Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

Antimicrobial and immunomodulatory activities of porcine cathelicidin Protegrin-1

Antimicrobial peptides (AMPs) are a promising alternative to antibiotics in the fight against multi-drug resistant and immune system-evading bacterial infections. Protegrins are porcine cathelicidins which have been identified in porcine leukocytes. Protegrin-1 is the best characterized family member and has broad antibacterial activity by interacting and permeabilizing bacterial membranes. Many host defense peptides (HDPs) like LL-37 or chicken cathelicidin 2 (CATH-2) have also been shown to have protective biological functions during infections. In this regard, it is interesting to study if Protegrin-1 has the immune modulating potential to suppress unnecessary immune activation by neutralizing endotoxins or by influencing the macrophage functionality in addition to its direct antimicrobial properties. This study showed that Protegrin-1 neutralized lipopolysaccharide- (LPS) and bacteria-induced activation of RAW macrophages by binding and preventing LPS from cell surface attachment. Furthermore, the peptide treatment not only inhibited bacterial phagocytosis by murine and porcine macrophages but also interfered with cell surface and intracellular bacterial survival. Lastly, Protegrin-1 pre-treatment was shown to inhibit the amastigote survival in Leishmania infected macrophages. These experiments describe an extended potential of Protegrin-1's protective role during microbial infections and add to the research towards clinical application of cationic AMPs.

Anticancer Mechanisms and Potential Anticancer Applications of Antimicrobial Peptides and Their Nano Agents

Traditional chemotherapy is one of the main methods of cancer treatment, which is largely limited by severe side effects and frequent development of multi-drug resistance by cancer cells. Antimicrobial peptides (AMPs) with high efficiency and low toxicity, as one of the most promising new drugs to replace chemoradiotherapy, have become a current research hotspot, attracting the attention of worldwide researchers. AMPs are natural-source small peptides from the innate immune system, and certain AMPs can selectively kill a broad spectrum of cancer cells while exhibiting less damage to normal cells. Although it involves intracellular mechanisms, AMPs exert their anti-cancer effects mainly through membrane destruction effect; thus, AMPs also hold unique advantages in fighting drug-resistant cancer cells. However, the poor stability and hemolytic toxicity of peptides limit their clinical application. Fortunately, functionalized nanoparticles have many possibilities in overcoming the shortcomings of AMPs, which provides a huge prospect for better application of AMPs. In this paper, we briefly introduce the characteristics and different sources of AMPs, review and summarize the mechanisms of action and the research status of AMPs used as an anticancer therapy, and finally focus on the further use of AMPs nano agents in the anti-cancer direction.

Biomimetic antimicrobial polymers—Design, characterization, antimicrobial, and novel applications

Biomimetic antimicrobial polymers have been an area of great interest as the need for novel antimicrobial compounds grows due to the development of resistance. These polymers were designed and developed to mimic naturally occurring antimicrobial peptides in both physicochemical composition and mechanism of action. These antimicrobial peptide mimetic polymers have been extensively investigated using chemical, biophysical, microbiological, and computational approaches to gain a deeper understanding of the molecular interactions that drive function. These studies have helped inform SARs, mechanism of action, and general physicochemical factors that influence the activity and properties of antimicrobial polymers. However, there are still lingering questions in this field regarding 3D structural patterning, bioavailability, and applicability to alternative targets. In this review, we present a perspective on the development and characterization of several antimicrobial polymers and discuss novel applications of these molecules emerging in the field. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.

Membrane mechanism of temporin-1CEc, an antimicrobial peptide isolated from the skin secretions of Rana chensinensis, and its systemic analogs

Antimicrobial peptides (AMPs) are new and powerful target molecules in the development of new antibacterial agents. Temporin-1CEc, a natural peptide isolated and purified from the skin secretions of the Chinese brown frog Rana chensinensis, exhibits low or no antibacterial activity against gram-negative and gram-positive bacteria, which limits its potential therapeutic use; however, it displays low hemolysis to human erythrocytes. Here, a series of temporin-1CEc analogs was designed and synthesized by amino acid residue substitutions based on cationicity, hydrophobicity, amphipathicity and secondary structure to understand the structure-activity relationships of this peptide in depth. The results showed that all of the analogs, except for 2K and 4K, had significantly improved antibacterial activity against the tested standard bacterial strains and multidrug-resistant bacterial strains compared to temporin-1CEc. 2K2L and 2K4L, but not 4K2L and 4K4L, showed the strongest antibacterial activity compared with their parent peptides 2K and 4K, suggesting that peptide hydrophobicity plays a more important role in antibacterial activity than cationicity for this series of AMPs. However, the antibacterial activity of the 6 Trp-containing analogs of 2K4L decreased with a further increase in hydrophobicity based on the results of 2K4L, indicating that it is more important to balance cationicity and hydrophobicity. Moreover, an increase in AMP hydrophobicity led to hemolysis. Notably, all of the peptides adopted α-helical structures in 50% trifluoroethanol/water and 30 mM SDS solutions. 2K2L and 2K4L displayed broad-spectrum antibacterial activity against sensitive and multidrug-resistant bacteria, effectively killing the tested multidrug resistant strain Staphylococcus epidermidis (MRSE1208). 2K2L and 2K4L were able to increase the permeability of the outer and inner membranes by depolarization and disturb the integration of the cytoplasmic membrane of MRSE1208 cells, leading to leakage of its cellular contents. In addition, 2K2L and 2K4L at low concentrations inhibited biofilm formation and degraded mature 1-day-old MRSE1208 biofilms. Notably, 2K2L and 2K4L inhibited the formation of MRSE1208 biofilms at concentrations below its MIC value, suggesting that the peptide may exert an inhibitory effect through not only direct antimicrobial activity but also a biofilm-specific mechanism. Collectively, these results suggest that 2K2L and 2K4L could be effective antibiotics against multidrug-resistant bacterial strains.

