Membrane Binding Of Peptides Research Articles

Computational investigation of the effect of BODIPY labelling on peptide-membrane interaction.

Optical monitoring of peptide binding to live cells is hampered by the abundance of naturally occurring fluorophores such as tryptophan. Unnatural amino acids incorporating synthetic fluorophores such as BODIPY overcome these optical limitations. A drawback to using fluorophores in lipid binding peptide design is their propensity to override other interactions, potentially causing the peptides to lose their binding selectivity. Here, the binding strength of a selection of peptides incorporating a variety of BODIPY derivatized amino acids has been studied via molecular dynamics simulations to quantify the impact of BODIPY incorporation on peptide-membrane binding behaviour.

Hydrophobic Matching Dictates over the Linear Rule of Mixtures in Binary Lipid Membranes.

Biological membranes feature heterogeneous mixtures of lipids with different head and tail characteristics. Their biophysical properties are dictated by the intimate interaction among different constituent lipids. Previous studies suggest that the membrane area-per-lipid (APL) deviates from the linear rule of mixtures (LRM) for binary lipid membranes, but the underlying mechanism remains elusive. Our molecular dynamics (MD) simulations of binary lipid membranes consisting of lipids with different tail characteristics reveal a competitive mechanism whereby lipids tend to deform each other to minimize the hydrophobic mismatch between their tails. Depending on the relative tail lengths and saturation levels, this may result in an either positive or negative deviation of APL from the LRM. As lipid packing plays an essential role in membrane fusion and peptide-membrane binding, our findings may help guide the selection of lipids for the effective rational design of nanoliposomes and membrane-targeting peptides.

Peptide-Membrane Binding: Effects of the Amino Acid Sequence.

An understanding of how the amino acid sequence affects the interaction of peptides with lipid membranes remains mostly unknown. This type of knowledge is required to rationalize membrane-induced toxicity of amyloid peptides and to design peptides that can interact with lipid bilayers. Here, we perform a systematic study of how variations in the sequence of the amphipathic Ac-(FKFE)2-NH2 peptide affect its interaction with zwitterionic lipid bilayers using extensive all-atom molecular dynamics simulations in explicit solvent. Our results show that peptides with a net positive charge bind more frequently to the lipid bilayer than neutral or negatively charged sequences. Moreover, neutral amphipathic peptides made with the same numbers of phenylalanine (F), lysine (K), and glutamic (E) amino acids at different positions in the sequence differ significantly in their frequency of binding to the membrane. We find that peptides bind with a higher frequency to the membrane if their positive lysine side chains are more exposed to the solvent, which occurs if they are located at the extremity (as opposed to the middle) of the sequence. Non-polar residues play an important role in accounting for the adsorption of peptides onto the membrane. In particular, peptides made with less hydrophobic non-polar residues (e.g., valine and alanine) are significantly less adsorbed to the membrane compared to peptides made with phenylalanine. We also find that sequences where phenylalanine residues are located at the extremities of the peptide have a higher tendency to be adsorbed.

Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism.

The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.

Peptide-membrane binding is not enough to explain bioactivity: A case study

Membrane-active peptides are a promising class of antimicrobial and anticancer therapeutics. For this reason, their molecular mechanisms of action are currently actively investigated. By exploiting Electron Paramagnetic Resonance, we study the membrane interaction of two spin-labeled analogs of the antimicrobial and cytotoxic peptide trichogin GA IV (Tri), with opposite bioactivity: Tri(Api8), able to selectively kill cancer cells, and Tri(Leu4), which is completely nontoxic. In our attempt to determine the molecular basis of their different biological activity, we investigate peptide impact on the lateral organization of lipid membranes, peptide localization and oligomerization, in the zwitter-ionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane We show that, despite their divergent bioactivity, both peptide analogs (i) are membrane-bound, (ii) display a weak tendency to oligomerization, and (iii) do not induce significant lipid rearrangement. Conversely, literature data show that the parent peptide trichogin, which is cytotoxic without any selectivity, is strongly prone to dimerization and affects the reorganization of POPC membranes. Its dimers are involved in the rotation around the peptide helix, as observed at cryogenic temperatures in the millisecond timescale. Since this latter behavior is not observed for the inactive Tri(Leu4), we propose that for short-length peptides as trichogin oligomerization and molecular motions are crucial for bioactivity, and membrane binding alone is not enough to predict or explain it. We envisage that small changes in the peptide sequence that affect only their ability to oligomerize, or their molecular motions inside the membrane, can tune the peptide activity on membranes of different compositions.

