Relating Molecular Dynamics Simulations to Functional Activity for Gly-Rich Membranolytic Helical Kiadin Peptides.

Kiadins are in silico designed peptides with a strong similarity to diPGLa-H, a tandem sequence of PGLa-H (KIAKVALKAL) and with single, double or quadruple glycine substitutions. They were found to show high variability in their activity and selectivity against Gram-negative and Gram-positive bacteria, as well as cytotoxicity against host cells, which are influenced by the number and placing of glycine residues along the sequence. The conformational flexibility introduced by these substitutions contributes differently peptide structuring and to their interactions with the model membranes, as observed by molecular dynamics simulations. We relate these results to experimentally determined data on the structure of kiadins and their interactions with liposomes having a phospholipid membrane composition similar to simulation membrane models, as well as to their antibacterial and cytotoxic activities, and also discuss the challenges in interpreting these multiscale experiments and understanding why the presence of glycine residues in the sequence affected the antibacterial potency and toxicity towards host cells in a different manner.

Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes.

Antimicrobial peptides (AMPs) can be directed to specific membranes based on differences in lipid composition. In this study, we performed atomistic and coarse-grained simulations of different numbers of the designed AMP adepantin-1 with a eukaryotic membrane, cytoplasmic Gram-positive and Gram-negative membranes, and an outer Gram-negative membrane. At the core of adepantin-1's behavior is its amphipathic α-helical structure, which was implemented in its design. The amphipathic structure promotes rapid self-association of peptide in water or upon binding to bacterial membranes. Aggregates initially make contact with the membrane via positively charged residues, but with insertion, the hydrophobic residues are exposed to the membrane's hydrophobic core. This adaptation alters the aggregate's stability, causing the peptides to diffuse in the polar region of the membrane, mostly remaining as a single peptide or pairing up to form an antiparallel dimer. Thus, the aggregate's proposed role is to aid in positioning the peptide into a favorable conformation for insertion. Simulations revealed the molecular basics of adepantin-1 binding to various membranes, and highlighted peptide aggregation as an important factor. These findings contribute to the development of novel anti-infective agents to combat the rapidly growing problem of bacterial resistance to antibiotics.

Anisaxins, helical antimicrobial peptides from marine parasites, kill resistant bacteria by lipid extraction and membrane disruption.

An infecting and propagating parasite relies on its innate defense system to evade the host's immune response and to survive challenges from commensal bacteria. More so for the nematode Anisakis, a marine parasite that during its life cycle encounters both vertebrate and invertebrate hosts and their highly diverse microbiotas. Although much is still unknown about how the nematode mitigates the effects of these microbiota, its antimicrobial peptides likely play an important role in its survival. We identified anisaxins, the first cecropin-like helical antimicrobial peptides originating from a marine parasite, by mining available genomic and transcriptomic data for Anisakis spp. These peptides are potent bactericidal agents in vitro, selectively active against Gram-negative bacteria, including multi-drug resistant strains, at sub-micromolar concentrations. Their interaction with bacterial membranes was confirmed by solid state NMR (ssNMR) and is highly dependent on the peptide concentration as well as peptide to lipid ratio, as evidenced by molecular dynamics (MD) simulations. MD results indicated that an initial step in the membranolytic mode of action involves membrane bulging and lipid extraction; a novel mechanism which may underline the peptides' potency. Subsequent steps include membrane permeabilization leading to leakage of molecules and eventually cell death, but without visible macroscopic damage, as shown by atomic force microscopy and flow cytometry. This membranolytic antibacterial activity does not translate to cytotoxicity towards human peripheral blood mononuclear cells (HPBMCs), which was minimal at well above bactericidal concentrations, making anisaxins promising candidates for further drug development. STATEMENT OF SIGNIFICANCE: Witnessing the rapid spread of antibiotic resistance resulting in millions of infected and dozens of thousands dying worldwide every year, we identified anisaxins, antimicrobial peptides (AMPs) from marine parasites, Anisakis spp., with potent bactericidal activity and selectivity towards multi-drug resistant Gram-negative bacteria. Anisaxins are membrane-active peptides, whose activity, very sensitive to local peptide concentrations, involves membrane bulging and lipid extraction, leading to membrane permeabilization and bacterial cell death. At the same time, their toxicity towards host cells is negligible, which is often not the case for membrane-active AMPs, therefore making them suitable drug candidates. Membrane bulging and lipid extraction are novel concepts that broaden our understanding of peptide interactions with bacterial functional structures, essential for future design of such biomaterials.

A Simple Two Dimensional Model of Methanol.

