Perfect confinement of crown ethers in MOF membrane for complete dehydration and fast transport of monovalent ions

Fast transport of monovalent ions is imperative in selective monovalent ion separation based on membranes. Here, we report the in situ growth of crown ether@UiO-66 membranes at a mild condition, where dibenzo-18-crown-6 (DB18C6) or dibenzo-15-crown-5 is perfectly confined in the UiO-66 cavity. Crown ether@UiO-66 membranes exhibit enhanced monovalent ion transport rates and mono-/divalent ion selectivity, due to the combination of size sieving and interaction screening effects toward the complete monovalent ion dehydration. Specifically, the DB18C6@UiO-66 membrane shows a permeation rate (e.g., K+) of 1.2 mol per square meter per hour and a mono-/divalent ion selectivity (e.g., K+/Mg2+) of 57. Theoretical calculations and simulations illustrate that, presumably, ions are completely dehydrated while transporting through the DB18C6@UiO-66 cavity with a lower energy barrier than that of the UiO-66 cavity. This work provides a strategy to develop efficient ion separation membranes via integrating size sieving and interaction screening and to illuminate the effect of ion dehydration on fast ion transport.

Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field

Molecular dynamics (MD) simulations are a commonly used method for investigating molecular behavior at the atomic level. Achieving reliable MD simulation results necessitates the use of an accurate force field. In the present work, we present a protocol to enhance the quality of group 1 monatomic ions (specifically Li+, Na+, K+, Rb+, and Cs+) with respect to their interactions with common polar model compounds in biomolecules in condensed phases in the context of the Drude polarizable force field. Instead of adjusting preexisting individual parameters for ions, model compounds, and water, we employ atom-pair specific Lennard-Jones (LJ) (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) terms to fine-tune the balance of ion-model compound, ion-water, and model compound-water interactions. This involved establishing a protocol for the optimization of NBFIX and NBTHOLE parameters targeting the difference between molecular mechanical (MM) and quantum mechanical (QM) potential energy scans (PES). It is shown that targeting PES involving complexes that include multiple model compounds and/or ions as trimers and tetramers yields parameters that produce condensed phase properties in agreement with experimental data. Validation of this protocol involved the reproduction of experimental thermodynamic benchmarks, including solvation free energies of ions in methanol and N-methylacetamide, osmotic pressures, ionic conductivities, and diffusion coefficients within the condensed phase. These results show the importance of including more complex ion-model compound complexes beyond dimers in the QM target data to account for many-body effects during parameter fitting. The presented parameters represent a significant refinement of the Drude polarizable force field, which will lead to improved accuracy for modeling ion-biomolecular interactions.

Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate-Ion Interactions and Comparison with CHARMM36

Phosphatidylinositol 4,5-bisphosphate (PIP2) is a critical lipid for cellular signaling. The specific phosphorylation of the inositol ring controls protein binding as well as clustering behavior. Two popular models to describe ion-mediated clustering of PIP2 are Martini3 (M3) and CHARMM36 (C36). Molecular dynamics simulations of PIP2-containing bilayers in solutions of potassium chloride, sodium chloride, and calcium chloride, and at two different resolutions are performed to understand the aggregation and the model parameters that drive it. The average M3 clusters of PIP2 in bilayers of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and PIP2 bilayers in the presence of K+, Na+, or Ca2+ contained 2.2, 2.6, and 6.4 times more PIP2 than C36 clusters, respectively. Indeed, the Ca2+-containing systems often formed a single large aggregate. Reparametrization of the M3 ion-phosphate Lennard-Jones interaction energies to reproduce experimental osmotic pressure of sodium dimethyl phosphate (DMP), K[DMP], and Ca[DMP]2 solutions, the same experimental target as C36, yielded comparably sized PIP2 clusters for the two models. Furthermore, C36 and the modified M3 predict similar saturation of the phosphate groups with increasing Ca2+, although the coarse-grained model does not capture the cooperativity between K+ and Ca2+. This characterization of the M3 behavior in the presence of monovalent and divalent ions lays a foundation to study cation/protein/PIP2 clustering.

A Mechanistic Understanding of the Modes of Ca2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration

The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.