Lipid Headgroup Charge Controls Melittin Oligomerization in Membranes: Implications in Membrane Lysis.

Melittin, a hemolytic peptide present in bee venom, represents one of the most well-studied amphipathic antimicrobial peptides, particularly in terms of its membrane interaction and activity. Nevertheless, no consensus exists on the oligomeric state of membrane-bound melittin. We previously reported on the differential microenvironments experienced by melittin in zwitterionic and negatively charged phospholipid membranes. In this work, we explore the role of negatively charged lipids in the oligomerization of membrane-bound melittin (labeled with 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)) utilizing a quantitative photobleaching homo-FRET assay. Our results show that the presence of negatively charged lipids decreases melittin oligomeric size to ∼50% of that observed in zwitterionic membranes. This is possibly due to differential energetics of binding of the peptide monomer to membranes of different compositions and could explain the reduced lytic activity yet tighter binding of melittin in negatively charged membranes. These results constitute one of the first experimental observations on the role of phospholipid headgroup charge in the oligomerization of melittin in membranes and is relevant in light of previous apparently contradictory reports on oligomerization of membrane-bound melittin. Our results highlight the synergistic interplay of peptide-membrane binding events and peptide oligomerization in modulating the organization, dynamics, and function of amphipathic α-helical peptides.

Membrane partitioning and lipid selectivity of the N-terminal amphipathic H0 helices of endophilin isoforms

Endophilin is an N-BAR protein, which is characterized by a crescent-shaped BAR domain and an amphipathic helix that contributes to the membrane binding of these proteins. The exact function of that H0 helix has been a topic of debate. In mammals, there are five different endophilin isoforms, grouped into A (three members) and B (two members) subclasses, which have been described to differ in their subcellular localization and function. We asked to what extent molecular properties of the H0 helices of these members affect their membrane targeting behavior.We found that all H0 helices of the endophilin isoforms display a two-state equilibrium between disordered and α-helical states in which the helical secondary structure can be stabilized through trifluoroethanol. The helicities in high TFE were strikingly different among the H0 peptides. We investigated H0-membrane partitioning by the monitoring of secondary structure changes via CD spectroscopy. We found that the presence of anionic phospholipids is critical for all H0 helices partitioning into membranes. Membrane partitioning is found to be sensitive to variations in membrane complexity. Overall, the H0 B subfamily displays stronger membrane partitioning than the H0 A subfamily. The H0 A peptide-membrane binding occurs predominantly through electrostatic interactions. Variation among the H0 A subfamily may be attributed to slight alterations in the amino acid sequence. Meanwhile, the H0 B subfamily displays greater specificity for certain membrane compositions, and this may link H0 B peptide binding to endophilin B's cellular function.

Flow Linear Dichroism of Protein-Membrane Systems.

Linear dichroism (LD) is the differential absorbance of light polarized parallel and perpendicular to an orientation direction. Any oriented sample will show a signal in its electronic as well as vibrational transitions. Model membrane small unilamellar vesicles or liposomes provide an oriented system when they are subject to shear flow in a Couette or other type of flow cell. Anything, including peptides and proteins, that is bound to the liposome also gives an LD signal whereas unbound analytes are invisible. Flow LD is the ideal technique for determining the orientation of different chromophores with respect to the membrane normal. To illustrate the power of the method, data for diphenyl hexatriene, fluorene, antimicrobial peptides (aurein 2.5 and gramicidin), are considered as well as another common chromophore, fluorene, often used to increase the hydrophobicity and hence membrane binding of peptides. How LD can be used both for geometry, structure analysis and probing kinetic processes is considered. Kinetic analysis usually involves identifying binding (appearance of an LD signal), insertion (sign change), often followed by loss of signal, if the inserted protein or peptide disrupts the membrane .

Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description.

