Protein-induced membrane disorder: a molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer

Structural Phenomena in a Vesicle Membrane Obtained through an Evolution Experiment: A Study Based on MD Simulations

The chemical evolution of biomolecules was clearly affected by the overall extreme environmental conditions found on Early Earth. Periodic temperature changes inside the Earth's crust may have played a role in the emergence and survival of functional peptides embedded in vesicular compartments. In this study, all-atom molecular dynamic (MD) simulations were used to elucidate the effect of temperature on the properties of functionalized vesicle membranes. A plausible prebiotic system was selected, constituted by a model membrane bilayer from an equimolar mixture of long-chain fatty acids and fatty amines, and an octapeptide, KSPFPFAA, previously identified as an optimized functional peptide in an evolution experiment. This peptide tends to form the largest spontaneous aggregates at higher temperatures, thereby enhancing the pore-formation process and the eventual transfer of essential molecules in a prebiotic scenario. The analyses also suggest that peptide-amphiphile interactions affect the structural properties of the membrane, with a significant increase in the degree of interdigitation at the lowest temperatures under study.

Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities

The emergence of new pathogens and multidrug resistant bacteria is an important public health issue that requires the development of novel classes of antibiotics. Antimicrobial peptides (AMPs) are a promising platform with great potential for the identification of new lead compounds that can combat the aforementioned pathogens due to their broad-spectrum antimicrobial activity and relatively low rate of resistance emergence. AMPs of multicellular organisms made their debut four decades ago thanks to ingenious researchers who asked simple questions about the resistance to bacterial infections of insects. Questions such as "Do fruit flies ever get sick?", combined with pioneering studies, have led to an understanding of AMPs as universal weapons of the immune system. This review focuses on a subclass of AMPs that feature a metal binding motif known as the amino terminal copper and nickel (ATCUN) motif. One of the metal-based strategies of hosts facing a pathogen, it includes wielding the inherent toxicity of copper and deliberately trafficking this metal ion into sites of infection. The sudden increase in the concentration of copper ions in the presence of ATCUN-containing AMPs (ATCUN-AMPs) likely results in a synergistic interaction. Herein, we examine common structural features in ATCUN-AMPs that exist across species, and we highlight unique features that deserve additional attention. We also present the current state of knowledge about the molecular mechanisms behind their antimicrobial activity and the methods available to study this promising class of AMPs.

Mechanistic Landscape of Membrane-Permeabilizing Peptides

Membrane permeabilizing peptides (MPPs) are as ubiquitous as the lipid bilayer membranes they act upon. Produced by all forms of life, most membrane permeabilizing peptides are used offensively or defensively against the membranes of other organisms. Just as nature has found many uses for them, translational scientists have worked for decades to design or optimize membrane permeabilizing peptides for applications in the laboratory and in the clinic ranging from antibacterial and antiviral therapy and prophylaxis to anticancer therapeutics and drug delivery. Here, we review the field of membrane permeabilizing peptides. We discuss the diversity of their sources and structures, the systems and methods used to measure their activities, and the behaviors that are observed. We discuss the fact that "mechanism" is not a discrete or a static entity for an MPP but rather the result of a heterogeneous and dynamic ensemble of structural states that vary in response to many different experimental conditions. This has led to an almost complete lack of discrete three-dimensional active structures among the thousands of known MPPs and a lack of useful or predictive sequence-structure-function relationship rules. Ultimately, we discuss how it may be more useful to think of membrane permeabilizing peptides mechanisms as broad regions of a mechanistic landscape rather than discrete molecular processes.

Computational studies of peptide-induced membrane pore formation

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers

Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers. As well as, the structure of zwitterionic membranes was more affected by the peptide than the anionic bilayers. Taken together, the study demonstrated that the cationic residues of pardaxin snorkeled toward the interface of lipid bilayers and all phenylalanine residues of the peptide played important roles in the peptide-membrane interactions. We hope that this work will provide a better understanding of the interactions of antimicrobial peptides with the membranes.

