The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations.

Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.

Effect of Ionic Strength on Ibuprofenate Adsorption on a Lipid Bilayer of Dipalmitoylphosphatidylcholine from Molecular Dynamics Simulations.

In this work, the free energy change in the process of transferring ibuprofenate from the bulk solution to the center of a model of the dipalmitoylphosphatidylcholine bilayer at different NaCl concentrations was calculated. Two minima were found in the free energy profile: a local minimum, located in the vicinity of the membrane, and the global free energy minimum, found near the headgroup region. The downward shift of free energy minima with increasing NaCl concentration is consistent with the results of previous works. Conversely, the upward shift of the free energy maximum with increasing ionic strength is due to the competition of sodium ions and lipids molecules to coordinate with ibuprofenate and neutralize its charge. In addition, normal molecular dynamics simulations were performed to study the effects of the ibuprofenate on the lipid bilayer and in the presence of a high ibuprofenate concentration. The effect of ionic strength on the properties of the lipid bilayer and on lipid-drug interactions was analyzed. The area per lipid shrinking with increasing ionic strength, volume of lipids, and thickness of the bilayer is consistent with the experimental results. At a very high ibuprofenate concentration, the lipid bilayer dehydrates, and it consequently transforms into the gel phase, thus blocking the permeation.

Pseudorotaxane formation affected by stereo-electronic effects. A theoretical and experimental study.

We report a theoretical and experimental study on different complexes of pseudorotaxanes possessing pyridine axles. In order to evaluate the stereo-electronic effects of the methyl substituents in the pyridine ring, complexes with different substitution patterns were synthesized. In this way, it was possible to analyze the different behaviors of these complexes according to the positions of their methyl substituents. Combined techniques of molecular dynamics and quantum mechanical calculations with the help of molecular electrostatic potentials for a simpler visualization of the electronic effects were employed. We have sought experimental support of NMR spectroscopy analysis to corroborate the conclusions obtained from the molecular simulations. Our results not only clearly demonstrate that both electronic and steric effects play key roles in the feasibility of the formation of such complexes, but also the simulations reported here might predict the degree of difficulty of their formation. The combination of computational techniques employed here seems to be an excellent approach to be able to predict whether or not a complex can be formed and with what degree of difficulty. In addition, our experimental and theoretical results have allowed us to visualize the formation of external complexes in the rotaxanes reported here. In this case, the use of bolaforms with trimethylammonium groups at both ends was very useful to evaluate in detail the formation of the so-called external complexes in these systems.

Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study.

In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.

Role of membrane curvature on the activation/deactivation of Carnitine Palmitoyltransferase 1A: A coarse grain molecular dynamic study.

Carnitine Palmitoyltransferase 1A (CPT 1A) is an enzyme anchored to the outer mitochondrial membrane (OMM), where it regulates the passage of fatty acids into the mitochondria and intervenes in the process of ß-oxidation of long-chain fatty acids. Although CPT 1A is inhibited by malonyl-CoA, its activity is also modulated by the curvature of OMM. This modulation depends on the behavior of the N-terminal domain (NTD), which can be adsorbed onto the OMM (nonactive CPT 1A) or interacting with the C-terminal domain (active CPT 1A). Aimed to provide mechanistic insights on the regulatory mechanism of CPT 1A, we studied the influence of the bilayer curvature on the NTD behavior through a series of coarse-grained (CG) molecular dynamics simulations using curved and planar membranes. Comparative analysis suggests that the main determinant for the activation/deactivation of the enzyme is the tilt angle orientation of the transmembrane (TM) domains. Planar membranes induce a wide variation on the tilt angle orientation of TM helices, while curved geometries promote small angles with the membrane normal. Our results identify the first TM domain as an important component of the membrane sensing mechanism.

Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer.

Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP2-, respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ mol-1 located at z = ±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP2- is ∼-35 kJ mol-1 located at z = ±â€¯1.4 nm (from the lipid bilayer center), and the maximum reaches ∼35 kJ mol-1 at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.

Modeling DMPC lipid membranes with SIRAH force-field.

Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www.sirahff.com ). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.

Theoretical and Experimental Study of Inclusion Complexes of ß-Cyclodextrins with Chalcone and 2',4'-Dihydroxychalcone.