Towards designing globular antimicrobial peptide mimics: role of polar functional groups in biomimetic ternary antimicrobial polymers

Using atomistic molecular dynamics simulations, we study the interaction of ternary methacrylate polymers, composed of charged cationic, hydrophobic and neutral polar groups, with model bacterial membrane. Our simulation data shows that the random ternary polymers can penetrate deep into the membrane interior and partitioning of even a single polymer has a pronounced effect on the membrane structure. Lipid reorganization, on polymer binding, shows a strong affinity of the ternary polymer for anionic POPG lipids and the same is compared with the control case of binary polymers (only cationic and hydrophobic groups). While binary polymers exhibit strong propensity of acquired amphiphilic conformations upon membrane insertion, our results strongly suggest that such amphiphilic conformations are absent in the case of random ternary polymers. The ternary polymers adopt a more folded conformation, staying aligned in the direction of the membrane normal and subsequently penetrating deeper into the membrane interior suggesting a novel membrane partitioning mechanism without amphiphilic conformations. Finally, we also examine the interactions of ternary polymer aggregates with model bacterial membranes, which show that replacing some of the hydrophobic groups by polar groups leads to weakly held ternary aggregates enabling them to undergo rapid partitioning and insertion into membrane interior. Our work thus underscores the role of inclusion of polar groups into the framework of traditional binary biomimetic antimicrobial polymers and suggests different mode of partitioning into bacterial membranes, mimicking antimicrobial mechanism of globular antimicrobial peptides like Defensin.

The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides

The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.

Protegrin 1 Enhances Innate Cellular Defense via the Insulin-Like Growth Factor 1 Receptor Pathway

Antimicrobial peptides (AMPs) represent a promising area of research to help combat the ever-growing problem of antibiotic resistance. Protegrin-1 is an AMP from the cathelicidin family. It is produced naturally in pigs and its mature form (mPG-1) has potent bactericidal properties and a unique β-hairpin structure that separates it from most AMPs found in mice and humans. While the antibacterial properties of protegrin-1 are well established, the role it plays in immune modulation has yet to be investigated, and our current study sought to explore this alternate role and potential mechanism behind. We found that mPG-1 stimulated intestinal cell migration, this is accompanied with altered expression of genes associated with cell migration, in addition to increased expression of pro-inflammatory cytokines and immune-related factors. Further study suggested that mPG-1 activates insulin-like growth factor 1 receptor (IGF1R) and through this receptor it modulates immune activity as well as cell migration. Our study revealed a novel function of mPG-1, and its associated pathway, suggesting therapeutic potential of the antimicrobial peptide for infection and/or immune disorders, particularly ones affecting the gastrointestinal tract such as inflammatory bowel syndrome.

Ordering of lipid membranes altered by boron nitride nanosheets

Boron nitride nanosheets are novel promising nanomaterials with a lower cytotoxicity than graphene making them a better candidate for biomedical applications.

Molecular dynamics and protein interaction studies of lipopeptide (Iturin A) on α- amylase of Spodoptera litura

The small mottled willow moth (Spodoptera litura) is one of the best-known agricultural pest insects. To understand the insecticidal activity, we have selected iturin A compound produced by Bacillus amyloliquefaciens RHNK22 which showed the strongest and most common inhibitory effect on the Spodoptera litura protein. In this work we have identified the action of iturin A on α- amylase is a major digestive enzyme of Spodoptera litura using docking studies. A 3D model of α- amylase from Spodoptera litura was generated using 2HPH as a template with the help of Modeller7v7. With the aid of the molecular mechanics and molecular dynamics methods, the final model is obtained and is further checked by Procheck and Verify 3D graph programs, which showed that the final refined model is reliable. With this model, a adjustable docking study was performed with iturin A using GOLD software. The results indicated that ARG 18, THR15, LEU42 in α- amylase are important determinant residues in binding as they have strong hydrogen bonding interactions with iturin A. These hydrogen binding interactions play an important role for the stability of the complex.

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.

High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles

PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.

Mapping activity elements of protegrin antimicrobial peptides by HomoSAR

HomoSAR has been able to shed light on the relationship between sequences of protegrin peptides and their activity on six specific micro-organisms.

Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs

Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2-3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in pre-formed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.