How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption?

Molecular dynamics (MD) simulations are conducted to suggest a mechanism of action for the aminopropyl dibromocarbazole derivative (P7C3) small molecule, which protects neurons from apoptotic cell death. At first, the influence of embedded Aβ₄₂ stacks on the structure of membrane is studied. Then, the effect of P7C3 molecules on the Aβ₄₂ fibril enriched membrane and Aβ₄₂ fibril depleted membrane (when Aβ₄₂ fibrils are originally dissolved in the aqueous phase) are evaluated. Also, the formation of an amyloid ion channel in the Aβ₄₂ enriched membrane is examined by calculating deuterium order parameter, density profile, and surface thickness. For Aβ₄₂ in the fully inserted state, ion channel-like structures are formed. The presence of P7C3 molecules in this case just postpones membrane destruction but could not prevent pore formation. In contrast, when both Aβ₄₂ and P7C3 molecules are embedded in the aqueous solution, the P7C3 molecules are self-assembled at membrane/ionic aqueous solution interface and prevent the precipitation and deposition of Aβ₄₂ fibrils into the membrane.

Aggregation and insertion of melittin and its analogue MelP5 into lipid bilayers at different concentrations: effects on pore size, bilayer thickness and dynamics

Melittin and its analogue MelP5 (five mutations T10A, R22A, K23A, R24Q, and Q26L of melittin) were simulated with lipid bilayers at different peptide/lipid molar ratios using all-atom and coarse-grained (CG) force fields.

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.

SLIM: an improved generalized Born implicit membrane model

In most implicit continuum models, membranes are represented as heterogeneous dielectric environments, but their treatment within computationally efficient generalized Born (GB) models is challenging. Despite several previous attempts, an adequate description of multiple dielectric regions in implicit GB-based membrane models that reproduce the qualitative and quantitative features of Poisson-Boltzmann (PB) electrostatics remains an unmet prerequisite of qualitatively correct implicit membrane models. A novel scheme (SLIM) to decompose one environment consisting of multiple dielectric regions into a sum of multiple environments consisting only of two dielectric regions each is proposed to solve this issue. These simpler environments can be treated with established GB methods. This approach captures qualitative features of PB electrostatic that are not present in previous models. Simulations of three membrane proteins demonstrate that this model correctly reproduces known properties of these proteins in agreement with experimental or other computational studies.

Vertical ordering sensitivity of solid supported DPPC membrane to alamethicin and the related loss of cell viability

BACKGROUND

Experimental studies of antimicrobial peptides interacting with lipid membranes recently attracted growing interest due to their numerous biomedical applications. However, the influence of such peptides on the structural organisation of lipid membranes in connection with the actual cell response still remains an elusive issue.

METHODS

X-ray diffraction was employed on detecting the sensitivity of the periodical spacing of dipalmitoyl-phosphatidyl-choline stacked as solid-supported bilayers to the presence of varying amounts of the peptide alamethicin in a wide range of peptide-to-lipid molar ratios. These results were then correlated with the effects of alamethicin on biological membranes in vitro as observed by optical microscopy and microculture tetrazolium assay on the tumour cells HeLa to provide a comprehensive and quantitative analysis of these effects, based on a dose-response relationship.

RESULTS

The experiments allowed correlating the periodical spacing and the peptide-to-lipid molar ratio on alamethicin-dipalmitoyl-phosphatidyl-choline samples. Two different trends of periodical spacing vs. peptide-to-lipid molar ratio clearly appeared at low and high hydration levels, showing intriguing non-linear profiles. Unexpected correspondences were observed between the peptide-to-lipid molar ratio range where the changes in dipalmitoyl-phosphatidyl-choline structure occur and the alamethicin doses which alter the viability and the plasma membrane morphology of HeLa.

CONCLUSIONS

Alamethicin might induce either mechanical or phase changes on dipalmitoyl-phosphatidyl-choline bilayers. Such easily accessible ordering information was well-calibrated to predict the alamethicin doses necessary to trigger cell death through plasma membrane alterations.

