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Lipid bilayers are active participants in many crucial biological processes. They can be observed in different phases, liquid and solid, respectively. The liquid phase is predominant in biological systems. The solid phase, both crystalline and gel phases, is under investigation due to its resilience to mechanical stress and tight packing of lipids. The mechanical properties of lipids affect their dynamics, therefore influencing the transformation of cell plasma and the endomembrane. Mechanical properties of lipid bilayers are also an important parameter in the design and production of supramolecular lipid-based drug delivery systems. To this end, in this work, we focused on investigating the effect of solid phases of lipid bilayers on their structural parameters and mechanical properties using theoretical molecular dynamics studies on atomistic models of whole vesicles. Those include area per lipid, membrane thickness, density vesicle profiles, bending rigidity coefficient, and area compressibility. Additionally, the bending rigidity coefficient was measured using the flicker noise spectroscopy. The two approaches produced very similar and consistent results. We showed that, contrary to our expectations, bending rigidity coefficients of solid-ordered bilayers for vesicles decreased with an increase in lipid transition temperature. This tendency was reverse in planar systems. Additionally, we have observed an increase of membrane thickness and area compressibility and a decrease of area per lipid. We hope these results will provide valuable mechanical insight for the behavior in solid phases and differences between spherical and planar confirmations.

Alzheimer&rsquo, s disease (AD) is a neurodegenerative disease that results in memory loss and the impairment of cognitive skills. Several mechanisms of AD&rsquo, s pathogenesis were proposed, such as the progressive accumulation of amyloid-&beta, (A&beta, ) and &tau, pathology. Nevertheless, the exact neurodegenerative mechanism of the A&beta, remains complex and not fully understood. This paper proposes an alternative hypothesis of the mechanism based on maintaining the neuron membrane&rsquo, s mechanical balance. The incorporation of A&beta, decreases the lipid membrane&rsquo, s elastic properties, which eventually leads to the impairment of membrane clustering, disruption of mechanical wave propagation, and change in gamma oscillations. The first two disrupt the neuron&rsquo, s ability to function correctly while the last one decreases sensory encoding and perception enabling. To begin discussing this mechanical-balance hypothesis, we measured the effect of two selected peptides, A&beta, 40 and A&beta, 42, as well as their fluorescently labeled modification, on membrane mechanical properties. The decrease of bending rigidity, consistent for all investigated peptides, was observed using molecular dynamic studies and experimental flicker-noise techniques. Additionally, wave propagation was investigated with molecular dynamic studies in membranes with and without incorporated neurodegenerative peptides. A change in membrane behavior was observed in the membrane system with incorporated A&beta

The spreading of antibiotic-resistant bacteria strains is one of the most serious problem in medicine to struggle nowadays. This triggered the development of alternative antimicrobial agents in recent years. One of such group is Gemini surfactants which are massively synthesised in various structural configurations to obtain the most effective antibacterial properties. Unfortunately, the comparison of antimicrobial effectiveness among different types of Gemini agents is unfeasible since various protocols for the determination of Minimum Inhibitory Concentration are used. In this work, we proposed alternative, computational, approach for such comparison. We designed a comprehensive database of 250 Gemini surfactants. Description of structure parameters, for instance spacer type and length, are included in the database. We parametrised modelled molecules to obtain force fields for the entire Gemini database. This was used to conduct in silico studies using the molecular dynamics to investigate the incorporation of these agents into model E. coli inner membrane system. We evaluated the effect of Gemini surfactants on structural, stress and mechanical parameters of the membrane after the agent incorporation. This enabled us to select four most likely membrane properties that could correspond to Gemini’s antimicrobial effect. Based on our results we selected several types of Gemini spacers which could demonstrate a particularly strong effect on the bacterial membranes.