Membranes are a crucial component of both bacterial and mammalian cells, being involved in signaling, transport, and compartmentalization. This versatility requires a variety of lipid species to tailor the membrane’s behavior as needed, increasing the complexity of the system. Molecular dynamics simulations have been successfully applied to study model membranes and their interactions with proteins, elucidating some crucial mechanisms at the atomistic detail and thus complementing experimental techniques. An accurate description of the functional interplay of the diverse membrane components crucially depends on the selected parameters that define the adopted force field. A coherent parameterization for lipids and proteins is therefore needed. In this work, we propose and validate new lipid head group parameters for the GROMOS 54A8 force field, making use of recently published parametrizations for key chemical moieties present in lipids. We make use additionally of a new canonical set of partial charges for lipids, chosen to be consistent with the parameterization of soluble molecules such as proteins. We test the derived parameters on five phosphocholine model bilayers, composed of lipid patches four times larger than the ones used in previous studies, and run 500 ns long simulations of each system. Reproduction of experimental data like area per lipid and deuterium order parameters is good and comparable with previous parameterizations, as well as the description of liquid crystal to gel-phase transition. On the other hand, the orientational behavior of the head groups is more realistic for this new parameter set, and this can be crucial in the description of interactions with other polar molecules. For that reason, we tested the interaction of the antimicrobial peptide lactoferricin with two model membranes showing that the new parameters lead to a weaker peptide–membrane binding and give a more realistic outcome in comparing binding to antimicrobial versus mammal membranes.

Synthesis and application of the blue fluorescent amino acid l-4-cyanotryptophan to assess peptide-membrane interactions.

Recently, l-4-cyanotryptophan has been shown to be an efficient blue fluorescence emitter, with the potential to enable novel applications in biological spectroscopy and microscopy. However, lack of facile synthetic routes to this unnatural amino acid limits its wide use. Herein, we describe an expedient approach to synthesize Fmoc protected l-4-cyanotryptophan with high optical purity (>99%). Additionally, we test the utility of this blue fluorophore in imaging cell-membrane-bound peptides and in determining peptide-membrane binding constants.

Molecular design of antimicrobial peptides based on hemagglutinin fusion domain to combat antibiotic resistance in bacterial infection.

Antimicrobial peptides are derived from the viral fusion domain of influenza virus hemagglutinin based on rational analysis of the intermolecular interaction between peptides and bacterial outer membrane. It is revealed that the isolated viral fusion domain is a negatively charged peptide HAfp1-23 that cannot effectively interact with the anionic membrane. Conversion of the native HAfp1-23 to a positively charged peptide HAfp1-23 _KK by E11K/D19K mutation can promote the peptide-membrane interaction substantially; this confers to the peptide a moderate antibacterial potency against antibiotic-resistant bacterial strains. Cyclization of the linear peptide HAfp1-23 _KK results in a cyclic peptide cHAfp1-23 _KK, which can largely minimize entropy penalty upon the peptide-membrane binding by pre-stabilizing peptide hairpin configuration in solvent, where the linear peptide would incur in a considerable conformational change/folding from intrinsic disorder (in water) to the structured hairpin conformation (in lipid). As might be expected, the cyclization considerably improves peptide antibacterial activity with minimum inhibitory concentration of 67 and 34μg/mL against multidrug-resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus, respectively.

First Example of Kinetic Modelling of Multi-state Membrane Binding, Exapnsion and Disruption for an Antimicrobial Peptide

Antimicrobial peptide disruption of the membrane bilayer involves a series of defined states during binding and insertion, and are all associated with significant changes in the bilayer structure. We recently identified a complex series of bilayer state changes for the binding of an analogue of magainin 2, (Ala-8,13,18)-Magainin 2-amide (MagA), to lipid bilayers. However, the presence of multiple structural states of the membrane prevented the determination of kinetic constants using currently available kinetic models, but this information is necessary to allow the full definition of the mechanism of action. In this study the binding and dissociation of MagA to lipid bilayers with different charge and fluidity properties was studied with dual polarization interferometry, an optical technique capable of measuring real-time simultaneous changes in mass and birefringence (an optical parameter representing bilayer order). The dependence of birefringence vs. mass were categorised into several discrete mechanistic profiles and new multiple-state kinetic models were developed and fitted to the experimental data, with a three-state model with lateral bilayer expansion providing distinctly superior fits to simpler model types. Overall this is the first study to quantitatively analyse complex peptide-membrane binding data in terms of specific states of membrane disruption by an antimicrobial peptide.