GENERAL SIGNIFICANCE

This benchmark combined study may be valuable to predict bioeffects of several antimicrobial peptides of biomedical relevance.

Molecular dynamic studies of transportan interacting with a DPPC lipid bilayer

Translocation of peptides through cellular membranes is a fundamental problem in developing antimicrobial peptides and in drug delivery. There is a class of peptides, known as cell-penetrating peptides, that are able to penetrate membranes without disrupting them. They can carry pharmacological compounds, thus a promising strategy for drug delivery. The physical mechanisms that facilitate translocation are not known. We have used large-scale molecular dynamics simulations to study the penetration of transportan across a zwitterionic dipalmitoyl-phosphatidyl-choline (DPPC) bilayer. We obtained the free energy profile for one peptide inside the bilayer and discuss the response of the bilayer to the presence of transportan. We also discuss the importance of lysine residues and speculate on the possible penetration mechanism of the peptide and propose a graded-like penetration process.

Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation

Bovine lactoferrampin (LFampinB) is a newly discovered antimicrobial peptide found in the N1-domain of bovine lactoferrin (268-284), and consists of 17 amino-acid residues. It is important to determine the orientation and structure of LFampinB in bacterial membranes to reveal the antimicrobial mechanism. We therefore performed (13)C and (31)P NMR, (13)C-(31)P rotational echo double resonance (REDOR), potassium ion-selective electrode, and quartz-crystal microbalance measurements for LFampinB with mimetic bacterial membrane and molecular-dynamics simulation in acidic membrane. (31)P NMR results indicated that LFampinB caused a defect in mimetic bacterial membranes. Ion-selective electrode measurements showed that ion leakage occurred for the mimetic bacterial membrane containing cardiolipin. Quartz-crystal microbalance measurements revealed that LFampinB had greater affinity to acidic phospholipids than that to neutral phospholipids. (13)C DD-MAS and static NMR spectra showed that LFampinB formed an α-helix in the N-terminus region and tilted 45° to the bilayer normal. REDOR dephasing patterns between carbonyl carbon nucleus in LFampinB and phosphorus nuclei in lipid phosphate groups were measured by (13)C-(31)P REDOR and the results revealed that LFampinB is located in the interfacial region of the membrane. Molecular-dynamics simulation showed the tilt angle to be 42° and the rotation angle to be 92.5° for Leu(3), which are in excellent agreement with the experimental values.

Molecular dynamics simulations and conductance studies of the interaction of VP1 N-terminus from Polio virus and gp41 fusion peptide from HIV-1 with lipid membranes

The icosahedral Polio virus capsid consists of 60 copies of each of the coat proteins VP1, VP2, VP3 and myristolyated VP4 (myrVP4). Catalyzed by the host cell receptor the Polio virus enters the host cell via externalization of myrVP4 and the N terminal part of VP1. There are several assumptions about the individual role of both of the proteins in the mechanism of membrane attachment and genome injection. We use the first 32 N terminal amino acids of VP1 and applied molecular dynamics simulations to assess its mechanism of function when attached and inserted into hydrated lipid membranes (POPC). Helical models are placed in various positions in regard to the lipid membrane to start with. As a comparison, the first 33 amino acids of the fusion peptide of gp41 of HIV-1 are simulated under identical conditions. Computational data support the idea that VP1 is not penetrating into the membrane to form a pore; it rather lays on the membrane surface and only perturbs the membrane. Furthermore, this idea is strengthened by channel recordings of both peptides showing irregular openings.

Molecular dynamics simulation of Bombolitin II in the dipalmitoylphosphatidylcholine membrane bilayer

The orientation behavior of Bombolitin II (BLT2) in the dipalmitoylphosphatidylcholine membrane bilayer was investigated by using molecular-dynamics simulation. During the 20-ns simulation, the BLT2 began to tilt and finally reached the angle of 51° from the membrane-normal. The structure of the peptide formed the amphipathic α-helical structure during the entire simulation time. The peptide tilts with its hydrophobic side faced to the hydrophobic core of the bilayer. We analyzed the mechanism of the tilting behavior of the peptide associated with the membrane in detail. The analysis showed that the hydrogen-bond interaction and the electrostatic interaction were found to exist between Lys(12) and a lipid molecule. These interactions are considered to work as an important factor in tilting the peptide to the membrane-normal.

Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.

Protein folding in a reverse micelle environment: the role of confinement and dehydration

Characterization of the molecular interactions that stabilize the folded state of proteins including hydrogen bond formation, solvation, molecular crowding, and interaction with membrane environments is a fundamental goal of theoretical biophysics. Inspired by recent experimental studies by Gai and co-workers, we have used molecular dynamics simulations to explore the structure and dynamics of the alanine-rich AKA(2) peptide in bulk solution and in a reverse micelle environment. The simulated structure of the reverse micelle shows substantial deviations from a spherical geometry. The AKA(2) peptide is observed to (1) remain in a helical conformation within a spherically constrained reverse micelle and (2) partially unfold when simulated in an unconstrained reverse micelle environment, in agreement with experiment. While aqueous solvation is found to stabilize the N- and C-termini random coil portions of the peptide, the helical core region is stabilized by significant interaction between the nonpolar surface of the helix and the aliphatic chains of the AOT surfactant. The results suggest an important role for nonpolar peptide-surfactant and peptide-lipid interactions in stabilizing helical geometries of peptides in reverse micelle environments.

Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer

We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces β-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal β-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment.

Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state (31)P and (13)C NMR spectroscopy. (31)P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (T(c)) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the T(c). (13)C NMR spectra of site-specifically (13)C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers.

Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes

Many physical chemical properties of lipid membranes, for example, the thickness, phase state, order parameter, and fluidity, can be understood straightforwardly. Water residence on a membrane is, however, an exception. To tackle this problem, we have performed molecular dynamics simulations of the distribution of water normal to the surface of several lipid membranes and from this deduced the associated water residence time. Our analysis of the results clearly indicates that lipid membranes have hydration shells on their surface, just as a solute in an aqueous solution does, and that the water residence time can be estimated from the potential for the mean force field derived from the distribution function of the water. We have done this atomic-scale analysis for ceramide bilayers and contrasted the calculation results with those for sphingomyelin bilayers, revealing that sphingomyelin bilayers can retain water molecules longer than ceramide bilayers and that the total number of water molecules retained on the membrane surface of sphingomyelin is larger than that for ceramide. In addition, we find that not only polar atoms of lipid molecules, such as oxygen, but also non-polar atoms, such as carbon, influence the motion of water on the membranes.

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.

Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study

The etiology of Alzheimer's disease is considered to be linked to interactions between amyloid beta-peptide (Abeta) and neural cell membranes. Membrane disruption and increased ion conductance have been observed in vitro in the presence of Abeta, and it is assumed that these same phenomena occur in the brain of an individual afflicted with Alzheimer's. The effects of Abeta on lipid behavior have been characterized experimentally, but details are lacking regarding how Abeta induces these effects. Simulations of Abeta in a bilayer environment can provide the resolution necessary to explain how the peptide interacts with the surrounding lipids. In the present study, we present an extensive analysis of lipid parameters for a model dipalmitoylphosphatidylcholine bilayer in the presence of the 40-residue Abeta peptide (Abeta40). The simulated systems examine the effects of the insertion depth of the peptide, temperature, the protonation state of the peptide, and ionic strength on the features of the lipid bilayer. The results show that Abeta40 is capable of disordering nearby lipids, as well as decreasing bilayer thickness and area per lipid headgroup. These phenomena arise as a result of the unfolding process of the peptide, which leads to a disordered, extended conformation that is capable of extensive electrostatic and hydrogen-bonding interactions between the peptide and the lipid headgroups. Comparisons are made using melittin-dipalmitoylphosphatidylcholine systems as positive controls of a membrane-disrupting peptide because these systems have previously been characterized experimentally as well as in molecular dynamics simulations.