The widespread problem of resistance development in bacteria has become a critical issue for modern medicine. To limit that phenomenon, many compounds have been extensively studied. Among them were derivatives of available drugs, but also alternative novel detergents such as Gemini surfactants. Over the last decade, they have been massively synthesized and studied to obtain the most effective antimicrobial agents, as well as the most selective aids for nanoparticles drug delivery. Various protocols and distinct bacterial strains used in Minimal Inhibitory Concentration experimental studies prevented performance benchmarking of different surfactant classes over these last years. Motivated by this limitation, we designed a theoretical methodology implemented in custom fast screening software to assess the surfactant activity on model lipid membranes. Experimentally based QSAR (quantitative structure-activity relationship) prediction delivered a set of parameters underlying the Diptool software engine for high-throughput agent-membrane interactions analysis. We validated our software by comparing score energy profiles with Gibbs free energy from the Adaptive Biasing Force approach on octenidine and chlorhexidine, popular antimicrobials. Results from Diptool can reflect the molecule behavior in the lipid membrane and correctly predict free energy of translocation much faster than classic molecular dynamics. This opens a new venue for searching novel classes of detergents with sharp biologic activity.

Inflammatory bowel disease (IBD) is a chronic, incurable disease involving the gastrointestinal tract. It is characterized by complex, unclear pathogenesis, increased prevalence worldwide, and a wide spectrum of extraintestinal manifestations and comorbidities. Recognition of IBD remains challenging and delays in disease diagnosis still poses a significant clinical problem as it negatively impacts disease outcome. The main diagnostic tool in IBD continues to be invasive endoscopy. We aimed to create an IBD machine learning prediction model based on routinely performed blood, urine, and fecal tests. Based on historical patients’ data (702 medical records: 319 records from 180 patients with ulcerative colitis (UC) and 383 records from 192 patients with Crohn’s disease (CD)), and using a few simple machine learning classificators, we optimized necessary hyperparameters in order to get reliable few-features prediction models separately for CD and UC. Most robust classificators belonging to the random forest family obtained 97% and 91% mean average precision for CD and UC, respectively. For comparison, the commonly used one-parameter approach based on the C-reactive protein (CRP) level demonstrated only 81% and 61% average precision for CD and UC, respectively. Results of our study suggest that machine learning prediction models based on basic blood, urine, and fecal markers may with high accuracy support the diagnosis of IBD. However, the test requires validation in a prospective cohort.

Flotillins are the major structural proteins in erythroid raft domains. We have shown previously that the dynamic nanoscale organization of raft domains in erythroid cells may depend on flotillin-MPP1 interactions. Here, by using molecular dynamic simulations and a surface plasmon resonance-based approach we determined that high-affinity complexes of MPP1 and flotillins are formed via a so far unidentified region within the D5 domain of MPP1. Significantly, this particular “flotillin binding motif” is of key physiological importance, as overexpression of peptides containing this motif inhibited endogenous MPP1-flotillin interaction in erythroid precursor cells, thereby causing lateral disorganization of raft domains. This was reflected by both reduction in the plasma membrane order and markedly decreased activation of signal transduction via the raft-dependent insulin receptor pathway. Our data highlight new molecular details concerning the mechanism whereby MPP1 functionally links flotillins to exert their physiological role in raft domain formation.

The increasing problem of antibiotic resistance in bacteria requires the development of new antimicrobial candidates. There are several well-known substances with commercial use, but their molecular mode of action is not fully understood. In this paper, we focus on two commonly used antimicrobial agents from the detergent family – octenidine dichloride (OCT) and chlorhexidine digluconate (CHX). Both of them are reported to be agents selectively attacking the cell membrane through interaction inducing membrane disruption by emulsification. They are believed to present electrostatic selectivity towards charged lipids. In this study, we tested this hypothesis and we revised previously proposed molecular mechanisms of action. Employing a variety of techniques such as molecular dynamics, zeta potential with dynamic light scattering, vesicle fluctuation spectroscopy, carboxyfluorescein (CXF) leakage measurement and fluorescence trimethylammonium-diphenylhexatriene (TMA-DPH) and DPH based studies for determination of OCT and CHX membrane location, we performed experimental studies using two model membrane systems – zwitterionic PC and negatively charged PG (18:1/18:1):PC (16:0/18:1) 3:7, respectively. These studies were extended by molecular dynamics simulations performed on a 3-component bacterial membrane model system to further test interactions with another negatively charged lipid, cardiolipin. In summary, our study demonstrated that detergent selectivity is far more complicated than supposed simple electrostatic interactions. While OCT does disrupt the membrane, our results suggest that its primary selectivity was more linked to mechanical properties of the membrane. On the other hand, CHX did not disrupt membranes as a primary activity, nor did it show any sign of electrostatic selectivity toward negatively charged membranes at any stage of interactions, which suggest membrane disruption by influencing more discrete membrane properties.