Osmotic Force Balance Evaluation of Aqueous Electrolyte Osmotic Pressures and Chemical Potentials

Concentrated aqueous salt solutions are ubiquitous in problems of biological and environmental relevance. The development of accurate force fields that capture the interactions between dissolved species in solution is crucial to simulating these systems to gain molecular insights into the underlying processes under saline conditions. The osmotic pressure is a relatively simple thermodynamic property connecting the experimental and simulation measurements of the associative properties of the ions in solution. Milner [C. Gillespie and S. T. Milner, Soft Matter, 16, 9816 (2020)] proposed a simulation approach to evaluate the osmotic pressures of salts in solution by applying a restraint potential to the ions alone in solution and determining the resulting pressure required to balance that potential, referred to here as the osmotic force balance. Here, we expand Milner's approach, demonstrating that the chemical potentials of the salts in solution as a function of concentration can be fitted to the concentration profiles determined from simulation, additionally providing an analytical expression for the osmotic pressure. This approach is used to determine the osmotic pressures of 15 alkali halide salts in water from simulations. The cross interactions between cations and anions in solution are subsequently optimized to capture their experimental osmotic pressures.

Parameter Dependence of the Solubility Limit for Disodium Phosphate

The solubility limit was calculated for supersaturated solutions of disodium phosphate in water as a function of the sodium-oxygen Lennard-Jones radius parameter Rmin. We found that changes in the sodium-oxygen Rmin were clearly exponentially related to the concentration of the solubility limit. Starting from standard force fields more suited to nucleic acids and phospholipids, only relatively small changes were required to achieve the experimentally known solubility limit. Simultaneously, we found that it was possible to achieve the solubility limit and the osmotic pressure with the same model parameters. Based on transferability, the adjusted Rmin parameter can be used to more accurately model phosphorylated proteins.

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key regulators in cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to the challenges associated with studying mucin domains. Here, we demonstrate that the mucinase SmE has a unique ability to cleave at residues bearing very complex glycans. SmE enables improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we perform molecular dynamics (MD) simulations of TIM-3 and -4 to understand how glycosylation affects structural features of these proteins. Finally, we use these models to investigate the functional relevance of glycosylation for TIM-3 function and ligand binding. Overall, we present a powerful workflow to better understand the detailed molecular structures and functions of the mucinome.

Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules

Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.

Membrane Domain Anti-Registration Induces an Intrinsic Transmembrane Potential

Plasma membrane segregation into various nanoscale membrane domains is driven by distinct interactions between diverse lipids and proteins. Among them, liquid-ordered (Lo) membrane domains are defined as "lipid rafts" and liquid-disordered (Ld) ones as "lipid non-rafts". Using model membrane systems, both intra-leaflet and inter-leaflet dynamics of these membrane domains are widely studied. Nevertheless, the biological impact of the latter, which is accompanied by membrane domain registration/anti-registration, is far from clear. Hence, in this work, we studied the biological relevance of the membrane domain anti-registration using both all-atom molecular dynamics (MD) simulations and confocal fluorescence microscopy. All-atom MD simulations suggested an intrinsic transmembrane potential for the case of the membrane anti-registration (Lo/Ld). Meanwhile, confocal fluorescence microscopy experiments of HeLa and 293T cell lines indicated that membrane cholesterol depletion could significantly alter the transmembrane potential of cells. Considering differences in the cholesterol content between Lo and Ld membrane domains, our confocal fluorescence microscopy experiments are consistent with our all-atom MD simulations. In short, membrane domain anti-registration induces local membrane asymmetry and, thus, an intrinsic transmembrane potential.

Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes

Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.

Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A

Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na+-dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na+. Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na+ -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a "trap-and-flip" mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.

Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels

The recent determination of cryo-EM structures of voltage-gated sodium (Na_v) channels has revealed many details of these proteins. However, knowledge of ionic permeation through the Na_v pore remains limited. In this work, we performed atomistic molecular dynamics (MD) simulations to study the structural features of various neuronal Na_v channels based on homology modeling of the cryo-EM structure of the human Na_v1.4 channel and, in addition, on the recently resolved configuration for Na_v1.2. In particular, single Na⁺ permeation events during standard MD runs suggest that the ion resides in the inner part of the Na_v selectivity filter (SF). On-the-fly free energy parametrization (OTFP) temperature-accelerated molecular dynamics (TAMD) was also used to calculate two-dimensional free energy surfaces (FESs) related to single/double Na⁺ translocation through the SF of the homology-based Na_v1.2 model and the cryo-EM Na_v1.2 structure, with different realizations of the DEKA filter domain. These additional simulations revealed distinct mechanisms for single and double Na⁺ permeation through the wild-type SF, which has a charged lysine in the DEKA ring. Moreover, the configurations of the ions in the SF corresponding to the metastable states of the FESs are specific for each SF motif. Overall, the description of these mechanisms gives us new insights into ion conduction in human Na_v cryo-EM-based and cryo-EM configurations that could advance understanding of these systems and how they differ from potassium and bacterial Na_v channels.