Multiscale Models of Antibiotic Probiotics

The discovery of antibiotics is one of the most important advances in the history of humankind. For eighty years human life expectancy and standards of living improved greatly thanks to antibiotics. But bacteria have been fighting back, developing resistance to our most potent molecules. New, alternative strategies must be explored as antibiotic therapies become obsolete because of bacterial resistance. Mathematical models and simulations guide the development of complex technologies, such as aircrafts, bridges, communication systems and transportation systems. Herein, models are discussed that guide the development of new antibiotic technologies. These models span multiple molecular and cellular scales, and facilitate the development of a technology that addresses a significant societal challenge. We argue that simulations can be a creative source of knowledge.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. III. Water clustering and vibrational energy transfer

Water clustering and connectivity around lipid bilayers strongly influences the properties of membranes and is important for functions such as proton and ion transport. Vibrational anisotropic pump-probe spectroscopy is a powerful tool for understanding such clustering, as the measured anisotropy depends upon the time-scale and degree of intra- and intermolecular vibrational energy transfer. In this article, we use molecular dynamics simulations and theoretical vibrational spectroscopy to help interpret recent experimental measurements of the anisotropy of water in lipid multi-bilayers as a function of both lipid hydration level and isotopic substitution. Our calculations are in satisfactory agreement with the experiments of Piatkowski, Heij, and Bakker, and from our simulations we can directly probe water clustering and connectivity. We find that at low hydration levels, many water molecules are in fact isolated, although up to 70% of hydration water forms small water clusters or chains. At intermediate hydration levels, water forms a wide range of cluster sizes, while at higher hydration levels, the majority of water molecules are part of a large, percolating water cluster. Therefore, the size, number, and nature of water clusters are strongly dependent on lipid hydration level, and the measured anisotropy reflects this through its dependence on intermolecular energy transfer.

Membrane interactions and pore formation by the antimicrobial peptide protegrin

Protegrin is an antimicrobial peptide with a β-hairpin structure stabilized by a pair of disulfide bonds. It has been extensively studied by solid-state NMR and computational methods. Here we use implicit membrane models to examine the binding of monomers on the surface and in the interior of the membrane, the energetics of dimerization, the binding to membrane pores, and the stability of different membrane barrel structures in pores. Our results challenge a number of conclusions based on previous experimental and theoretical work. The burial of monomers into the membrane interior is found to be unfavorable for any membrane thickness. Because of its imperfect amphipathicity, protegrin binds weakly, at most, on the surface of zwitterionic membranes. However, it binds more favorably onto toroidal pores. Anionic charge on the membrane facilitates the binding due to electrostatic interactions. Solid-state NMR results have suggested a parallel NCCN association of monomers in dimers and association of dimers to form octameric or decameric β-barrels. We find that this structure is not energetically plausible for binding to bilayers, because in this configuration the hydrophobic sides of two monomers point in opposite directions. In contrast, the antiparallel NCCN and especially the parallel NCNC octamers are stable and exhibit a favorable binding energy to the pore. The results of 100-ns simulations in explicit bilayers corroborate the higher stability of the parallel NCNC barrel compared with the parallel NCCN barrel. The ability to form pores in zwitterionic membranes provides a rationalization for the peptide's cytotoxicity. The discrepancies between our results and experiment are discussed, and new experiments are proposed to resolve them and to test the validity of the models.

Dynamics in the interior of AOT lamellae investigated with two-dimensional infrared spectroscopy

The dynamics inside the organic regions of aerosol-OT (AOT)/water mixtures in the lamellar mesophase, bicontinuous cubic (BC) phase, and in an analogous molecule without the charged sulfonate headgroup are investigated by observing spectral diffusion, orientational relaxation and population relaxation using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy and IR pump-probe experiments on the asymmetric CO stretch of a vibrational probe, tungsten hexacarbonyl (W(CO)6). The water layer thickness between the bilayer planes in the lamellar phase was varied. For comparison, the dynamics of W(CO)6 in the normal liquid bis(2-ethylhexyl) succinate (EHS), which is analogous to AOT but has no charged sulfonate headgroup, were also studied. The 2D IR experiments measure spectral diffusion, which results from the structural evolution of the system. Spectral diffusion is quantified by the frequency-frequency correlation function (FFCF). In addition to a homogeneous component, the FFCFs are biexponential decays with fast and slow time components of ∼12.5 and ∼150 ps in the lamellar phase. Both components of the FFCF are independent of the number of water molecules per headgroup for the lamellae, but they slow somewhat in the BC phase. The dynamics in the ordered phases are in sharp contrast to the dynamics in EHS, which displays fast and slow components of the FFCF of 5 and 80 ps, respectively. As the hydration level of AOT increases, vibrational lifetime decreases, suggesting some change in the local environment of W(CO)6 with water content.

Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup's phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

Molecular basis for membrane pore formation by Bax protein carboxyl terminus

Bax protein plays a key role in mitochondrial membrane permeabilization and cytochrome c release upon apoptosis. Our recent data have indicated that the 20-residue C-terminal peptide of Bax (BaxC-KK; VTIFVAGVLTASLTIWKKMG), when expressed intracellularly, translocates to the mitochondria and exerts lethal effect on cancer cells. Moreover, the BaxC-KK peptide, as well as two mutants where the two lysines are replaced with glutamate (BaxC-EE) or leucine (BaxC-LL), have been shown to form relatively large pores in lipid membranes, composed of up to eight peptide molecules per pore. Here the pore structure is analyzed by polarized Fourier transform infrared, circular dichroism, and fluorescence experiments on the peptides reconstituted in phospholipid membranes. The peptides assume an α/β-type secondary structure within membranes. Both β-strands and α-helices are significantly (by 30-60 deg) tilted relative to the membrane normal. The tryptophan residue embeds into zwitterionic membranes at 8-9 Å from the membrane center. The membrane anionic charge causes a deeper insertion of tryptophan for BaxC-KK and BaxC-LL but not for BaxC-EE. Combined with the pore stoichiometry determined earlier, these structural constraints allow construction of a model of the pore where eight peptide molecules form an "α/β-ring" structure within the membrane. These results identify a strong membranotropic activity of Bax C-terminus and propose a new mechanism by which peptides can efficiently perforate cell membranes. Knowledge on the pore forming mechanism of the peptide may facilitate development of peptide-based therapies to kill cancer or other detrimental cells such as bacteria or fungi.

Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations

In a previous report, we calculated the infrared absorption spectrum and both the isotropic and anisotropic pump-probe signals for the OD stretch of isotopically dilute water in dilauroylphosphatidylcholine (DLPC) multi-bilayers as a function of the lipid hydration level. These results were then compared to recent experimental measurements and are in generally good agreement. In this paper, we will further investigate the structure and dynamics of hydration water using molecular dynamics simulations and calculations of the two-dimensional infrared and vibrational echo peak shift observables for hydration water in DLPC membranes. These observables have not yet been measured experimentally, but future comparisons may provide insight into spectral diffusion processes and hydration water heterogeneity. We find that at low hydration levels the motion of water molecules inside the lipid membrane is significantly arrested, resulting in very slow spectral diffusion. At higher hydration levels, spectral diffusion is more rapid, but still slower than in bulk water. We also investigate the effects of several common approximations on the calculation of spectroscopic observables by computing these observables within multiple levels of theory. The impact of these approximations on the resulting spectra affects our interpretation of these measurements and reveals that, for example, the cumulant approximation, which may be valid for certain systems, is not a good approximation for a highly heterogeneous environment such as hydration water in lipid multi-bilayers.

Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers

We report altogether 3-μs molecular dynamics (MD) simulations of the antimicrobial peptide CM15 to systematically investigate its interaction with two model lipid bilayers, pure POPC and mixed POPG:POPC (1:2). Starting with either an α-helical or a random-coil conformation, CM15 is found to insert into both bilayers. Peptide-lipid interaction is stronger with the anionic POPG:POPC than the zwitterionic POPC, which is largely attributed to the electrostatic attraction between CM15 and the negatively charged POPG. Simulations initiated with CM15 as a random coil allowed us to study peptide folding at the lipid-water interface. Interestingly, CM15 folding appears to be faster in POPC than POPG:POPC, which may be explained by a lower activation energy barrier of structural rearrangement in the former system. Our data also suggest that compared with the random-coil conformation, CM15 in a pre-folded α-helix has significantly reduced interactions with the lipids, indicating that peptide initial structures may bias the simulation results considerably on the 100-ns timescale. The implications of this result should be considered when preparing and interpreting future AMP simulations.

Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer

Molecular dynamics (MD) simulations are used to study the pathway for the insertion of the cationic antimicrobial peptide protegrin-1 (PG1) into mixed anionic lipid bilayers composed of palmitoyl-oleoyl-phosphatidylglycerol (POPG) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE) in a 1:3 ratio (POPG/POPE). We calculate the potential of mean force (PMF) during the transfer of the peptide from the bulk aqueous phase to the transmembrane (TM) configuration using the adaptive biasing force (ABF) method. We find that the PMF has two energy minima separated by an energy barrier. One minimum corresponds to the fully transmembrane inserted state, with a free energy of -20.1 kcal/mol. The second PMF minimum, which corresponds to adsorption to the membrane surface, has a value of -2.5 kcal/mol. The PMF also shows the existence of a free energy barrier of +6.3 kcal/mol for the insertion process. Using the Kramers theory Langevin equation and the Grote-Hynes theory generalized Langevin equation, we calculated the transmission coefficient for PG1 diffusion through the potential barrier. We focus on the use of the PMF and the time correlation function of the fluctuation of the instantaneous force to calculate the rate constants for insertion/deinsertion of PG1 from the mixed POPG/POPE membrane. The influence of the activation free energy barrier on the dynamics of the insertion and permeation of peptides through the membrane are discussed.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.

Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Protegrin-1 (PG-1) belongs to the family of antimicrobial peptides. It interacts specifically with the membrane of a pathogen and kills the pathogen by releasing its cellular contents. To fully understand the energetics governing the orientation of PG-1 in different membrane environments and its effects on the physicochemical properties of the peptide and membrane bilayers, we have performed the potential of mean force (PMF) calculations as a function of its tilt angle at four distinct rotation angles in explicit membranes composed of either DLPC (1,2-dilauroylphosphatidylcholine) or POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid molecules. The resulting PMFs in explicit lipid bilayers were then used to search for the optimal hydrophobic thickness of the EEF1/IMM1 implicit membrane model in which a two-dimensional PMF in the tilt and rotation space was calculated. The PMFs in explicit membrane systems clearly reveal that the energetically favorable tilt angle is affected by both the membrane hydrophobic thickness and the PG-1 rotation angle. Local thinning of the membrane around PG-1 is observed upon PG-1 tilting. The thinning is caused by both hydrophobic mismatch and arginine-lipid head group interactions. The two-dimensional PMF in the implicit membrane is in good accordance with those from the explicit membrane simulations. The ensemble-averaged Val16 (15)N and (13)CO chemical shifts weighted by the two-dimensional PMF agree fairly well with the experimental values, suggesting the importance of peptide dynamics in calculating such ensemble properties for direct comparison with experimental observables.