Hereditary spherocytosis (HS), the most commonly inherited hemolytic anemia in northern Europeans, comprises a group of diseases whose heterogeneous genetic basis results in a variable clinical presentation. High-throughput genome sequencing methods have made a leading contribution to the recent progress in research on and diagnostics of inherited diseases and inspired us to apply whole exome sequencing (WES) to identify potential mutations in HS. The data presented here reveal a novel mutation probably responsible for HS in a single Polish family. Patients with clinical evidence of HS (clinical symptoms, hematological data, and EMA test) were enrolled in the study. The examination of the resulting WES data showed a number of polymorphisms in 71 genes associated with known erythrocyte pathologies (including membranopathies, enzymopathies, and hemoglobinopathies). Only a single SPTB gene variant indicated the possible molecular mechanism of the disease in the studied family. The new missense mutation p.C183Y was identified using WES in the SPTB gene, which is most likely the cause of clinical symptoms typical of hereditary spherocytosis (membranopathy) due to structural and functional impairments of human β-spectrin. This mutation allows for a better understanding of the molecular mechanism(s) of one of the membranopathies, hereditary spherocytosis.

GABAA receptors (GABAARs) are crucial in mediating inhibition in the adult mammalian brain. Although the kinetics of this receptor has been extensively studied, the molecular picture of interactions occurring at various channel conformations remains elusive. While electrophysiology combined with mutagenesis sheds light on the role of specific residues, ultrastructural studies reveal static structures which, in the case of GABAARs, are limited to the β3 homomer. To take advantage of the newest crystal structures of cys-loop receptors, a homology model of α1β2γ2 GABAAR in the unbound closed state was built using a template of the homomeric glycine receptor in the closed state. The template model contained strychnine molecules at the binding sites which were removed and molecular dynamics was used to study the system relaxation. The modeled GABAAR preserved the closed conformation. Two interfaces forming orthosteric binding sites (β2/α1) exhibited opening due to the outward shift of loop C. Similar movement, although less pronounced, was observed at the α1/γ2 (modulatory) interface. In contrast, interfaces α1/β2 and γ2/β2 remained closed. The former one, due to interactions mediated mainly by loops C and F, affected the neighboring β2/α1 interface leading to asymmetry between the orthosteric binding sites. Such interactions were not observed at the β2/α1 interface preceded by a γ2 subunit. As expected, in the channel pore, the conserved leucine gate and selectivity filter were present. However, an additional constriction was found at the top of the pore which differed from a typical hydrophobic channel gate as it consisted of charged residues. Interestingly, this site showed a capacity to trap chloride ions and to undergo conformation transition-like expansion, suggesting an impact on pore properties. In conclusion, our homology model faithfully reproduced major features of heteromeric GABAARs offering insight into the underlying mechanisms of stabilizing the shut conformation and chloride ion interaction with the channel pore.

In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.

Faced with the worldwide spread of multidrug-resistant (MDR) bacterial strains, together with a lack of any appropriate treatment, urgent steps to combat infectious diseases should be taken. Usually, bacterial components are studied to understand, by analogy, the functioning of human proteins. However, molecular data from bacteria gathered over the past decades provide a sound basis for the search for novel approaches in medical care. With this current work, we want to direct attention to inhibition of the vSGLT glucose transporter from Vibrio parahaemolyticus belonging to the sodium solute symporter (SSS) family, to block sugar transport into the bacterial cell and, as a consequence, to limit its growth. Potential bacteriostatic properties can be drawn from commercially available drugs developed for human diseases. This goal can also be reached with natural components from traditional herbal medicine. The presented data from the numerical analysis of 44 known inhibitors of sodium glucose symporters shed light on potential novel approaches in fighting Gram-negative multidrug-resistant microorganisms. Graphical abstract Molecular view on vSGLT channel inhibition by gneyulin B, the compound of natural origin.