Insights into the solubility of γ $$ \gamma $$ D-crystallin from multiscale atomistic simulations

The molecular basis underlying the rich phase behavior of globular proteins remains poorly understood. We use atomistic multiscale molecular simulations to model the solution-state conformational dynamics and interprotein interactions of γ $$ \gamma $$ D-crystallin and its P23T-R36S mutant, which drastically limits the protein solubility, at both infinite dilution and at a concentration where the mutant fluid phase and crystalline phase coexist. We find that while the mutant conserves the protein fold, changes to the surface exposure of residues in the neighborhood of residue-36 enhance protein-protein interactions and develop specific protein-protein contacts found in the protein crystal lattice.

The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter

The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.

The pH Response of a Peptoid Oligomer

Polypeptoids are N-substituted glycine polymers, which differ from peptides in the placement of the side chain on the amide nitrogen rather than the C_α carbon. A peptoid with a chiral side chain containing both an aromatic group and carboxylic acid has a structure that responds to pH changes. All-atom molecular dynamics simulations using a force field specifically tuned for peptoids were carried out with an advanced sampling method for the peptoid (S)-N-(1-carboxy-2-phenylethyl)glycine in the high and low pH limits. The simulations show that the structure changes from mostly cis amide bonds at low pH to mostly trans bonds at high pH. The structural changes are driven by side chain-backbone hydrogen bonds at low pH and side chain repulsions and increased water contact at high pH.

The impact of pathogenic and artificial mutations on Claudin-5 selectivity from molecular dynamics simulations

Tight-junctions (TJs) are multi-protein complexes between adjacent endothelial or epithelial cells. In the blood-brain-barrier (BBB), they seal the paracellular space and the Claudin-5 (Cldn5) protein forms their backbone. Despite the fundamental role in brain homeostasis, little is known on Cldn5-based TJ assemblies. Different structural models were suggested, with Cldn5 protomers generating paracellular pores that restrict the passage of ions and small molecules. Recently, the first Cldn5 pathogenic mutation, G60R, was identified and shown to induce Cl^--selective channels and Na⁺ barriers in BBB TJs, providing an excellent opportunity to validate the structural models. Here, we used molecular dynamics to study the permeation of ions and water through two distinct G60R-Cldn5 paracellular architectures. Only the so-called Pore I reproduces the functional modification observed in experiments, displaying a free energy (FE) minimum for Cl^- and a barrier for Na⁺ consistent with anionic selectivity. We also studied the artificial Q57D and Q63D mutations in the constriction region, Q57 being conserved in Cldns except for cation permeable homologs. In both cases, we obtain FE profiles consistent with facilitated passage of cations. Our calculations provide the first in-silico description of a Cldn5 pathogenic mutation, further assessing the TJ Pore I model and yielding new insight on BBB's paracellular selectivity.

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

Structure of POPC Lipid Bilayers in OPLS3e Force Field

It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters S_CH of POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid bilayers at varying hydration conditions and ion concentrations. The results show that OPLS3e behaves similarly to the CHARMM36 force field and relatively accurately follows the experimentally measured S_CH for the lipid headgroup, the glycerol backbone, and the acyl tails. Thus, OPLS3e is a good choice for POPC bilayer simulations under many biologically relevant conditions. The exception are systems with an abundancy of ions, as similarly to most other force fields OPLS3e strongly overestimates the membrane-binding of cations, especially Ca²⁺. This leads to undesirable positive charge of the membrane surface and drastically lowers the concentration of Ca²⁺ in the surrounding solvent, which might cause issues in systems sensitive to correct charge distribution profiles across the membrane.

Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions

Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.