Methanol is the simplest alcohol and possible energy carrier because it is easier to store than hydrogen and burns cleaner than fossil fuels. It is a colorless liquid, completely miscible with water and organic solvents and is very hygroscopic. Here, simple two-dimensional models of methanol, based on Mercedes-Benz (MB) model of water, are examined by Monte Carlo simulations. Methanol particles are modeled as dimers formed by an apolar Lennard-Jones disk, mimicking the methyl group, and a sphere with two hydrogen bonding arms for the hydroxyl group. The used models are the one proposed by Hribar-Lee and Dill (Acta Chimica Slovenica, 53:257, 2006.) with the overlapping discs and a new model with tangentially fused dimers. The comparison was done between the models, in connection to the MB water, as well as with experimental results and with new simulations done for 3D models of methanol. Both 2D models show similar trends in structuring and thermodynamics. The difference is the most pronounced at lower temperatures, where the smaller model exhibits spontaneous crystallization, while the larger model shows metastable states. The 2D structural organization represents well the clustering tendency observed in 3D models, as well as in experiments. The models qualitatively agree with the bulk methanol thermodynamic properties like density and isothermal compressibility, however, heat capacity at the constant pressure shows trend more similar to the water behavior. This work on the smallest amphiphilic organic solute provides a simple testing ground to study the competition between polar and non-polar effects within the molecule and physical properties.

Designed peptide with a flexible central motif from ranatuerins adapts its conformation to bacterial membranes.

The long-standing goal in the field of peptide antibiotics has been to design lead compounds that have a wide spectrum of excellent antibacterial activity but are nontoxic to human cells. Gram-negative and Gram-positive bacteria have very different membranes, which are additionally modified in some drug-resistant species, presenting a challenge for the design of a single membrane-active peptide able to adapt its conformation to various physical properties of membrane microenvironments. In this paper, we describe how a peptide sequence can be constructed starting from an adaptable dynamic turn tandem motif in a central location. The peptide, named flexampin, has been examined firstly by molecular dynamics simulations. It uses a flexible central motif and designed helix-forming cationic amphipathic arms to form a boomerang-like, L-shape, V-shape, and hairpin, super-secondary structures, whichever is the best in matching amphipathic and hydrophobic microenvironments it encounters. Secondly, activity measurements showed that flexampin is bactericidal at low micromolar concentrations against Gram-positive and Gram-negative strains including some multidrug resistant clinical isolates, while it is nontoxic for human circulating blood cells, does not cause DNA damage, and has good selectivity for bacterial cells in comparison to human cells. It is the first membrane-active peptide designed with the ability to self-adjust the orientation of its two cationic helical arms, 3D-hydrophobic moment, and dipole moment for obtaining a better grasp of anionic polar head groups at bacterial membrane surfaces.

Antibacterial Activity Affected by the Conformational Flexibility in Glycine-Lysine Based α-Helical Antimicrobial Peptides.

Antimicrobial peptides often show broad-spectrum activity due to a mechanism based on bacterial membrane disruption, which also reduces development of permanent resistance, a desirable characteristic in view of the escalating multidrug resistance problem. Host cell toxicity however requires design of artificial variants of natural AMPs to increase selectivity and reduce side effects. Kiadins were designed using rules obtained from natural peptides active against E. coli and a validated computational algorithm based on a training set of such peptides, followed by rational conformational alterations. In vitro activity, tested against ESKAPE strains (ATCC and clinical isolates), revealed a varied activity spectrum and cytotoxicity that only in part correlated with conformational flexibility. Peptides with a higher proportion of Gly were generally less potent and caused less bacterial membrane alteration, as observed by flow cytometry and AFM, which correlate to structural characteristics as observed by circular dichroism spectroscopy and predicted by molecular dynamics calculations.

PGLa-H tandem-repeat peptides active against multidrug resistant clinical bacterial isolates.

Antimicrobial peptides (AMPs) are promising candidates for new antibiotic classes but often display an unacceptably high toxicity towards human cells. A naturally produced C-terminal fragment of PGLa, named PGLa-H, has been reported to have a very low haemolytic activity while maintaining a moderate antibacterial activity. A sequential tandem repeat of this fragment, diPGLa-H, was designed, as well as an analogue with a Val to Gly substitution at a key position. These peptides showed markedly improved in vitro bacteriostatic and bactericidal activity against both reference strains and multidrug resistant clinical isolates of Gram-negative and Gram-positive pathogens, with generally low toxicity for human cells as assessed by haemolysis, cell viability, and DNA damage assays. The glycine substitution analogue, kiadin, had a slightly better antibacterial activity and reduced haemolytic activity, which may correlate with an increased flexibility of its helical structure, as deduced using molecular dynamics simulations. These peptides may serve as useful lead compounds for developing anti-infective agents against resistant Gram-negative and Gram-positive species.

The microscopic structure of cold aqueous methanol mixtures.

The evolution of the micro-segregated structure of aqueous methanol mixtures, in the temperature range 300 K-120 K, is studied with computer simulations, from the static structural point of view. The structural heterogeneity of water is reinforced at lower temperatures, as witnessed by a pre-peak in the oxygen-oxygen structure factor. Water tends to form predominantly chain-like clusters at lower temperatures and smaller concentrations. Methanol domains have essentially the same chain-like cluster structure as the pure liquid at high concentrations and becomes monomeric at smaller ones. Concentration fluctuations decrease with temperature, leading to quasi-ideal Kirkwood-Buff integrals, despite the enhanced molecular interactions, which we interpret as the signature of non-interacting segregated water and methanol clusters. This study throws a new light on the nature of the micro-heterogeneous structure of this mixture: the domain segregation is essentially based on the appearance of linear water clusters, unlike other alcohol aqueous mixtures, such as with propanol or butanol, where the water domains are more bulky.

