Spontaneous Formation of a Barrel-Stave Pore in a Coarse-Grained Model of the Synthetic LS3 Peptide and a DPPC Lipid Bilayer

The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation

Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.

Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel

Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K⁺ and Cl^- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K⁺, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl^- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.

Inhalation Delivery of Host Defense Peptides (HDP) using Nano- Formulation Strategies: A Pragmatic Approach for Therapy of Pulmonary Ailments

Host defense peptides (HDP) are small cationic molecules released by the immune systems of the body, having multidimensional properties including anti-inflammatory, anticancer, antimicrobial and immune-modulatory activity. These molecules gained importance due to their broad-spectrum pharmacological activities, and hence being actively investigated. Presently, respiratory infections represent a major global health problem, and HDP has an enormous potential to be used as an alternative therapeutics against respiratory infections and related inflammatory ailments. Because of their short half-life, protease sensitivity, poor pharmacokinetics, and first-pass metabolism, it is challenging to deliver HDP as such inside the physiological system in a controlled way by conventional delivery systems. Many HDPs are efficacious only at practically high molar-concentrations, which is not convincing for the development of drug regimen due to their intrinsic detrimental effects. To avail the efficacy of HDP in pulmonary diseases, it is essential to deliver an appropriate payload into the targeted site of lungs. Inhalable HDP can be a potentially suitable alternative for various lung disorders including tuberculosis, Cystic fibrosis, Pneumonia, Lung cancer, and others as they are active against resistant microbes and cells and exhibit improved targeting with reduced adverse effects. In this review, we give an overview of the pharmacological efficacy of HDP and deliberate strategies for designing inhalable formulations for enhanced activity and issues related to their clinical implications.

Graphene Oxide for Integrated Photonics and Flat Optics

With superior optical properties, high flexibility in engineering its material properties, and strong capability for large-scale on-chip integration, graphene oxide (GO) is an attractive solution for on-chip integration of 2D materials to implement functional integrated photonic devices capable of new features. Over the past decade, integrated GO photonics, representing an innovative merging of integrated photonic devices and thin GO films, has experienced significant development, leading to a surge in many applications covering almost every field of optical sciences such as photovoltaics, optical imaging, sensing, nonlinear optics, and light emitting. This paper reviews the recent advances in this emerging field, providing an overview of the optical properties of GO as well as methods for the on-chip integration of GO. The main achievements made in GO hybrid integrated photonic devices for diverse applications are summarized. The open challenges as well as the potential for future improvement are also discussed.

Interaction of peptides with cell membranes: insights from molecular modeling

The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.

In silico design of antimicrobial peptides

The rapid spread of drug-resistant pathogenic microbial strains has created an urgent need for the development of new anti-infective molecules, having different mechanism of action in comparison to existing drugs. Natural antimicrobial peptides (AMPs) represent a novel class of molecules with a broad spectrum of activity and a low rate in inducing bacterial resistance. In particular, linear alpha-helical cationic antimicrobial peptides are among the most widespread membrane-disruptive AMPs in nature, representing a particularly successful structural arrangement of the innate defense against microbes. However, until now, many AMPs have failed in clinical trials because of several drawbacks that strongly limit their applicability such as degradation, cytotoxicity, and high production cost. Thus, to overcome the limitations of native peptides, a rational in silico approach to AMPs design becomes a promising strategy that drastically reduce production costs and the time required for evaluation of activity and toxicity. This chapter focuses on the strategies and methods for de novo design of potentially active AMPs. In particular, statistical-based design strategies and MD methods for modelling AMPs are elucidated.

Peptide-lipid interactions: experiments and applications

The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining new potent pharmaceutical agents whose biological action is dependent on the binding of peptides to lipid-bilayers. Several issues need to be addressed such as secondary structure, orientation, oligomerization and localization inside the membrane. At the same time, the structural effects which the peptides cause on the lipid bilayer are important for the interactions and need to be elucidated. The structural characterization of membrane active peptides in membranes is a harsh experimental challenge. It is in fact accepted that no single experimental technique can give a complete structural picture of the interaction, but rather a combination of different techniques is necessary.