Computational study of ion permeation through claudin-4 paracellular channels

Claudins (Cldns) form a large family of protein homologs that are essential for the assembly of paracellular tight junctions (TJs), where they form channels or barriers with tissue-specific selectivity for permeants. In contrast to several family members whose physiological role has been identified, the function of claudin 4 (Cldn4) remains elusive, despite experimental evidence suggesting that it can form anion-selective TJ channels in the renal epithelium. Computational approaches have recently been employed to elucidate the molecular basis of Cldns' function, and hence could help in clarifying the role of Cldn4. In this work, we use structural modeling and all-atom molecular dynamics simulations to transfer two previously introduced structural models of Cldn-based paracellular complexes to Cldn4 to reproduce a paracellular anion channel. Free energy calculations for ionic transport through the pores allow us to establish the thermodynamic properties driving the ion-selectivity of the structures. While one model shows a cavity permeable to chloride and repulsive to cations, the other forms barrier to the passage of all the major physiological ions. Furthermore, our results confirm the charge selectivity role of the residue Lys65 in the first extracellular loop of the protein, rationalizing Cldn4 control of paracellular permeability.

The Structures of Heterogeneous Membranes and Their Interactions with an Anticancer Peptide: A Molecular Dynamics Study

We conduct molecular dynamics simulations of model heterogeneous membranes and their interactions with a 24-amino acid peptide-NAF-144-67. NAF-144-67 is an anticancer peptide that selectively permeates and kills malignant cells; it does not permeate normal cells. We examine three membranes with different binary mixtures of lipids, DOPC-DOPA, DOPC-DOPS, and DOPC-DOPE, with a single peptide embedded in each as models for the diversity of biological membranes. We illustrate that the peptide organization in the membrane depends on the types of nearby phospholipids and is influenced by the charge and size of the head groups. The present study sheds light on early events of permeation and the mechanisms by which an amphiphilic peptide crosses from an aqueous solution to a hydrophobic membrane. Understanding the translocation mechanism is likely to help the design of new permeants.

The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase

TMEM16F is a Ca2+-activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.

Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments

Interactions of charged molecules with biomembranes regulate many of their biological activities, but their binding affinities to lipid bilayers are difficult to measure experimentally and model theoretically. Classical molecular dynamics (MD) simulations have the potential to capture the complex interactions determining how charged biomolecules interact with membranes, but systematic overbinding of sodium and calcium cations in standard MD simulations raises the question of how accurately force fields capture the interactions between lipid membranes and charged biomolecules. Here, we evaluate the binding of positively charged small molecules, etidocaine, and tetraphenylphosphonium to a phosphatidylcholine (POPC) lipid bilayer using the changes in lipid head-group order parameters. We observed that these molecules behave oppositely to calcium and sodium ions when binding to membranes: (i) their binding affinities are not overestimated by standard force field parameters, (ii) implicit inclusion of electronic polarizability increases their binding affinity, and (iii) they penetrate into the hydrophobic membrane core. Our results can be explained by distinct binding mechanisms of charged small molecules with hydrophobic moieties and monoatomic ions. The binding of the former is driven by hydrophobic effects, while the latter has direct electrostatic interactions with lipids. In addition to elucidating how different kinds of charged biomolecules bind to membranes, we deliver tools for further development of MD simulation parameters and methodology.

The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16

The TMEM16 family of transmembrane proteins includes Ca2+-activated phospholipid scramblases (PLS) that can also function as non-selective ion channels. Extensive structural and functional studies have established that a membrane-exposed hydrophilic groove in TMEM16 PLS can serve as a translocation pathway for lipids. However, it is still unclear how the TMEM16 PLS conduct ions. A “protein-delimited pore” model suggests that ions are translocated through a narrow opening of the groove region, which is not sufficiently wide to allow lipid movement, whereas a “proteolipidic pore” model envisions ions and lipids translocating through an open conformation of the groove. We investigated the dynamic path of potassium ion (K+) translocation that occurs when an open groove state of nhTMEM16 is obtained from long atomistic molecular dynamics (MD) simulations, and calculated the free energy profile of the ion movement through the groove with umbrella sampling methodology. The free energy profile identifies effects of specific interactions along the K+ permeation path. The same calculations were performed to investigate ion permeation through a groove closed to lipid permeation in the nhTMEM16 L302A mutant which exhibits a stable conformation of the groove that does not permit lipid scrambling. Our results identify structural and energy parameters that enable K+ permeation, and suggest that the presence of lipids in the nhTMEM16 groove observed in the simulations during scrambling or in/out diffusion, affect the efficiency of K+ permeation to various extents.