Micro-heterogeneity versus clustering in binary mixtures of ethanol with water or alkanes.

Ethanol is a hydrogen bonding liquid. When mixed in small concentrations with water or alkanes, it forms aggregate structures reminiscent of, respectively, the direct and inverse micellar aggregates found in emulsions, albeit at much smaller sizes. At higher concentrations, micro-heterogeneous mixing with segregated domains is found. We examine how different statistical methods, namely correlation function analysis, structure factor analysis and cluster distribution analysis, can describe efficiently these morphological changes in these mixtures. In particular, we explain how the neat alcohol pre-peak of the structure factor evolves into the domain pre-peak under mixing conditions, and how this evolution differs whether the co-solvent is water or alkane. This study clearly establishes the heuristic superiority of the correlation function/structure factor analysis to study the micro-heterogeneity, since cluster distribution analysis is insensitive to domain segregation. Correlation functions detect the domains, with a clear structure factor pre-peak signature, while the cluster techniques detect the cluster hierarchy within domains. The main conclusion is that, in micro-segregated mixtures, the domain structure is a more fundamental statistical entity than the underlying cluster structures. These findings could help better understand comparatively the radiation scattering experiments, which are sensitive to domains, versus the spectroscopy-NMR experiments, which are sensitive to clusters.

Simple and complex disorder in binary mixtures with benzene as a common solvent.

Substituting benzene for water in computer simulations of binary mixtures allows one to study the various forms of disorder, without the complications often encountered in aqueous mixtures. In particular, we study the relationship between the local order generated by different types of molecular interactions and the nature of the global disorder, by analyzing the relationship between the concentration fluctuations and the correlation functions and the associated structure factors. Alkane-benzene mixtures are very close to ideal mixtures, despite appreciable short range shape mismatch interactions, acetone-benzene mixtures appear as a good example of regular mixtures, and ethanol-benzene mixtures show large micro-segregation. In the latter case, we can unambiguously demonstrate, unlike in the case of water, the appearance of domain-domain correlations, both in the correlation functions and the structure factor calculated in computer simulations. This finding helps to confirm the existence of a pre-peak in the structure factor associated with the micro-heterogeneity, which was speculated from several of our previous simulations of aqueous-alcohol mixtures. The fact that benzene as a solvent allows us to solve some of the problems that could not be solved with water points towards some of the particularities of water as a solvent, which we discuss herein. The concept of molecular emulsion put forward in our earlier work is useful in formulating these differences between water and benzene through the analogy with direct and inverse micellar aggregates.

Concentration fluctuations and microheterogeneity in aqueous amide mixtures.

The relationship between concentration fluctuations and the microheterogeneous status of aqueous amide mixtures is addressed through the molecular dynamics study of three different amides, namely, formamide, N-methylformamide, and dimethylformamide. The computer simulations provide structural evidence that these mixtures exhibit considerable microheterogeneity, in apparent contrast to the experimentally obtained Kirkwood-Buff integrals which indicate that these mixtures should be near ideal. This contradiction is addressed by distinguishing microheterogeneity from concentration fluctuations. The former is the result of mixing H-bonding species under specific constraints due to various bonding possibilities between the molecules, while the second is related to the average relative distribution of the molecules. The relationship between these two different quantities is analyzed and illustrated in terms of the partial site-site structure factors. Small wave-number prepeaks relate to the microheterogeneity while zero wave-number value relates to the concentration fluctuations. A simple analytical statistical model for the microheterogeneity is formulated, which allows to discuss the small wave-number behavior of these structure factors in terms of the kinetics of the transient cluster formation, as observed in the computer simulations.

Microstructure of neat alcohols.

Formation of microstructure in homogeneous associated liquids is analyzed through the density-density pair correlation functions, both in direct and reciprocal space, as well as an effective local one-body density function. This is illustrated through a molecular dynamics study of two neat alcohols, namely, methanol and tert-butanol, which have a rich microstructure: chainlike molecular association for the former and micellelike for the latter. The relation to hydrogen bonding interaction is demonstrated. The apparent failure to find microstructure in water--a stronger hydrogen bonding liquid--with the same tools is discussed.

Microstructure of neat alcohols: a molecular dynamics study.

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.

Basic charge clusters and predictions of membrane protein topology.

The topology predictor SPLIT 4.0 (http://pref.etfos.hr) predicts the sequence location of transmembrane helices by performing an automatic selection of optimal amino acid attribute and corresponding preference functions. The best topological model is selected by choosing the highest absolute bias parameter that combines the bias in basic charge motifs and the bias in positive residues (the "positive inside rule") with the charge difference across the first transmembrane segment. Basic charge motifs, such as the BBB, BXXBB, and BBXXB motifs in alpha-helical integral membrane proteins, are significantly more frequent near cytoplasmic membrane surface than expected from the Arg/Lys (B) frequency. The predictor's accuracy is 99% for predicting 178 transmembrane helices in all membrane proteins or subunits of known 3D structure.