The inclusion complexes formed by chalcone and 2',4'-dihydroxychalcone with ß-cyclodextrin have been studied combining experimental (phase solubility diagrams, Fourier transform infrared spectroscopy) and molecular modeling (molecular dynamics, quantum mechanics/molecular mechanics calculations) techniques. The formation constants of the complexes were determined at different temperatures, and the thermodynamic parameters of the process were obtained. The inclusion of chalcone in ß-cyclodextrin is an exothermic process, while the inclusion of 2',4'-dihydroxychalcone is endothermic. Free energy profiles, derived from umbrella sampling using molecular dynamics simulations, were constructed to analyze the binding affinity and the complexation reaction at a molecular level. Hybrid QM/MM calculations were also employed to obtain a better description of the energetic and structural aspects of the complexes. The intermolecular interactions that stabilize both inclusion complexes were characterized by means of quantum atoms in molecules theory and reduce density gradient method. The calculated interactions were experimentally observed using FTIR.

Study of the effect of Na+ and Ca2+ ion concentration on the structure of an asymmetric DPPC/DPPC + DPPS lipid bilayer by molecular dynamics simulation.

A molecular dynamics simulation study of the steady and dynamic properties of an asymmetric phospholipid bilayer was carried out in the presence of sodium or calcium ions. The asymmetric lipid bilayer was seen to resemble a cellular membrane of an eukaryotic cell, which was modeled by dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylserine (DPPS), placing the DPPS in one of the two leaflets of the lipid bilayer. From a numerical analysis of the simulated trajectories, information was obtained with atomic resolution for both membrane leaflet concerning the effect of bilayer asymmetry on different properties of the lipid/water interface, such as the translational diffusion coefficient and rotational relaxation time of the water molecules, lipid hydration, and residence time of water around different lipid atoms. In addition, information related to lipid conformation, and lipid-lipid interactions was also analyzed.

Study of the benzocaine transfer from aqueous solution to the interior of a biological membrane.

The precise molecular mechanism of general anesthetics remains unknown. It is therefore important to understand where molecules with anesthetic properties localize within biological membranes. We have determined the free energy profile of a benzocaine molecule (BZC) across a biological membrane using molecular dynamics simulation. We use an asymmetric phospholipid bilayer with DPPS in one leaflet of a DPPC bilayer (Lopez Cascales et al. J. Phys. Chem. B 2006, 110, 2358-2363) to model a biological bilayer. From the free energy profile, we predict the zone of actuation of a benzocaine is located in the hydrocarbon region or at the end of the lipid head, depending of the presence of charged lipids (DPPS) in the leaflet. We observe a moderate increase in the disorder of the membrane and in particular an increase in the disorder of DPPS. Static and dynamic physicochemical properties of the benzocaine, such as its dipole orientation, translational diffusion coefficient, and rotational relaxation time were measured.

Analysis of trace metal humic acid interactions using counterion condensation theory.

Recent extensions of counterion condensation theory, originally developed for well-defined linear polyelectrolytes, enable us to analyze the interaction of trace metals with humic acid. In the present model, the heterogeneity of the macromolecule is taken into account as well as the chemical binding of the considered metal ions to the humic material. Experimentally, potentiometric titrations have been performed for humic acid in solution in the presence of different environmentally important (heavy) metals (Ca, Cd, Cu, Ni, and Pb) at various metal concentrations by titrating with potassium hydroxide without additional salt. From proton release data obtained for the initial point in the titration, it was estimated that the interaction of the different metals with the humic acid in terms of binding strength increased in the order Ca < Cd approximately = Ni < Pb approximately = Cu. These results were confirmed by model analysis. Experimentally obtained apparent dissociation constants were in good agreement for the humic acid systems containing Ca, Cd, and Ni at concentrations ranging from 0 up to 0.75 x 10(-3) mol L(-1) and polymer dissociation degree from about 0.1 up to approximately 0.8. Also for the Cu/humic acid and Pb/humic acid systems, the agreement between experimental data and calculated data was satisfactory atthe lowest metal concentrations over the complete titration curve. For elevated levels of Cu and Pb, the agreement between experimental data and theoretical calculations becomes less satisfactory at low degrees of dissociation of the humic acid. This distortion of the potentiometric curves is probably due to changes in the intrinsic pK of the functional groups due to metal binding. This complex process is not included in present polyelectrolytic models.