Rational design of amphiphilic fluorinated peptides: evaluation of self-assembly properties and hydrogel formation

Advanced peptide-based nanomaterials composed of self-assembling peptides (SAPs) are of emerging interest in pharmaceutical and biomedical applications. The introduction of fluorine into peptides, in fact, offers unique opportunities to tune their biophysical properties and intermolecular interactions. In particular, the degree of fluorination plays a crucial role in peptide engineering as it can be used to control the characteristics of fluorine-specific interactions and, thus, peptide conformation and self-assembly. Here, we designed and explored a series of amphipathic peptides by incorporating the fluorinated amino acids (2S)-4-monofluoroethylglycine (MfeGly), (2S)-4,4-difluoroethylglycine (DfeGly) and (2S)-4,4,4-trifluoroethylglycine (TfeGly) as hydrophobic components. This approach enabled studying the impact of fluorination on secondary structure formation and peptide self-assembly on a systematic basis. We show that the interplay between polarity and hydrophobicity, both induced differentially by varying degrees of side chain fluorination, does affect peptide folding significantly. A greater degree of fluorination promotes peptide fibrillation and subsequent formation of physical hydrogels in physiological conditions. Molecular simulations revealed the key role played by electrostatically driven intra-chain and inter-chain contact pairs that are modulated by side chain fluorination and give insights into the different self-organization behaviour of selected peptides. Our study provides a systematic report about the distinct features of fluorinated oligomeric peptides with potential applications as peptide-based biomaterials.

Filling the Gap with Long n-Alkanes: Incorporation of C20 and C30 into Phospholipid Membranes

Investigating how hydrophobic molecules mix with phospholipid bilayers and how they affect membrane properties is commonplace in biophysics. Despite this, a molecular-level empirical description of a membrane model as simple as a phospholipid bilayer with long linear hydrophobic chains incorporated is still missing. Here, we present an unprecedented molecular characterization of the incorporation of two long n-alkanes, n-eicosane (C20) and n-triacontane (C30) with 20 and 30 carbons, respectively, in phosphatidylcholine (PC) bilayers using a combination of experimental techniques (²H NMR, ³¹P NMR, ¹H-¹³C dipolar recoupling solid-state NMR, X-ray scattering, and cryogenic electron microscopy) and atomistic molecular dynamics (MD) simulations. At low hydration, deuterated C20 and C30 yield ²H NMR spectra evidencing anisotropic-motion, which demonstrates their miscibility in PC membranes up to a critical alkane-to-acyl-chain volume fraction, ϕ_c. The acquired ²H NMR spectra of C20 and C30 have notably different lineshapes. At low alkane volume fractions below ϕ_c, CHARMM36 MD simulations predict such ²H NMR spectra qualitatively and thus enable an atomistic-level interpretation of the spectra. Above ϕ_c, the ²H NMR lineshapes become characteristic of motions in the intermediate-regime that, together with the MD simulation results, suggest the onset of immiscibility between the alkane molecules and the acyl chains. For all the systems investigated, the phospholipid molecular structure is unperturbed by the presence of the alkanes. However, at conditions of excess hydration and at surprisingly low alkane fractions below ϕ_c, a peak characteristic of isotropic motion is observed in both the ²H spectra of the alkanes and ³¹P spectra of the phospholipids, strongly indicating that the incorporation of the alkanes induces a reduction on the average radius of the lipid vesicles.

Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes

Although molecular dynamics (MD) simulations have been used extensively to study the structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based systems has been more limited. One contributing factor to this disparity is the historically lower level of accuracy of the physical models used in such simulations to describe interactions involving nucleic acids. By modifying nonbonded and torsion parameters of a force field from the Amber family of models, we recently developed force field parameters for RNA that achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Here we report force field parameters for DNA, which we developed by transferring nonbonded parameters from our recently reported RNA force field and making subsequent adjustments to torsion parameters. We have also modified the backbone charges in both the RNA and DNA parameter sets to make the treatment of electrostatics compatible with our recently developed variant of the Amber protein and ion force field. We name the force field resulting from the union of these three parameter sets (the new DNA parameters, the revised RNA parameters, and the existing protein and ion parameters) DES-Amber. Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, especially for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein–nucleic acid complexes.

