Lipid Membrane Surface Research Articles

Understanding Antimicrobial Peptide Synergy: Differential Binding Interactions and Their Impact on Membrane Integrity.

Research on antimicrobial peptides (AMPs) has been conducted as a solution to overcome antibiotic resistance. In particular, the synergistic effect that appears when two or more AMPs are used in combination has been observed. To find an effective synergistic combination, it is necessary to understand the underlying mechanism. However, a consistent explanation for this phenomenon has not yet been provided due to limitations in experimentally determining or predicting the structure of the heteroaggregates formed by the interactions between different AMPs and the interaction of the aggregate surface with the lipid membrane surface. In this study, we conducted molecular dynamics simulations for two heterogeneous aggregates of melittin-indolicidin and pexiganan-indolicidin to observe their structures in the solution phase and their interactions with the lipid membrane. We aimed to determine how the surfaces of these aggregates interact with the lipid membrane. Due to the different amino acid residue sequence characteristics of melittin and pexiganan, we found that when the two AMPs bind to indolicidin, they form aggregates with completely different structural characteristics. Accordingly, the sequence characteristics of pexiganan, which exhibits a relatively unstable structure compared to melittin in aqueous solution or on lipid membranes, allow for a more stable interaction with the lipid membrane when forming aggregates with indolicidin, effectively inhibiting the integrity of the lipid membranes. We also found that the amino acid residues forming the surface of the AMP aggregate show differential binding strengths to different lipid species forming the lipid membrane, thereby disrupting the membrane in a way that weakens its integrity. Through this, we provided insight into the basic principle of how the synergistic effect of AMPs occurs.

Variable Non-Gaussian Transport of Nanoplastic on Supported Lipid Bilayers in Saline Conditions.

Nanoplastic-lipid interaction is vital to understanding the nanoscale mechanism of plastic adsorption and aggregation on a lipid membrane surface. However, a single-particle mechanistic picture of the nanoplastic transport process on a lipid surface remains unclear. Here, we report a salt-dependent non-Gaussian transport mechanism of polystyrene particles on a supported 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer surface. Particle stickiness on the POPC surface increases with salt concentration, where the particles stay longer at the surface and diffuse to shorter distances. Additionally, a non-Gaussian diffusion state dominates the transport process at high salt concentrations. Our current study provides insight into the transport mechanism of polystyrene (PS) particles on supported lipid membranes, which is essential to understanding fundamental questions regarding the adsorption mechanisms of nanoplastics on lipid surfaces.

Thermodynamics of oligomerization and Helix-to-sheet structural transition of amyloid β-protein on anionic phospholipid vesicles

Understanding oligomerization and aggregation of the amyloid-β protein is important to elucidate the pathological mechanisms of Alzheimer's disease, and lipid membranes play critical roles in this process. In addition to studies reported by other groups, our group has also reported that the negatively-charged lipid bilayers with a high positive curvature induced α-helix-to-β-sheet conformational transitions of amyloid-β-(1–40) upon increase in protein density on the membrane surface and promoted amyloid fibril formation of the protein. Herein, we investigated detailed mechanisms of the conformational transition and oligomer formation of the amyloid-β protein on the membrane surface. Changes in the fractions of the three protein conformers (free monomer, membrane-bound α-helix-rich conformation, and β-sheet-rich conformation) were determined from the fluorescent spectral changes of the tryptophan probe in the protein. The helix-to-sheet structural transition on the surface was described by a thermodynamic model of octamer formation driven by entropic forces including hydrophobic interactions. These findings provide useful information for understanding the self-assembly of amyloidogenic proteins on lipid membrane surfaces.

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling.

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

Second Harmonic Generation as a Noninvasive Method to Study Molecular Processes on the Surface of Lipid Membranes (Brief Review)

The development and implementation of modern experimental methods in interdisciplinary projects promote the solution of fundamental problems in molecular biology and medicine. One of these problems is the understanding of the physics of molecular interactions in a narrow (1 nm) surface layer of cellular lipid membranes (hydration layer of the membrane), where most of the important electrochemical interactions with ions and proteins, transmembrane transport of molecules, and endocytosis occur. The solution of this problem requires noninvasive methods sensitive to changes in the molecular structure of the surface layer of membranes. The aims of this work are to describe advantages of nonlinear optical microscopy and spectroscopy for the study of structural and electrostatic features of lipid membranes, to present the developed method for the visualization of the hydration of lipid membranes, and to discuss the limits of applicability of this method.

Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces.

Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.

Improved Protein Model in SPICA Force Field.

The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and the stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was overstabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study, we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and reoptimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radii of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems.