Monitoring orientation and dynamics of membrane-bound melittin utilizing dansyl fluorescence

Melittin is a cationic hemolytic peptide isolated from the European honey bee, Apis mellifera. In spite of a number of studies, there is no consensus regarding the orientation of melittin in membranes. In this study, we used a melittin analogue that is covalently labeled at its amino terminal (Gly-1) with the environment-sensitive 1-dimethylamino-5-sulfonylnaphthalene (dansyl) group to obtain information regarding the orientation and dynamics of the amino terminal region of membrane-bound melittin. Our results show that the dansyl group in Dns-melittin exhibits red edge excitation shift in vesicles of 1,2-dioleoyl-sn-glycero-3-phosphocholine, implying its localization in a motionally restricted region of the membrane. This is further supported by wavelength-dependent anisotropy and lifetime changes and time-resolved emission spectra characterized by dynamic Stokes shift, which indicates relatively slow solvent relaxation in the excited state. Membrane penetration depth analysis using the parallax method shows that the dansyl group is localized at a depth of approximately 18 A from the center of the bilayer in membrane-bound Dns-melittin. Further analysis of dansyl and tryptophan depths in Dns-melittin shows that the tilt angle between the helix axis of membrane-bound melittin and the bilayer normal is approximately 70 degrees. Our results therefore suggest that melittin adopts a pseudoparallel orientation in DOPC membranes at low concentration.

Molecular dynamics simulations of Na+/Cl(-)-dependent neurotransmitter transporters in a membrane-aqueous system

We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate 5-HT or the selective serotonin reuptake inhibitor escitalopram. We have also included a transporter homologue, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystallographic B factors. Furthermore, key interactions identified in the X-ray structure of LeuT are maintained throughout the simulations indicating that our simple membrane system is suitable for studying the transmembrane protein hSERT in complex with 5-HT or escitalopram. For these transporter complexes, only relatively small fluctuations are observed in the ligand-binding cleft. Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitalopram complexes. Our findings are in good agreement with predictions from mutagenesis studies.

The impact of peptides on lipid membranes

We review the fundamental strategies used by small peptides to associate with lipid membranes and how the different strategies impact on the structure and dynamics of the lipids. In particular we focus on the binding of amphiphilic peptides by electrostatic and hydrophobic forces, on the anchoring of peptides to the bilayer by acylation and prenylation, and on the incorporation of small peptides that form well-defined channels. The effect of lipid-peptide interactions on the lipids is characterized in terms of lipid acyl-chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation, as well as acyl-chain dynamics. The different situations are illustrated by specific cases for which experimental observations can be interpreted and supplemented by theoretical modeling and simulations. A comparison is made with the effect on lipids of trans-membrane proteins. The various cases are discussed in the context of the possible roles played by lipid-peptide interactions for the biological, physiological, and pharmacological function of peptides.

A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer

Because the amyloid beta-peptide (Abeta) functions as approximately half of the transmembrane domain of the amyloid precursor protein and interaction of Abeta with membranes is proposed to result in neurotoxicity, the association of Abeta with membranes likely is important in the etiology of Alzheimer's disease. Atomic details of the interaction of Abeta with membranes are not accessible with most experimental techniques, but computational methods can provide this information. Here, we present the results of ten 100-ns molecular dynamics (MD) simulations of the 40-residue amyloid beta-peptide (Abeta40) embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer. The present study examines the effects of insertion depth, protonation state of key residues, and ionic strength on Abeta40 in a DPPC bilayer. In all cases, a portion of the peptide remained embedded in the bilayer. In the case of deeper insertion depth, Abeta40 adopted a near-transmembrane orientation, drawing water molecules into the bilayer to associate with its charged amino acids. In the case of shallower insertion, the most widely-accepted construct, the peptide associated strongly with the membrane-water interface and the phosphatidylcholine headgroups of the bilayer. In most cases, significant disordering of the extracellular segment of the peptide was observed, and the brief appearance of a beta-strand was noted in one case. Our results compare well with a variety of experimental and computational findings. From this study, we conclude that Abeta associated with membranes is dynamic and capable of adopting a number of conformations, each of which may have significance in understanding the progression of Alzheimer's disease.