How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.

Design principles of PI(4,5)P2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

SignificanceClustering of phosphatidylinositol 4,5-bisphosphate (PIP₂) with proteins into what are known as "PIP₂ rafts" is a critical component of intracellular signaling, yet little is known about PIP₂ clusters at the atomic level. Using molecular dynamics simulations and network theory, this paper shows that Ca²⁺ generates large clusters by linking PIP₂ dimers already formed by doubly charged P4/P5 phosphates, while monovalent cations form smaller and less-stable clusters by adding PIP₂ monomers preferentially via weaker interactions with P4/P5 (for Na⁺) or with glycerol P1 (for K⁺). Synergy arises between K⁺ and Ca²⁺ because each ion forms linkages with different phosphates, thereby giving clusters more ways to grow. This explains why Ca²⁺ is pumped into cells by ion channels to form PIP₂ rafts.

Cholesterol occupies the lipid translocation pathway to block phospholipid scrambling by a G protein-coupled receptor

Class A (rhodopsin-like) G protein-coupled receptors (GPCRs) are constitutive phospholipid scramblases as evinced after their reconstitution into liposomes. Yet phospholipid scrambling is not detectable in the resting plasma membrane of mammalian cells that is replete with GPCRs. We considered whether cholesterol, a prominent component of the plasma membrane, limits the ability of GPCRs to scramble lipids. Our previous Markov State Model (MSM) analysis of molecular dynamics simulations of membrane-embedded opsin indicated that phospholipid headgroups traverse a dynamically revealed hydrophilic groove between transmembrane helices (TM) 6 and 7 while their tails remain in the bilayer. Here, we present comparative MSM analyses of 150-μs simulations of opsin in cholesterol-free and cholesterol-rich membranes. Our analyses reveal that cholesterol inhibits phospholipid scrambling by occupying the TM6/7 interface and stabilizing the closed groove conformation while itself undergoing flip-flop. This mechanism may explain the inability of GPCRs to scramble lipids at the plasma membrane.

Highly Ion-Permselective Porous Organic Cage Membranes with Hierarchical Channels

Membranes of high ion permselectivity are significant for the separation of ion species at the subnanometer scale. Here, we report porous organic cage (i.e., CC3) membranes with hierarchical channels including discrete internal cavities and cage-aligned external cavities connected by subnanometer-sized windows. The windows of CC3 sieve monovalent ions from divalent ones and the dual nanometer-sized cavities provide pathways for fast ion transport with a flux of 1.0 mol m^-2 h^-1 and a mono-/divalent ion selectivity (e.g., K⁺/Mg²⁺) up to 10³, several orders of magnitude higher than the permselectivities of reported membranes. Molecular dynamics simulations illustrate the ion transport trajectory from the external to internal cavity via the CC3 window, where ions migrate in diverse hydration states following the energy barrier sequence of K⁺ < Na⁺ < Li⁺ ≪ Mg²⁺. This work sheds light on ion transport properties in porous organic cage channels of discrete frameworks and offers guidelines for developing membranes with hierarchical channels for efficient ion separation.

Binding of polar and hydrophobic molecules at the LiCoO2 (001)-water interface: force field development and molecular dynamics simulations

A classical model in the framework of the INTERFACE force field has been developed for treating the LiCoO₂ (LCO) (001)/water interface. In comparison to ab initio molecular dynamics (MD) simulations based on density functional theory, MD simulations using the classical model lead to generally reliable descriptions of interfacial properties, such as the density distribution of water molecules. Water molecules in close contact with the LCO surface form a strongly adsorbed layer, which leads to a free energy barrier for the adsorption of polar or charged molecules to the LCO surface. Moreover, due to the strong hydrogen bonding interactions with the LCO surface, the first water layer forms an interface that exhibits hydrophobic characters, leading to favorable adsorption of non-polar molecules to the interface. Therefore, despite its highly polar nature, the LCO (001) surface binds not only polar/charged but also non-polar solutes. As an application, the model is used to analyze the adsorption of reduced nicotinamide adenine dinucleotide (NADH) and its molecular components to the LCO (001) surface in water. The results suggest that recently observed redox activity of NADH at the LCO/water interface was due to the co-operativity between the ribose component, which drives binding to the LCO surface, and the nicotinamide moiety, which undergoes oxidation.