Computational studies of protegrin antimicrobial peptides: a review

Antimicrobial peptides (AMPs) are small, naturally occurring peptides that exhibit strong antibacterial properties generally believed to be a result of selective bacterial membrane disruption. As a result, there has been significant interest in the development of therapeutic antibiotics based on AMPs; however, the poor understanding of the fundamental mechanism of action of these peptides has largely hampered such efforts. We present a summary of computational and theoretical investigations of protegrin, a particularly potent peptide that is both an excellent model for the mechanism of action of AMPs and a promising therapeutic candidate. Experimental investigations have shed light on many of the key steps in the action of protegrin: protegrin monomers are known to dimerize in various lipid environments; protegrin peptides interact strongly with lipid bilayer membranes, particularly anionic lipids; protegrins have been shown to form pores in lipid bilayers, which results in uncontrolled ion transport and may be a key factor in bacterial death. In this work, we present a comprehensive review of the computational and theoretical studies that have complemented and extended the information obtained from experimental work with protegrins, as well as a brief survey of the experimental biophysical studies that are most pertinent to such computational work. We show that a consistent, mechanistic description of the bactericidal mechanism of action of protegrins is emerging, and briefly outline areas where the current understanding is deficient. We hope that the research reviewed herein offers compelling evidence of the benefits of computational investigations of protegrins and other AMPs, as well as providing a useful guide to future work in this area.

Dimerization of protegrin-1 in different environments

The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1) is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize the cells. PG1 dimers are found in two distinct, parallel and antiparallel, conformations, known as important intermediate structural units of the active pore oligomers. What is not clear is the sequence of events from PG1 monomers in solution to pores inside membranes. The step we focus on in this work is the dimerization of PG1. In particular, we are interested in determining where PG1 dimerization is most favorable. We use extensive molecular dynamics simulations to determine the potential of mean force as a function of distance between two PG1 monomers in the aqueous subphase, the surface of model lipid bilayers and the interior of these bilayers. We investigate the two known distinct modes of dimerization that result in either a parallel or an antiparallel β-sheet orientation. The model bilayer membranes are composed of anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE) in a 1:3 ratio (POPG:POPE). We find the parallel PG1 dimer association to be more favorable than the antiparallel one in water and inside the membrane. However, we observe that the antiparallel PG1 β-sheet dimer conformation is somewhat more stable than the parallel dimer association at the surface of the membrane. We explore the role of hydrogen bonds and ionic bridges in peptide dimerization in the three environments. Detailed knowledge of how networks of ionic bridges and hydrogen bonds contribute to peptide stability is essential for the purpose of understanding the mechanism of action for membrane-active peptides as well as for designing peptides which can modulate membrane properties. The findings are suggestive of the dominant pathways leading from individual PG1 molecules in solution to functional pores in bacterial membranes.

Current trends in antimicrobial agent research: chemo- and bioinformatics approaches

Databases and chemo- and bioinformatics tools that contain genomic, proteomic and functional information have become indispensable for antimicrobial drug research. The combination of chemoinformatics tools, bioinformatics tools and relational databases provides means of analyzing, linking and comparing online search results. The development of computational tools feeds on a diversity of disciplines, including mathematics, statistics, computer science, information technology and molecular biology. The computational approach to antimicrobial agent discovery and design encompasses genomics, molecular simulation and dynamics, molecular docking, structural and/or functional class prediction, and quantitative structure-activity relationships. This article reviews progress in the development of computational methods, tools and databases used for organizing and extracting biological meaning from antimicrobial research.

Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer

The free energies of adsorption of the monomer or dimer of the cationic beta-hairpin antimicrobial peptide protegrin-1 (PG1) in a specific binding orientation on a lipid bilayer are determined using molecular dynamics (MD) simulations and Poisson-Boltzmann calculations. The bilayer is composed of anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE) with ratio 1:3 (POPG/POPE). PG1 is believed to kill bacteria by binding on their membranes. There, it forms pores that lyse the bacteria. Herein we focus on the thermodynamics of binding. In particular, we explore the role of counterion release from the lipid bilayer upon adsorption of either the monomeric or the dimeric form of PG1. Twenty-two 4-ns-long MD trajectories of equilibrated systems are generated to determine the free energy profiles for the monomer and dimer as a function of the distance between the peptide(s) and the membrane surface. The MD simulations are conducted at 11 different separations from the membrane for each of the two systems, one with PG1, the second with a PG1 dimer of only a specific orientation of the monomer and dimer without taking into account the change of entropy for the peptide. To calculate the potential of mean force for each peptide/membrane system, a variant of constrained MD and thermodynamic integration is used. We observed that PG1 dimer binds more favorably to the POPG/POPE membrane. A simple method for relating the free energy profile to the PG1-membrane binding constant is employed to predict a free energy of adsorption of -2.4 +/- 0.8 kcal/mol. A corresponding PG1-dimer-membrane binding constant is calculated as -3.5 +/- 1.1 kcal/mol. Free energy profiles from MD simulation were extensively analyzed and compared with results of Poisson-Boltzmann theory. We find the peptide-membrane attraction to be dominated by the entropy increase due to the release of counterions in a POPG/POPE lipid bilayer.

Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli

Antimicrobial peptides (AMPs), important effector molecules of the innate immune system, also provide templates for designing novel antibiotics. Protegrin, an especially potent AMP found in porcine leukocytes, was recently shown to form octameric transmembrane pores. We have employed a combination of experiments and models spanning length scales from the atomistic to the cellular level in order to elucidate the microbicidal mechanism of protegrin. Comparison of the modeling and experimental data suggests that approximately 10-100 protegrin pores are necessary to explain the observed rates of potassium leakage and Escherichia coli death in exponential-phase bacteria. The kinetics of viability loss suggest that bacterial death results largely from uncontrolled ion exchange processes and decay of transmembrane potential. However, ion exchange processes alone cannot account for the experimentally observed cell swelling and osmotic lysis-a redundant "overkill" mechanism most likely to occur in locales with high protegrin concentrations. Although our study is limited to protegrin and E. coli, the timeline of events described herein is likely shared by other AMPs that act primarily by permeabilizing microbial membranes. This work provides many of the missing links in describing antimicrobial action, as well as providing a quantitative connection between several previous experimental and simulation studies of protegrin.

Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers

Antimicrobial peptides interact specifically with the membrane of a pathogen and kill the pathogen by releasing its cellular contents. Protegrin-1 (PG-1), a beta-hairpin antimicrobial peptide, is known to exist as a transmembrane monomer in a 1,2-dilauroylphosphatidylcholine (DLPC) bilayer and shows concentration-dependent oligomerization in a 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) bilayer. To examine its structure, dynamics, orientation, and interaction in membranes, we performed comparative molecular dynamics simulations of PG-1 monomer and dimer in DLPC and POPC bilayers for a total of 840 ns. The PG-1 monomer exhibits larger tilting in DLPC than in POPC due to a hydrophobic mismatch. PG-1 tilting is dependent on its rotation angle. The specific orientation of PG-1 in membranes is governed by the interactions of its aromatic residues with lipid headgroups. The calculated (15)N and (13)CO chemical shifts of Val(16) in DLPC reveal that there are different sets of tilt and rotation angles that satisfy the experimental values reasonably, suggesting that more experiments are needed to determine its orientation. The dimer simulations show that the dimer interface is better preserved in POPC than in DLPC because POPC's greater hydrophobic thickness causes reduced flexibility of the C-terminal strands. Both monomer and dimer simulations show membrane thinning around PG-1, largely due to arginine-lipid interactions.

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function

Understanding the delicate balance of forces governing helix or beta-hairpin interactions in transmembrane (TM) proteins is central to understanding membrane structure and function. These membrane constituent interactions play an essential role in determining the structure and function of membrane proteins, and protein interactions in membranes, and thus form the basis for many vital processes, including TM signaling, transport of ions and small molecules, energy transduction, and cell-cell recognition. "Why does a single-pass TM helix or beta-hairpin have specific orientations in membranes?" "What are the roles of hydrogen bonds, close packing, and helix-lipid or beta-hairpin-lipid interactions in helix or beta-hairpin associations in membranes?" "How do these interactions change the membrane structures?" "How do TM domains transmit signals across membranes?" These are important membrane biophysical questions that can be addressed by understanding the delicate balance of forces governing helix or beta-hairpin interactions with/in membranes. In this work, we summarize a series of helix/beta-hairpin restraint potentials that we have developed, and illustrate their applications that begin to address the complicated energetics and molecular mechanisms of these interactions at the atomic level by calculating the potentials of mean force (PMFs) along reaction coordinates relevant to helix/beta-hairpin motions in membranes and dissecting the total PMF into the contributions arising from physically important microscopic forces.

Membrane-disruptive properties of the bioinsecticide Jaburetox-2Ec: implications to the mechanism of the action of insecticidal peptides derived from ureases

Jaburetox-2Ec, a recombinant peptide derived from an urease isoform (JBURE-II), displays high insecticidal activity against important pests such as Spodoptera frugiperda and Dysdercus peruvianus. Although the molecular mechanism of action of ureases-derived peptides remains unclear, previous ab initio data suggest the presence of structural motifs in Jaburetox-2Ec with characteristics similar to those found in a class of pore-forming peptides. Here, we investigated the molecular aspects of the interaction between Jaburetox-2Ec and large unilamellar vesicles. Jaburetox-2Ec displays membrane-disruptive ability on acidic lipid bilayers and this effect is greatly influenced by peptide aggregation. Corroborating with this finding, molecular modeling studies revealed that Jaburetox-2Ec might adopt a well-defined beta-hairpin conformation similar to those found in antimicrobial peptides with membrane disruption properties. In addition, molecular dynamics simulations suggest that the protein is able to anchor at a polar/non-polar interface. In the light of these findings, for the first time it was possible to point out some evidence that the peptide Jaburetox-2Ec interacting with lipid vesicles promotes membrane permeabilization.

Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance

We have developed a set of restraint potentials for beta-hairpin tilt relative to the membrane normal, beta-hairpin rotation around the beta-hairpin axis, and hairpin-hairpin distance. Such restraint potentials enable us to characterize the molecular basis of specific beta-hairpin tilt and rotation in membranes and hairpin-hairpin interactions at the atomic level by sampling their conformational space along these degrees of freedom, i.e., reaction coordinates, during molecular dynamics simulations. We illustrate the efficacy of the beta-hairpin restraint potentials by calculating the potentials of mean force (PMFs) as a function of tilt and rotation angles of protegrin-1 (PG-1), a beta-hairpin antimicrobial peptide, in an implicit membrane model. The peptide association in the membrane is also examined by calculating the PMFs as a function of distance between two PG-1 peptides in various dimer interfaces. These novel restraint potentials are found to perform well in each of these cases and are expected to be a useful means to study the microscopic driving forces of insertion, tilting, and rotation of beta-hairpin peptides in membranes as well as their association in aqueous solvent or membrane environments particularly when combined with explicit solvent models.