Melittin: a membrane-active peptide with diverse functions

Melittin is the principal toxic component in the venom of the European honey bee Apis mellifera and is a cationic, hemolytic peptide. It is a small linear peptide composed of 26 amino acid residues in which the amino-terminal region is predominantly hydrophobic whereas the carboxy-terminal region is hydrophilic due to the presence of a stretch of positively charged amino acids. This amphiphilic property of melittin has resulted in melittin being used as a suitable model peptide for monitoring lipid-protein interactions in membranes. In this review, the solution and membrane properties of melittin are highlighted, with an emphasis on melittin-membrane interaction using biophysical approaches. The recent applications of melittin in various cellular processes are discussed.

Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers

We have previously demonstrated that some poly(alkylthiophenes) (PATs) are able to increase the electrical conductance of unsupported phospholipid bilayers and have hypothesized that this effect is due to the ability of some PAT side chains to permit stable insertion into the bilayer. We have further proposed the development of long-term intracellular electrodes based on that phenomenon. In this article, we apply molecular dynamics techniques to study the insertion of two model PATs into a patch of a lipid bilayer. Steered molecular dynamics is used to obtain potential trajectories of insertion, followed by umbrella sampling to determine the free-energy change upon insertion. Our results indicate that both branched-side-chain poly(3-(2-ethylhexyl)thiophene) (EHPT) and straight-side-chain poly(3-hexylthiophene) (HPT) are able to enter the bilayer but only EHPT can cross the center of the membrane and establish an electrical bridge. HPT penetrates the head groups but is not able to enter the alkyl tail phase. These findings support the feasibility of our electrode concept and raise questions regarding the mechanisms by which branched side chains grant PATs greater solubility in a lipid bilayer environment. The parameters and methods used in this study establish a novel framework for studying these and similar systems, and the results hold promise for the use of EHPT in biosensing and neural interfacing.

Molecular dynamics studies of the molecular structure and interactions of cholesterol superlattices and random domains in an unsaturated phosphatidylcholine bilayer membrane

The effect of the molecular organization of lipid components on the properties of the bilayer membrane has been a topic of increasing interest. Several experimental and theoretical studies have suggested that cholesterol is not randomly distributed in the fluid-state lipid bilayer but forms nanoscale domains. Several cholesterol-enriched nanodomain structures have been proposed, including rafts, regular or maze arrays, complexes, and superlattices. At present, the molecular mechanisms by which lipid composition influences the formation and stability of lipid nanodomains remain unclear. In this study, we have used molecular dynamics (MD) simulations to investigate the effects of the molecular organization of cholesterol--superlattice versus random--on the structure of and interactions between lipids and water in lipid bilayers of cholesterol and 1-palmitoyl-2-oleoylphosphatidylcholine (cholesterol/POPC) at a fixed cholesterol mole fraction of 0.40. On the basis of four independent replicates of 200-ns MD simulations for a superlattice or random bilayer, statistically significant differences were observed in the lipid structural parameters, area per lipid, density profile, and acyl chain order profile, as well as the hydrogen bonding between various pairs (POPC and water, cholesterol and water, and POPC and cholesterol). The time evolution of the radial distribution of the cholesterol hydroxy oxygen suggests that the lateral distribution of cholesterol in the superlattice bilayer is more stable than that in the random bilayer. Furthermore, the results indicate that a relatively long simulation time, more than 100 ns, is required for these two-component bilayers to reach equilibrium and that this time is influenced by the initial lateral distribution of lipid components.