Microtubule modification influences cellular response to amyloid-β exposure

During the normal aging process, cytoskeletal changes such as a reduction in density or disruption of cytoskeletal components occur that can affect neuronal function. As aging is the biggest risk factor for Alzheimer's disease (AD), this study sought to determine how microtubule (MT) modification influences cellular response upon exposure to β-amyloid1-42 (Aβ1-42), which is implicated in AD. The MT networks of hypothalamic GT1-7 neurons were modified by common disrupting or stabilizing drugs, and then the physical and mechanical properties of the modified neurons were determined. The MT modified neurons were then exposed to Aβ1-42 and the ability of the neurons to cope with this exposure was determined by a variety of biochemical assays. Flow cytometry studies indicated that MT disruption reduced the binding of Aβ1-42 to the plasma membrane by 45% per cell compared to neurons with stabilized or unaltered MTs. Although the cells with disrupted MTs experienced less peptide-membrane binding, they experienced similar or increased levels of cytotoxicity caused by the Aβ1-42 exposure. In contrast, MT stabilization delayed toxicity caused by Aβ1-42. These results demonstrate that MT modification significantly influences the ability of neurons to cope with toxicity induced by Aβ1-42.

Peptide-Membrane Interactions by Spin-Labeling EPR.

Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a well-established method that has recently grown in popularity as an experimental technique, with multiple applications in protein and peptide science. The growth is driven by development of labeling strategies, as well as by considerable technical advances in the field, that are paralleled by an increased availability of EPR instrumentation. While the method requires an introduction of a paramagnetic probe at a well-defined position in a peptide sequence, it has been shown to be minimally destructive to the peptide structure and energetics of the peptide-membrane interactions. In this chapter, we describe basic approaches for using SDSL EPR spectroscopy to study interactions between small peptides and biological membranes or membrane mimetic systems. We focus on experimental approaches to quantify peptide-membrane binding, topology of bound peptides, and characterize peptide aggregation. Sample preparation protocols including spin-labeling methods and preparation of membrane mimetic systems are also described.

Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion

We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid–polymer–oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide–membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning–folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide-pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precede fusion.

Early stages of interactions of cell-penetrating peptide penetratin with a DPPC bilayer

Cell-penetrating-peptides (CPPs) can deliver themselves together with a macromolecular cargo into cells and, hence, have promising applications in drug delivery. The detailed physical mechanisms that underlie and determine their cellular uptake remain unknown. We used molecular dynamics (MD) simulations to study the interaction of a well-known CPP, namely penetratin, with a zwitterionic di-palmitoyl-phosphatidyl-choline (DPPC) bilayer. Our study shows that the arginine and lysine residues play a crucial role in peptide-membrane binding through charge-pair and hydrogen bond interactions. We also characterize peptide conformation and show that it remains helical near the N-terminus but can fold into a variety of other conformations in the residues close to the C-terminus. The response of membrane to the peptide is also investigated.

Effect of Liposome Surface Charge and Peptide Side Chain Charge Density on Antimicrobial Peptide-Membrane Binding as Determined by Circular Dichroism

In this investigation the effect of varying the surface charge and hydrophobicity of liposomes of mixed phospholipid compositions on the binding of four of the AMPs was determined using Circular Dichroism Spectroscopy,1H NMR and Diffusion Ordered Spectroscopy NMR methods. The following mixed anionic liposomes: 3:1 POPC/POPG, 4:1 POPC/POPG, 5:1 POPC/POPG, 3:1 POPC/POPS, 4:1 POPC/POPS, 5:1 POPC/POPS, and the following mixed zwitter ionic liposomes: 3:1 POPC/POPE, 4:1 POPC/POPE and 5:1 POPC/POPE were used in this investigation. The results obtained from the mixed anionic liposomes study indicated even when the net change on the liposome are the same, local differences in charge density and hydrophobicity will result in different physicochemical surface properties that will dramatically affect the mechanism of AMP binding. The results obtained from the mixed zwitterionic liposomes study indicated that very small changes in the charged amine going from an ammonium salt to a quaternary amine salt will result in different physicochemical surface properties that can inhibit or dramatically reduce AMP binding. This observation is particularly important when designing physicochemical investigations of model membrane of Gram Negative bacteria.