Exploring Fullerenol-C60(OH)24 interactions with lipid bilayers: Molecular dynamics study of agglomeration and surface deposition

In this work, the physical–chemical properties of lipid membranes interacting with Fullerenol-C60(OH)24 molecules immersed in an aqueous solution were studied using Molecular Dynamics (MD) simulations. In order to analyze the role played by the concentration of Fullerene-C60(OH)24 in the interaction with lipid membranes, we carried out simulations with variations in the number (n = 1, 2, 4, 8, 12, 16 or 20) of Fullerene-C60(OH)24 molecules present in the solution in which the lipid membrane was immersed. The lipid membrane simulated was composed of DOPC (dipalmitoylphosphatidylcholine) with 30% of cholesterol molecules (DOPC/CHOL(30%)). The average behavior of the Coulomb and vdW interaction energy shows that as the Fullerenol-C60(OH)24 molecules concentration increases, insertion of Fullerenol in the lipid bilayer becomes energetically unfavorable since they tend to interact with each other, leading to the formation of clusters. From the mass density, we confirmed that there is a decrease in the insertion of Fullerenol-C60(OH)24 molecules in the bilayer as n increases. We noticed that Fullerenol molecules get closer to each other and are deposited on the surface of the lipid bilayers but do not penetrate them. The diffusion coefficient (MSD) reveals a decrease in the mobility of Fullerenol molecules as n increases. This observation confirms the agglomeration of Fullerenol on the lipid membrane’s surface. A detailed analysis of hydrogen bonds (HB) involving Fullerenol–Fullerenol, Fullerenol–DOPC, and Fullerenol–Water pairs provides insight into this phenomenon. While the average number of HBs in the Fullerenol–Water pair remains relatively constant as n increases, there is a significant increase in HB interactions for the Fullerenol–Fullerenol pair. In contrast, the Fullerenol–DOPC pair experiences a decrease in HBs, underscoring the preference of Fullerenol to agglomerate and deposit onto the lipid membrane's surface.

Electrostatic Potentials Caused by the Release of Protons from Photoactivated Compound Sodium 2-Methoxy-5-nitrophenyl Sulfate at the Surface of Bilayer Lipid Membrane.

Lateral transport and release of protons at the water-membrane interface play crucial roles in cell bioenergetics. Therefore, versatile techniques need to be developed for investigating as well as clarifying the main features of these processes at the molecular level. Here, we experimentally measured the kinetics of binding of protons released from the photoactivated compound sodium 2-methoxy-5-nitrophenyl sulfate (MNPS) at the surface of a bilayer lipid membrane (BLM). We developed a theoretical model of this process describing the damage of MNPS coupled with the release of the protons at the membrane surface, as well as the exchange of MNPS molecules and protons between the membrane and solution. We found that the total change in the boundary potential difference across the membrane, ∆ϕb, is the sum of opposing effects of adsorption of MNPS anions and release of protons at the membrane-water interface. Steady-state change in the ∆ϕb due to protons decreased with the concentration of the buffer and increased with the pH of the solution. The change in the concentration of protons evaluated from measurements of ∆ϕb was close to that in the unstirred water layer near the BLM. This result, as well as rate constants of the proton exchange between the membrane and the bulk solution, indicated that the rate-limiting step of the proton surface to bulk release is the change in the concentration of protons in the unstirred layer. This means that the protons released from MNPS remain in equilibrium between the BLM surface and an adjacent water layer.

Second Harmonic Generation as a Noninvasive Method to Study Molecular Processes on the Surface of Lipid Membranes (Brief Review)

Second Harmonic Generation as a Noninvasive Method to Study Molecular Processes on the Surface of Lipid Membranes (Brief Review)

Surface-induced phase separation of reconstituted nascent integrin clusters on lipid membranes

Integrin adhesion complexes are essential membrane-associated cellular compartments for metazoan life. The formation of initial integrin adhesion complexes is a dynamic process involving focal adhesion proteins assembled at the integrin cytoplasmic tails and the inner leaflet of the plasma membrane. The weak multivalent protein interactions within the complex and with the plasma membrane suggest that liquid-liquid phase separation could play a role in the nascent adhesion assembly. Here, we report that solid-supported lipid membranes supplemented with phosphoinositides induce the phase separation of minimal integrin adhesion condensates composed of integrin β1 tails, kindlin, talin, paxillin, and FAK at physiological ionic strengths and protein concentrations. We show that the presence of phosphoinositides is key to enriching kindlin and talin on the lipid membrane, which is necessary to further induce the phase separation of paxillin and FAK at the membrane. Our data demonstrate that lipid membrane surfaces set the local solvent conditions for steering the membrane-localized phase separation even in a regime where no condensate formation of proteins occurs in bulk solution.

Ion Pairing of Cationic and Anionic Ir(III) Photosensitizers for Photocatalytic CO2 Reduction at Lipid-Membrane Surfaces.