Transmembrane Helix Packing of ErbB/Neu Receptor in Membrane Environment: A Molecular Dynamics Study

Dimerization or oligomerization of the ErbB/Neu receptors are necessary but not sufficient for initiation of receptor signaling. The two intracellular domains must be properly oriented for the juxtaposition of the kinase domains allowing trans-phosphorylation. This suggests that the transmembrane (TM) domain acts as a guide for defining the proper orientation of the intracellular domains. Two structural models, with the two helices either in left-handed or in right-handed coiling have been proposed as the TM domain structure of the active receptor. Because experimental data do not distinguish clearly helix-helix packing, molecular dynamics (MD) simulations are used to investigate the energetic factors that drive Neu TM-TM interactions of the wild and the oncogenic receptor (Val664/Glu mutation) in DMPC or in POPC environments. MD results indicate that helix-lipid interactions in the bilayer core are extremely similar in the two environments and raise the role of the juxtamembrane residues in helix insertion and helix-helix packing. The TM domain shows a greater propensity to adopt a left-handed structure in DMPC, with helices in optimal position for strong inter-helical Hbonds induced by the Glu mutation. In POPC, the right-handed structure is preferentially formed with the participation of water in inter-helical Hbonds. The two structural arrangements of the Neu(TM) helices both with GG4 residue motif in close contact at the interface are permissible in the membrane environment. According to the hypothesis of a monomer-dimer equilibrium of the proteins it is likely that the bilayer imposes structural constraints that favor dimerization-competent structure responsible of the proper topology necessary for receptor activation.

Orientation and dynamics of melittin in membranes of varying composition utilizing NBD fluorescence

Melittin is a cationic hemolytic peptide isolated from the European honey bee, Apis mellifera. The organization of membrane-bound melittin has earlier been shown to be dependent on the physical state and composition of membranes. In this study, we covalently labeled the N-terminal (Gly-1) and Lys-7 of melittin with an environment-sensitive fluorescent probe, the NBD group, to monitor the influence of negatively charged lipids and cholesterol on the organization and dynamics of membrane-bound melittin. Our results show that the NBD group of melittin labeled at its N-terminal end does not exhibit red edge excitation shift in DOPC and DOPC/DOPG membranes, whereas the NBD group of melittin labeled at Lys-7 exhibits REES of approximately 8 nm. This could be attributed to difference in membrane microenvironment experienced by the NBD groups in these analogs. Interestingly, the membrane environment of the NBD groups is sensitive to the presence of cholesterol, which is supported by time-resolved fluorescence measurements. Importantly, the orientation of melittin is found to be parallel to the membrane surface as determined by membrane penetration depth analysis using the parallax method in all cases. Our results constitute the first report to our knowledge describing the orientation of melittin in cholesterol-containing membranes. These results assume significance in the overall context of the role of membrane lipids in the orientation and function of membrane proteins and peptides.

Phospholipid Bilayer Free Volume Analysis Employing the Thermal Ring-Closing Reaction of Merocyanine Molecular Switches

The free volume properties of phospholipid bilayers have been determined using a new assay that applies the photochromic and solvatochromic properties of merocyanines. The orientation and embedding depth of the merocyanines in the bilayer are controlled using substitution on the merocyanine indole moiety. The free volume changes at the aqueous interface (region 1), the phospholipid headgroup (region 2), and the aliphatic interior (region 3) of the bilayer are compared by analyzing the rate constants for the merocyanine ring-closing reaction. Free volume variations during the P(beta)(')(gel) <--> L(alpha)(liquid) phase transition are observed in region 1, in accordance with large structural rearrangements between the gel and the liquid phases in this region. The largest free volume is found in region 3, and the smallest is found in region 2. This distribution of free volume in the bilayer agrees with computational studies of these systems. Comparison of the free volume in region 2 of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids shows that this method is sensitive to small structural differences between lipids. In region 2, the free volume is found to be approximately 2 times larger in DPPC bilayers, which could be related to different merocyanine interactions with the two phosphatidylcholines. Free volume properties determined on picosecond and second time scales are compared based on an analysis of merocyanine formation and decoloration reactions.

Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level.