The Application of Biophysical Techniques to Study Antimicrobial Peptides

The increasing bacteria resistance to conventional antibiotics has led to the need for alternative therapies. Being part of the human innate defence system and with a broad spectrum of activity against bacteria, viruses, protozoa, and cancer cells, antimicrobial peptides (AMPs) are a very promising alternative. The mechanism of action of AMPs seems to broadly correlate with their ability to target the bacterial cell membrane. To understand and improve their effect, it is of major importance to unravel their mechanism of action and, in particular, to understand the peptide-membrane binding. Several biophysical techniques such as fluorescence spectroscopy, circular dichroism, zeta potential determination, and atomic force microscopy can be used to achieve this goal. Characteristics of AMPs-membranes interactions and the use of these biophysical techniques will be discussed.

Cell-Cell Membrane Fusion Induced by p15 Fusion-associated Small Transmembrane (FAST) Protein Requires a Novel Fusion Peptide Motif Containing a Myristoylated Polyproline Type II Helix

The p15 fusion-associated small transmembrane (FAST) protein is a nonstructural viral protein that induces cell-cell fusion and syncytium formation. The exceptionally small, myristoylated N-terminal ectodomain of p15 lacks any of the defining features of a typical viral fusion protein. NMR and CD spectroscopy indicate this small fusion module comprises a left-handed polyproline type II (PPII) helix flanked by small, unstructured N and C termini. Individual prolines in the 6-residue proline-rich motif are highly tolerant of alanine substitutions, but multiple substitutions that disrupt the PPII helix eliminate cell-cell fusion activity. A synthetic p15 ectodomain peptide induces lipid mixing between liposomes, but with unusual kinetics that involve a long lag phase before the onset of rapid lipid mixing, and the length of the lag phase correlates with the kinetics of peptide-induced liposome aggregation. Lipid mixing, liposome aggregation, and stable peptide-membrane interactions are all dependent on both the N-terminal myristate and the presence of the PPII helix. We present a model for the mechanism of action of this novel viral fusion peptide, whereby the N-terminal myristate mediates initial, reversible peptide-membrane binding that is stabilized by subsequent amino acid-membrane interactions. These interactions induce a biphasic membrane fusion reaction, with peptide-induced liposome aggregation representing a distinct, rate-limiting event that precedes membrane merger. Although the prolines in the proline-rich motif do not directly interact with membranes, the PPII helix may function to force solvent exposure of hydrophobic amino acid side chains in the regions flanking the helix to promote membrane binding, apposition, and fusion.

A Molecular Dynamics Study on the Binding and Interaction of the Amyloid-Beta (1-42) Peptide with Phospholipid Bilayers

The Amyloid-Beta (A-Beta) peptide is a key aggregate species in Alzheimer's disease. While aspects of the A-Beta peptide aggregation pathway have previously been elucidated, the initial conversion of monomer peptides into an oligomer during aggregation is not clearly understood. One potential mediator of these early stages of aggregation is interactions of A-Beta with cell membranes, particularly anionic cell membranes. We use unconstrained and umbrella sampling molecular dynamics simulations to investigate interactions between the 42-amino acid A-Beta peptide and model bilayers consisting of zwitterionic dipalmitoylphophatidylcholine (DPPC) lipids and anionic dioleoylphosphatidylserine (DOPS) lipids. From this work, we determine that A-Beta binds to the surface of DPPC and DOPS bilayers over the small length scales used in simulations. Our results also support the hypothesis that the charge on the bilayer surface and on the peptide affects both the free energy of peptide-membrane binding and the distribution of the peptide on the bilayer surface. Finally, no significant secondary structure change is observed in the peptide during the timescales used in these simulations. This result may indicate all-atom simulation times are too short to observe secondary structure changes in this system or that structure change during the oligomerization process requires peptide-peptide interactions. Our work demonstrates that interactions between the A-Beta peptide and lipid bilayers promote a peptide distribution on the bilayer surface that is prone to peptide-peptide interactions, which can influence the propensity of A-Beta to aggregate into higher order structures.