Coupling molecular dynamics simulations with experiments for the rational design of indolicidin-analogous antimicrobial peptides

Antimicrobial peptides (AMPs) have attracted much interest in recent years because of their potential use as new-generation antibiotics. Indolicidin (IL) is a 13-residue cationic AMP that is effective against a broad spectrum of bacteria, fungi, and even viruses. Unfortunately, its high hemolytic activity retards its clinical applications. In this study, we adopted molecular dynamics (MD) simulations as an aid toward the rational design of IL analogues exhibiting high antimicrobial activity but low hemolysis. We employed long-timescale, multi-trajectory all-atom MD simulations to investigate the interactions of the peptide IL with model membranes. The lipid bilayer formed by the zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was chosen as the model erythrocyte membrane; lipid bilayers formed from a mixture of POPC and the negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol were chosen to model bacterial membranes. MD simulations with a total simulation time of up to 4 micros revealed the mechanisms of the processes of IL adsorption onto and insertion into the membranes. The packing order of these lipid bilayers presumably correlated to the membrane stability upon IL adsorption and insertion. We used the degree of local membrane thinning and the reduction in the order parameter of the acyl chains of the lipids to characterize the membrane stability. The order of the mixed 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol/POPC lipid bilayer reduced significantly upon the adsorption of IL. On the other hand, although the order of the pure-POPC lipid bilayer was perturbed slightly during the adsorption stage, the value was reduced more dramatically upon the insertion of IL into the membrane's hydrophobic region. The results imply that enhancing IL adsorption on the microbial membrane may amplify its antimicrobial activity, while the degree of hemolysis may be reduced through inhibition of IL insertion into the hydrophobic region of the erythrocyte membrane. In addition, through simulations, we identified the amino acids that are most responsible for the adsorption onto or insertion into the two model membranes. Positive charges are critical to the peptide's adsorption, whereas the presence of hydrophobic Trp8 and Trp9 leads to its deeper insertion. Combining the hypothetical relationships between the membrane disordering and the antimicrobial and hemolytical activities with the simulated results, we designed three new IL-analogous peptides: IL-K7 (Pro7-->Lys), IL-F89 (Trp8 and Trp9-->Phe), and IL-K7F89 (Pro7-->Lys; Trp8 and Trp9-->Phe). The hemolytic activity of IL-F89 is considerably lower than that of IL, whereas the antimicrobial activity of IL-K7 is greatly enhanced. In particular, the de novo peptide IL-K7F89 exhibits higher antimicrobial activity against Escherichia coli; its hemolytic activity decreased to only 10% of that of IL. Our simulated and experimental results correlated well. This approach-coupling MD simulations with experimental design-is a useful strategy toward the rational design of AMPs for potential therapeutic use.

Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model

Continuum models that describe the effects of solvent and biological membrane molecules on the structure and behavior of antimicrobial peptides, holds a promise to improve our understanding of the mechanisms of antimicrobial action of these peptides. In such methods, a lipid bilayer model membrane is implicitly represented by multiple layers of relatively low dielectric constant embedded in a high dielectric aqueous solvent, while an antimicrobial peptide is accounted for by a dielectric cavity with fixed partial charge at the center of each one of its atoms. In the present work, we investigate the ability of continuum approaches to predict the most probable orientation of the β-hairpin antimicrobial peptide Protegrin-1 (PG-1) in DLPC lipid bilayers by calculating the difference in the transfer free energy from an aqueous environment to a membrane-water environment for multiple orientations. The transfer free energy is computed as a sum of two terms; polar/electrostatic and non-polar. They both include energetic and entropic contributions to the free energy. We numerically solve the Poisson-Boltzmann equation to calculate the electrostatic contribution to the transfer free energy, while the non-polar contribution to the free energy is approximated using a linear solvent accessible surface area relationships. The most probable orientation of PG-1 is that with the lowest relative transfer free energy. Our simulation results indicate that PG-1 assumes an oblique orientation in DLPC lipid bilayers. The predicted most favorable orientation was with a tilt angle of 19°, which is in qualitative agreement with the experimentally observed orientations derived from solid-state NMR data.

Effect of lipid composition on buforin II structure and membrane entry

Buforin II is a 21-amino acid polycationic antimicrobial peptide derived from a peptide originally isolated from the stomach tissue of the Asian toad Bufo bufo gargarizans. It is hypothesized to target a wide range of bacteria by translocating into cells without membrane permeabilization and binding to nucleic acids. Previous research found that the structure and membrane interactions of buforin II are related to lipid composition. In this study, we used molecular dynamics (MD) simulations along with lipid vesicle experiments to gain insight into how buforin II interacts differently with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) lipids. Fluorescent spectroscopic measurements agreed with the previous assertion that buforin II does not interact with pure PC vesicles. Nonetheless, the reduced entry of the peptide into anionic PG membranes versus neutral PC membranes during simulations correlates with the experimentally observed reduction in BF2 translocation through pure PG membranes. Simulations showing membrane entry into PC also provide insight into how buforin II may initially penetrate cell membranes. Our MD simulations also allowed us to consider how neutral PE lipids affect the peptide differently than PC. In particular, the peptide had a more helical secondary structure in simulations with PE lipids. A change in structure was also apparent in circular dichroism measurements. PE also reduced membrane entry in simulations, which correlates with decreased translocation in the presence of PE observed in previous studies. Together, these results provide molecular-level insight into how lipid composition can affect buforin II structure and function and will be useful in efforts to design peptides with desired antimicrobial and cell-penetrating properties.