We synthesized an ion pair comprising cationic and anionic Ir(III) photosensitizers ([Ir1+][Ir2-]) for photocatalytic CO2 reduction and showed that the cationic component imparts stability, while the cyclometalating ligands in the anionic component ensure effective visible-light absorption. The triplet excited state of [Ir1+] is the key photoredox species in this system and is mainly generated through the transfer of triplet excitation energy from the anionic moiety due to Coulombic interactions and appropriate triplet energy alignment between the two ionic components. The positive photosensitization effect of ion pairing was demonstrated by photocatalytic CO2 reduction in cooperation with a Re(I) molecular catalyst incorporated into a vesicle membrane.

Exploring the Role of Anionic Lipid Nanodomains in the Membrane Disruption and Protein Folding of Human Islet Amyloid Polypeptide Oligomers on Lipid Membrane Surfaces Using Multiscale Molecular Dynamics Simulations.

The aggregation of human Islet Amyloid Polypeptide (hIAPP) on cell membranes is linked to amyloid diseases. However, the physio-chemical mechanisms of how these hIAPP aggregates trigger membrane damage are unclear. Using coarse-grained and all-atom molecular dynamics simulations, we investigated the role of lipid nanodomains in the presence or absence of anionic lipids, phosphatidylserine (PS), and a ganglioside (GM1), in the membrane disruption and protein folding behaviors of hIAPP aggregates on phase-separated raft membranes. Our raft membranes contain liquid-ordered (Lo), liquid-disordered (Ld), mixed Lo/Ld (Lod), PS-cluster, and GM1-cluster nanosized domains. We observed that hIAPP aggregates bound to the Lod domain in the absence of anionic lipids, but also to the GM1-cluster- and PS-cluster-containing domains, with stronger affinity in the presence of anionic lipids. We discovered that L16 and I26 are the lipid anchoring residues of hIAPP binding to the Lod and PS-cluster domains. Finally, significant lipid acyl chain order disruption in the annular lipid shells surrounding the membrane-bound hIAPP aggregates and protein folding, particularly beta-sheet formation, in larger protein aggregates were evident. We propose that the interactions of hIAPP and both non-anionic and anionic lipid nanodomains represent key molecular events of membrane damage associated with the pathogenesis of amyloid diseases.

The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data

Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.

Membrane remodeling and vesicle formation by biomolecular condensates: A coarse grained simulation study.

Intrinsically disordered peptides (IDPs) can undergo liquid-liquid phase separation (LLPS) which is essential for membrane-less organelle formation and intracellular compartmentalization. Several experimental studies observed LLPS at or near the lipid membrane surface, leading to the alteration of the membrane morphology. Processes such as tubulation, endocytosis, exocytosis, and multilamellar membrane formation have also been observed in recent experiments. However, the molecular mechanisms and the governing molecular interactions remain unclear. Here we employ molecular dynamics simulations with different levels of coarse-graining to understand these long timescale processes. We study the coacervation of oppositely charged polypeptide sequences, namely, poly-glutamate (E30) and poly-lysine (K30) mixtures in the presence of lipid bilayers containing different ratios of POPC and POPG, with Martini 3.0 explicit solvent forcefield. We find that at least 20% anionic lipids are required to observe successful events of adsorption, followed by wetting, of the EK-coacervate on the bilayer. Upon wetting, the coacervate produces negative curvature to the bilayer and induces local demixing of lipids. Interestingly, the number of contacts between the polyelectrolytes decreases, unlike previous suggestions that predicted an increased overlap among the polyelectrolytes as the driving force of negative curvature formation. Next, we investigate the sensitivity of membrane deformation to the sequence (or charge patterns) of the IDPs. We observe that the IDPs with segregated charge patterns can remodel the membrane more prominently than IDPs with well-mixed charges. In order to understand the biologically relevant length- and time-scales, we developed a solvent-free coarse grained model for such systems. By tuning the IDP-lipid and IDP-IDP interactions, we observe endocytosis, exocytosis, and multilamellarity induced by the LLPS droplet into the bilayer vesicle.

Surfactant-Assisted Purification of Hydrophobic DNA Nanostructures.

Purification of functional DNA nanostructures is an essential step in achieving intended functions because misfolded structures and the remaining free DNA strands in a solution can interact and affect their behavior. However, due to hydrophobicity-mediated aggregation, it is difficult to purify DNA nanostructures modified with hydrophobic molecules by conventional methods. Herein, we report the purification of cholesterol-modified DNA nanostructures by using a novel surfactant-assisted gel extraction. The addition of sodium cholate (SC) to the sample solution before structure folding prevented aggregation; this was confirmed by gel electrophoresis. We also found that adding sodium dodecyl sulfate (SDS) to the sample inhibited structural folding. The cholesterol-modified DNA nanostructures prepared with SC were successfully purified by gel extraction, and their ability to bind to the lipid membrane surfaces was maintained. This method will facilitate the purification of DNA nanostructures modified with hydrophobic molecules and expand their applicability in the construction of artificial cell-like systems.