Multiscale molecular dynamics simulations of membrane proteins

The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.

Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study

Molecular mechanisms of the action of antimicrobial peptides on bacterial membranes were studied by large scale coarse-grained simulations of magainin 2-dipalmitoylphosphatidylcholine/palmitoyloleoylphosphatidylglycerol (DPPC/POPG) mixed bilayer systems with spatial extents up to 0.1 μm containing up to 1600 peptides. Equilibrium simulations exhibit disordered toroidal pores stabilized by peptides. However, when a layer of peptides is placed near the lipid head groups on one side of the bilayer only, their incorporation leads to a spontaneous buckling of the bilayer. This buckling is followed by the formation of a quasi-spherical vesicular bud connected to the bilayer by a narrow neck. The mean curvature of the budding region is consistent with what is expected based on the dependence of the area per lipid on the peptide-to-lipid ratio in equilibrium simulations. Our simulations suggest that the incorporation of antimicrobial peptides on the exterior surface of a vesicle or a bacterial cell leads to buckling and vesicle budding, presumably accompanied by nucleations of giant transient pores of sizes that are much larger than indicated by equilibrium measurements and simulations.

Structural aspects of lipid monolayers: computer simulation analyses

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided.

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

Antimicrobial peptides (AMPs) comprise a large family of peptides that include small cationic peptides, such as magainins, which permeabilize lipid membranes. Previous atomistic level simulations of magainin-H2 peptides show that they act by forming toroidal transmembrane pores. However, due to the atomistic level of description, these simulations were necessarily limited to small system sizes and sub-microsecond time scales. Here, we study the long-time relaxation properties of these pores by evolving the systems using a coarse-grain (CG) description. The disordered nature and the topology of the atomistic pores are maintained at the CG level. The peptides sample different orientations but at any given time, only a few peptides insert into the pore. Key states observed at the CG level are subsequently back-transformed to the atomistic level using a resolution-transformation protocol. The configurations sampled at the CG level are stable in the atomistic simulation. The effect of helicity on pore stability is investigated at the CG level and we find that partial helicity is required to form stable pores. We also show that the current CG scheme can be used to study spontaneous poration by magainin-H2 peptides. Overall, our simulations provide a multi-scale view of a fundamental biophysical membrane process involving a complex interplay between peptides and lipids.

Cause and effect of melittin-induced pore formation: a computational approach

Melittin embedded in a palmitoyl oleyl phosphatidylcholine bilayer at a high peptide/lipid ratio (1:30) was simulated in the presence of explicit water and ions. The simulation results indicate the incipience of an ion-permeable water pore through collective membrane perturbation by bound peptides. The positively charged residues of melittin not only act as "anchors" but also disrupt the membrane, leading to cell lysis. A detailed analysis of the lipid tail order parameter profile depicts localized membrane perturbation. The lipids in the vicinity of the aqueous cavity adopt a tilted conformation, which allows local bilayer thinning. The prepore thus formed can be considered as the melittin-induced structural defects in the bilayer membrane. Because of the strong cationic nature, the melittin-induced prepore exhibits selectivity toward anions over cations. As Cl(-) ions entered into the prepore, they are electrostatically entrapped by positively charged residues located at its wall. The confined motion of the Cl(-) ions in the membrane interior is obvious from calculated diffusion coefficients. Moreover, reorientation of the local lipids occurs in such a way that few lipid heads along with peptide helices can line the surface of the penetrating aqueous phase. The flipping of lipids argued in favor of melittin-induced toroidal pore over a barrel-stave mechanism. Thus, our result provides atomistic level details of the mechanism of membrane disruption by antimicrobial peptide melittin.

Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure

The rugged energy landscape of biomolecules and associated large-scale conformational changes have triggered the development of many innovative enhanced sampling methods, either based or not based on molecular dynamics (MD) simulations. Surveyed here are methods in the latter class - including Monte Carlo methods, harmonic approximations, and coarse graining - many of which yield valuable conformational insights into biomolecular structure and flexibility, despite altered kinetics. MD-based methods are surveyed in an upcoming issue of F1000 Biology Reports.