We report a multistep strategy of biochemical surface modifications that resulted in the synthesis of new, effective and biocompatible intravascular implants coating with immobilized anti-CD133 antibodies, that proved to be the most effective in endothelial progenitor cells capture and reduced smooth muscle cells growth. Biomolecules were immobilized on differently functionalized surfaces. The distribution, nanostructural characteristics and intramolecular interactions of anti-CD133 molecules as well as their ability to bind EPCs was evaluated. We also tempted to build a molecular model of the CD133 protein to study antigen-antibody interactions. CD133 protein is expressed in endothelial progenitor cells (EPCs). Absence of preferential interaction site on CD133, but rather a presence of a small binding area, may be the specificity of reconnaissance sequence, thus importantly increasing the probability of CD133 protein binding. After all, regarding our molecular model, we are convinced that specific, and large enough interactions between anti-CD133 coating stent surface and CD133 present on EPCs will reduce risk of restenosis by favoring the endothelial growth. Additionally, the safety study of the vivo performance of modified titania based surface was performed using small animal models. No allergological or toxical local or systemic adverse effects of the developed coatings were noted.

The condensing effect of aminoglycoside antibiotics on the structure of double-stranded DNA was examined. The selective condensation of DNA by small molecules is an interesting approach in biotechnology. Here, we present the interaction between calf thymus DNA and three types of antibiotic molecules: tobramycin, kanamycin, and neomycin. Several techniques were applied to study this effect. Atomic force microscopy, transmission electron microscopy images, and nuclear magnetic resonance spectra showed that the interaction of tobramycin with double-stranded DNA caused the rod, toroid, and sphere formation and very strong condensation of DNA strands, which was not observed in the case of other aminoglycosides used in the experiment. Studies on the mechanisms by which small molecules interact with DNA are important in understanding their functioning in cells, in designing new and efficient drugs, or in minimizing their adverse side effects. Specific interactions between tobramycin and DNA double helix was modeled using molecular dynamics simulations. Simulation study shows the aminoglycoside specificity to bend DNA double helix, shedding light on the origins of toroid formation. This phenomenon may lighten the ototoxicity or nephrotoxicity issues, but also other adverse reactions of aminoglycoside antibiotics in the human body. Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1095-9) contains supplementary material, which is available to authorized users.

The confinement and the understanding of ion transport through ionic channels when they are confined inside solid-state nanopores smaller than 10 nm remains a challenge. Here we report on the fabrication of biomimetic nanopores with high length (5 μm)/diameter (smaller than 10 nm) ratio obtained using both a track-etched technique and atomic layer deposition on flexible membranes. These membranes present uniform hydrophobic nanopores with a low roughness inside the pores. Gramicidin A is then confined inside nanopores (diameter 10.6, 5.7, and ∼2 nm) leading to the NaCl ionic transport mechanism through a hybrid nanopore similar to the biological ones especially for small diameter (5.7 and ∼2 nm).

We report the production of a robust hybrid polyene/artificial solid-state membrane. The production of this membrane is based on the confinement of Amphotericin B inside the cylindrical nanopores of a polymeric membrane. The experiments supported by molecular dynamics simulations reveal new filtration properties never seen in biological membranes. Indeed this biomimetic membrane exhibits higher permeability to anions than to monovalent (Na+ and K+) and divalent (Ca2+) cations. This work opens a new route of separation in the domain of nanobiofiltration, especially for tunable nanodevices based on differential ion conduction, using a fundamental understanding of the confinement mechanism.

We explore with Molecular Dynamics simulations and a statistical model, the ability of carbon nanotubes to be internalized into a model lipid bilayer as a function of their length. The hydrophobicity is one of the key factors responsible for the insertion process. The membrane asymmetry is also needed to drive a complete translocation. Our data demonstrates that shorter nanotubes have a stronger propensity to passively penetrate the bilayer and reach the cytoplasm. Carbon nanotubes excretion appears mostly impossible whatever their length.

International audience; Bioactive molecules, cationic peptides among them, are nowadays well-recognized in modern pharmacology for their drug potential. However, they usually suffer from poor translocation across cell membranes, and specific drug carriers should be designed to circumvent this problem. In the present study, the uptake mechanism of fullerene bearing cationic ammonium groups by membranes modeled as lipid bilayers is investigated using extensive molecular dynamics simulations and free-energy calculations. Three main results issued from this work can be drawn. First, the fullerene core appears to be a good drug vector since it greatly enhances the uptake of the cationic groups by the membrane. Second, we show that the amino derivatives should be deprotonated at the lipid headgroup level in order to fully translocate the membrane by passive diffusion. Finally, the fullerenes bearing too many cationic groups display mostly a hydrophilic character; thus, the lipophilic fullerene core is not anymore effective as an insertion enhancer. Therefore, the lipid bilayer appears to be very selective with respect to the amount of amino groups conjugated with C60.