Water at the surfaces of aligned phospholipid multibilayer model membranes probed with ultrafast vibrational spectroscopy

The dynamics of water at the surface of artificial membranes composed of aligned multibilayers of the phospholipid dilauroyl phosphatidylcholine (DLPC) are probed with ultrafast polarization selective vibrational pump-probe spectroscopy. The experiments are performed at various hydration levels, x = 2 - 16 water molecules per lipid at 37 degrees C. The water molecules are approximately 1 nm above or below the membrane surface. The experiments are conducted on the OD stretching mode of dilute HOD in H 2O to eliminate vibrational excitation transfer. The FT-IR absorption spectra of the OD stretch in the DLPC bilayer system at low hydration levels shows a red-shift in frequency relative to bulk water, which is in contrast to the blue-shift often observed in systems such as water nanopools in reverse micelles. The spectra for x = 4 - 16 can be reproduced by a superposition of the spectra for x = 2 and bulk water. IR Pump-probe measurements reveal that the vibrational population decays (lifetimes) become longer as the hydration level is decreased. The population decays are fit well by biexponential functions. The population decays, measured as a function of the OD stretch frequency, suggest the existence of two major types of water molecules in the interfacial region of the lipid bilayers. One component may be a clathrate-like water cluster near the hydrophobic choline group and the other may be related to the hydration water molecules mainly associated with the phosphate group. As the hydration level increases, the vibrational lifetimes of these two components decrease, suggesting a continuous evolution of the hydration structures in the two components associated with the swelling of the bilayers. The agreement of the magnitudes of the two components obtained from IR spectra with those from vibrational lifetime measurements further supports the two-component model. The vibrational population decay fitting also gives an estimation of the number of phosphate-associated water molecules and choline-associated water molecules, which range from 1 to 4 and 1 to 12, respectively, as x increases from 2 to 16. Time-dependent anisotropy measurements yield the rate of orientational relaxation as a function of x. The anisotropy decay is biexponential. The fast component is almost independent of x, and is interpreted as small orientational fluctuations that occur without hydrogen-bond rearrangement. The slower component becomes very long as the hydration level decreases. This component is a measure of the rate of complete orientational randomization, which requires H-bond rearrangement and is discussed in terms of a jump reorientation model.

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity

The therapeutic, antibiotic potential of antimicrobial peptides can be prohibitively diminished because of the cytotoxicity and hemolytic profiles they exhibit. Quantifying and predicting antimicrobial peptide toxicity against host cells is thus an important goal of AMP related research. In this work, we present quantitative structure activity relationships for toxicity of protegrin-like antimicrobial peptides against human cells (epithelial and red blood cells) based on physicochemical properties, such as interaction energies and radius of gyration, calculated from molecular dynamics simulations of the peptides in aqueous solvent. The hypothesis is that physicochemical properties of peptides, as manifest by their structure and interactions in a solvent and as captured by atomistic simulations, are responsible for their toxicity against human cells. Protegrins are beta-hairpin peptides with high activity against a wide variety of microbial species, but in their native state are toxic to human cells. Sixty peptides with experimentally determined toxicities were used to develop the models. We test the resulting relationships to determine their ability to predict the toxicity of several protegrin-like peptides. The developed QSARs provide insight into the mechanism of cytotoxic action of antimicrobial peptides. In a subsequent blind test, the QSAR correctly ranked four of five protegrin analogues newly synthesized and tested for toxicity.

On the nature of antimicrobial activity: a model for protegrin-1 pores

We conducted over 150 ns of simulation of a protegrin-1 octamer pore in a lipid bilayer composed of palmitoyloleoyl-phosphatidylethanolamine (POPE) and palmitoyloleoyl-phosphatidylglycerol (POPG) lipids mimicking the inner membrane of a bacterial cell. The simulations improve on a model of a pore proposed from recent NMR experiments and provide a coherent understanding of the molecular mechanism of antimicrobial activity. Although lipids tilt somewhat toward the peptides, the simulated protegrin-1 pore more closely follows the barrel-stave model than the toroidal-pore model. The movement of ions is investigated through the pore. The pore selectively allows negatively charged chloride ions to pass through at an average rate of one ion every two nanoseconds. Only two events are observed of sodium ions crossing through the pore. The potential of mean force is calculated for the water and both ion types. It is determined that the chloride ions move through the pore with ease, similarly to the water molecules with the exception of a zone of restricted movement midway through the pore. In bacteria, ions moving through the pore will compromise the integrity of the transmembrane potential. Without the transmembrane potential as a countermeasure, water will readily flow inside the higher osmolality cytoplasm. We determine that the diffusivity of water through a single PG-1 pore is sufficient to cause fast cell death by osmotic lysis.

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.