Structures and Dynamics of Anionic Lipoprotein Nanodiscs

Nanolipoprotein particles known as nanodiscs (NDs) have emerged as versatile and powerful tools for the stabilization of membrane proteins permitting a plethora of structural and biophysical studies. Part of their allure is their flexibility to accommodate many types of lipids and precise control of the composition. However, little is known about how variations in lipid composition impact their structures and dynamics. Herein, we investigate how the introduction of the anionic lipid POPG into POPC NDs impacts these features. Small-angle X-ray and neutron scattering (SAXS and SANS) of variable-composition NDs are complemented with molecular dynamics simulations to interrogate how increasing the concern of POPG impacts the ND shape, structure of the lipid core, and the dynamics of the popular membrane scaffold protein, MSP1D1(-). A convenient benefit of including POPG is that it eliminates D₂O-induced aggregation observed in pure POPC NDs, permitting studies by SANS at multiple contrasts. SAXS and SANS data could be globally fit to a stacked elliptical cylinder model as well as an extension of the model that accounts for membrane curvature. Fitting to both models supports that the introduction of POPG results in strongly elliptical NDs; however, MD simulations predict the curvature of the membrane, thereby supporting the use of the latter model. Trends in the model-independent parameters suggest that increases in POPG reduce the conformational heterogeneity of the MSP1D1(-), which is in agreement with MD simulations that show that the incorporation of sufficient POPG suppresses disengagement of the N-terminal helix from the lipid core. These studies highlight novel structural changes in NDs in response to an anionic lipid and will inform the interpretation of future structural studies of membrane proteins embedded in NDs of mixed lipid composition.

Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks

Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.

High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations

Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing rules for Lennard-Jones (LJ) interactions. This, however, does not guarantee their reliability. In fact, compared to the quantum mechanical reference data, Lorentz-Berthelot mixing rules substantially underestimate the binding energies of Na⁺ ions with small-molecule analogues of lipid headgroups, yielding errors on the order of 80 and 130 kJ/mol, respectively, for methyl acetate and diethyl phosphate. Previously, errors associated with mixing force fields have been reduced using approaches such as "NB-fix" in which LJ interactions are computed using explicit cross terms rather than those from mixing rules. Building on this idea, we derive explicit lipid-ion cross terms that also may implicitly include many-body cooperativity effects. Additionally, to account for the interdependency between cross terms, we optimize all cross terms simultaneously by performing high-dimensional searches using our ParOpt software. The cross terms we obtain reduce the errors due to mixing rules to below 10 kJ/mol. MD simulation of the lipid bilayer conducted using these optimized cross terms resolves the structural discrepancies between our previous simulations and small-angle X-ray and neutron scattering experiments. These results demonstrate that simulations of lipid bilayers with ions that are accurate up to structural data from scattering experiments can be performed without explicit polarization terms. However, it is worth noting that such NB-fix cross terms are not based on any physical principle; a polarizable lipid model would be more realistic and is still desired. Our approach is generic and can be applied to improve the accuracies of simulations employing mixed force fields.

Lipid21: Complex Lipid Membrane Simulations with AMBER

We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage

Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments.

Envenomation following bites from recluse spiders (Loxosceles) causes loxoscelism, a necrotic tissue breakdown in mammals, and leads to skin degeneration and systemic reactions in the worst case. Recluse spiders belong to the Sicariidae family which also includes six-eyed sand spiders in the genera Sicarius and Hexopthalma. While sicariid spiders are found natively on all continents except Australia, treatments of loxoscelism are typically antibody based and available in some regions of the Americas. Sphingomyelinase D/phospholipase D enzymes are one of the major toxins in venom of sicariid spiders, and have been divided in two clades called α and β. The activity of α and β clades toxins differs; most α clade toxins present high activity against lipids with choline headgroups (-N (CH₃)₃⁺) such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (-NH₃⁺). When comparing the structures of two α clade toxins and one β clade toxin, we noticed the presence in the α clade toxins only of a cage consisting of three aromatic amino acids. In this work we used numerical molecular simulations to probe the role of this cage in the preference of α clade toxins for choline head groups over ethanolamine head groups.