International audience; Most studies of the interactions of neat and functionalized fullerenes with cells have focused so far on their ability to cross the cell membrane envelopes. Membranes are, however, also host to a large number of proteins responsible for various cellular functions. Among these, ion channels are prominent components of the nervous system. Recently, it was shown that fullerenes may act as blockers or modulators of a variety of K+ channels. Here we use computer simulations to investigate the propensity of such nanocompounds to bind to K+ channels. Our results based on extensive atomistic molecular dynamics simulations reveal a variety of specific binding sites depending on the structure and properties of the channel. The corresponding binding free energies and putative mechanisms suggest that C60 may indeed effectively hinder the function of K+ channels and hence induce toxicity.

Study of the mechanisms understanding how chemically functionalized carbon nanotubes internalize into mammalian cells is important in view of their design as new tools for therapeutic and diagnostic applications. The initial contact between the nanotube and the cell membrane allows elucidation of the types of interaction that are occurring and the contribution from the types of functional groups at the nanotube surface. Here we offer a combination of experimental and theoretical evidence of the initial phases of interaction between functionalized carbon nanotubes with model and cellular membranes. Both experimental and theoretical data reveal the critical parameters to determine direct translocation of the nanotubes through the membrane into the cytoplasm as a result of three distinct processes that can be summarized as landing, piercing and uptake. journal article research support, non-u.s. gov't 2013 Nov 07 2013 09 05 imported

International audience; Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based onquantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for thehigh flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organ-ometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies.

Catestatin, a cationic and hydrophobic 21-amino acid fragment of chromogranin A, is known to be a non-competitive nicotinic antagonist acting through nicotinic acetylcholine receptors (nAChRs) to inhibit catecholamine release. Since this receptor is the target of several neuronal and non-neuronal disorder prophylaxes and treatments, this study aims at the elucidation of the binding of human catestatin to the entire nAChR reconstructed in lipid bilayers by means of docking followed by full atomistic molecular dynamics simulations. The obtained results show that the minimum free energy for the binding of the peptide and the receptor attains minimal values for locations at the pore site and in the outer beta subunit. This result is consistent with previous studies showing that catestatin occludes the pore opening. A new finding is an additional even stronger binding seat at the beta subunit and that membrane presence could be an important factor. Specific amino acids involved in catestatin binding have been identified, indicating targets for point mutation studies. In addition to improving the understanding of the interaction between the peptide and muscle-type and even other nAChR subtypes, the results of this study provide directions for future peptidomimetic research.

Cholesterol is essential for the proper organization of the biological membrane. Therefore, predicting which proteins can bind cholesterol is important in understanding how proteins participate in lateral membrane organization. In this study, a simple bioinformatics approach was used to establish whether MPP1, a member of the MAGUK protein family, is capable of binding cholesterol. Modelled and experimentally-validated fragment structures were mined from online resources and searched for CRAC and CRAC-like motifs. Several of these motifs were found in the primary structure of MPP1, and these were structurally visualized to see whether they localized to the protein surface. Since all of the CRAC and CRAC-like motifs were found at the surface of MPP1 domains, in silico docking experiments were performed to assess the possibility of interaction between CRAC motifs and cholesterol. The results obtained show that MPP1 can bind cholesterol via CRAC and CRAC-like motifs with moderate to high affinity (KI in the nano- to micro-molar range). It was also found that palmitoylation-mimicking mutations (C/F or C/M) did not affect the affinity of MPP1 towards cholesterol. Data presented here may help to understand at least one of the molecular mechanisms via which MPP1 affects lateral organization of the membrane.

The hybrid biological/polymeric solid-state nanopore membrane offers several opportunities to combine the advantage of biological channel (selectivity) and material (robustness). Based on this technology, the challenge is to obtain selective ionic exchange membranes, with no energy intake. The direct insertion of an ionic channel inside a nanopore should be a promise solution. Here, the authors report a hybrid nanopore based on nystatin A1 confinement in commercial nanopore membrane. Ionic transport and selectivity studies show that the hybrid nanopores exhibit mainly an anionic behaviour, on the contrary to biological conditions. However, the order of magnitude between the different ratios of permeation of several cationic species is retained even if the blocking of divalent cation is not totally proved.