Pro-inflammatory protein S100A9 alters membrane organization by dispersing ordered domains

Pro-inflammatory, calcium-binding protein S100A9 is localized in the cytoplasm of many cells and regulates several intracellular and extracellular processes. S100A9 is involved in neuroinflammation associated with the pathogenesis of Alzheimer's disease (AD). The number of studies on the impact of S100A9 in co-aggregation processes with amyloid-like proteins is increasing. However, there is still a lack of data on how this protein interacts with lipid membranes. We employed atomic force microscopy (AFM), dynamic light scattering (DLS), and fluorescence measurements (Laurdan and Thioflavin-T) to study the interaction between protein and the membrane surface. We used lipid vesicles in bulk and planar tethered lipid bilayers as biomimetic membrane models. We demonstrated that the protein accumulates on negatively charged lipid bilayers but with no further loss of the bilayer's integrity. The most important result is that the initial adsorption and accumulation of apo-form of S100A9 on the lipid membrane surface is lipid phase-sensitive. The breaking down of raft-like and disappearance of gel-like domains indicate that protein incorporates into the hydrophobic part of the lipid bilayer. We observed the most noticeable loss of integrity in lipid bilayers constructed from a lipid mixture (brain total lipid extract). Understanding the function and interactions of these proteins in cellular environments might expand the development of new diagnostic and therapeutic approaches for AD or other related diseases.

Local Attraction of Substrates and Co-Substrates Enhances Weak Acid and Base Transmembrane Transport.

The transmembrane transport of weak acid and base metabolites depends on the local pH conditions that affect the protonation status of the substrates and the availability of co-substrates, typically protons. Different protein designs ensure the attraction of substrates and co-substrates to the transporter entry sites. These include electrostatic surface charges on the transport proteins and complexation with seemingly transport-unrelated proteins that provide substrate and/or proton antenna, or enzymatically generate substrates in place. Such protein assemblies affect transport rates and directionality. The lipid membrane surface also collects and transfers protons. The complexity in the various systems enables adjustability and regulation in a given physiological or pathophysiological situation. This review describes experimentally shown principles in the attraction and facilitation of weak acid and base transport substrates, including monocarboxylates, ammonium, bicarbonate, and arsenite, plus protons as a co-substrate.

Stable binding to phosphatidylserine-containing membranes requires conserved arginine residues in tandem C domains of blood coagulation factor VIII.

At sites of vascular damage, factor VIII (fVIII) is proteolytically activated by thrombin and binds to activated platelet surfaces with activated factor IX (fIXa) to form the intrinsic "tenase" complex. Previous structural and mutational studies of fVIII have identified the C1 and C2 domains in binding to negatively charged membrane surfaces through β-hairpin loops with solvent-exposed hydrophobic residues and a ring of positively charged basic residues. Several hemophilia A-associated mutations within the C domains are suggested to disrupt lipid binding, preventing formation of the intrinsic tenase complex. In this study, we devised a novel platform for generating recombinant C1, C2, and C1C2 domain constructs and performed mutagenesis of several charged residues proximal to the putative membrane binding region of each C domain. Binding measurements between phosphatidylserine (PS)-containing lipid membrane surfaces and fVIII C domains demonstrated an ionic strength dependence on membrane binding affinity. Mutations to basic residues adjacent to the surface-exposed hydrophobic regions of C1 and C2 differentially disrupted membrane binding, with abrogation of binding occurring for mutations to conserved arginine residues in the C1 (R2163) and C2 (R2320) domains. Lastly, we determined the X-ray crystal structure of the porcine fVIII C2 domain bound to o-phospho-L-serine, the polar headgroup of PS, which binds to a basic cleft and makes charge-charge contact with R2320. We conclude that basic clefts in the fVIII C domains bind to PS-containing membranes through conserved arginine residues via a C domain modularity, where each C domain possesses modest electrostatic-dependent affinity and tandem C domains are required for high affinity binding.

Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.

Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a pore-forming structure upon acidification; but its mechanism of conformational transition has been debated. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures of PFN2 in pre-pore and pore conformations in isolation and bound to liposomes. In isolation and upon acidification, the pre-assembled complete pre-pore rings convert to pores in both flat ring and twisted conformations. On membranes, insitu assembled PFN2 pre-pores display various degrees of completeness; whereas PFN2 pores are mainly incomplete arc structures that follow the same subunit packing arrangements as found in isolation. Both assemblies on membranes use their P2 β-hairpin for binding to the lipid membrane surface. Overall, these structural snapshots suggest a molecular mechanism for PFN2 pre-pore to pore transition on a targeted membrane, potentially using the twisted pore as an intermediate or alternative state to the flat conformation, with the capacity to cause bilayer distortion during membrane insertion.