International audience; The curvature of biological membranes is known to be an important influence on important phenomena such as membrane fusion, endocytosis, and the functioning of integral membrane proteins. There is a growing demand for analytical tools that are able accommodate molecular dynamics trajectories of significantly curved lipid bilayers. In this work, an algorithm for determining the shape and curvature of a nonplanar lipid bilayer in molecular dynamics simulations is proposed. The algorithm calculates the coordinates of the midline and the curvature of the bilayer as well as the local normal to it at any point on the membrane, which is bent arbitrarily in a single plane and is topologically equivalent to an infinite bilayer. The algorithm is implemented as a C++ program and tested by exploring the molecular dynamic trajectories of a highly curved meander-like asymmetric lipid bilayer. The algorithm is general enough to allow it to be easily applied to other geometries of nonplanar membrane systems.

Detection of a single macromolecule based on the use of artificial nanopores is an attractive and promising field of research. In this work, we report a device based on a 5 nm single nanopore with a high length/diameter ratio, tailored by the track etching and atomic layer deposition techniques. The translocation of neutral polyethylene glycol (PEG) and charged polyethylene glycol-carboxylate (PEG-carboxylate) molecules of low molar masses (200 and 600 g mol(-1)) through this nanodevice was studied. It was shown that charged PEG-carboxylate molecules, which permeate through the pore, promote an unusual blockade of ionic current whereas the neutral PEG molecules do not show such behaviour. The molecular dynamics simulation shows that both neutral and charged PEGs permeate through the nanopore close to its inner surface. The main difference between the two macromolecules is the existence of a structured shell of cations around the charged PEG, which is likely to cause the observed unusual current blockade.

International audience; Biological ion channels present unique ionic properties. They can be highly permeable to ions, while selecting only one type of ions, without external energy supply. An important research field has been developed to transfer these properties to solid state nanoporous membranes in order to develop artificial biomimetic nanofilters. One of the promising ways to develop biomimetic structures is based on the direct insertion of the gramicidin A, i.e. an ionic channel, inside a nanopore. Experiments have recently proved the feasibility of such a hybrid membrane with very interesting results regarding the ionic selectivity. Here, we propose to interpret these experiments using theoretical molecular dynamic simulations which allow us to analyze more profoundly the structures of the proteins confined inside the nanopore and the relation between their conformation and the observed ionic properties.

International audience; We report molecular dynamic simulations showing that a DNA molecule constituted by five unique bases can be spontaneously inserted into single walled carbon nanotube (SWCNT) in normal conditions (P, T and water environment) depending on the tube radius value. The van der Waals and electrostatic interactions play a central role for the rapid insertion process. Our study shows also that the Guanine molecule inserts the fastest compared to thymine, adenine and cytosine bases, respectively. The differences of insertion time could be exploited for applications concerning for example DNA sequencing

Development of fluorescence methods involves the necessity of understanding the fluorescent probes behavior in their ground and excited states. In the case of biological membranes, the position of the dyes in the lipid bilayer and their response after excitation are necessary parameters to correctly analyze the experiments. In the present work, we focus on two fluorescent markers, Laurdan (6-lauroyl-2-(N,N-dimethylamino)naphthalene) and its derivative C-Laurdan (6-dodecanoyl-2-[N-methyl-N-(carboxymethyl)amino]naphthalene), recently proposed for lipid raft visualization [Kim, H. M.; et al. ChemBioChem 2007, 8, 553]. C-Laurdan, by the presence of an additional carboxyl group, has an advantage over Laurdan since it has a higher sensitivity to the membrane polarity at the lipid headgroup region and a higher water solubility. This theoretical study, based on quantum mechanical (QM) and molecular dynamics (MD) simulations in a fully hydrated lipid membrane model, compare the equilibrium and dynamic properties of both probes taking into account their fluorescence lifetimes. C-Laurdan is found to be more stable than Laurdan in the headgroup region of the membrane and also much more aligned with the lipids. This study suggests that, besides the lipid raft imaging, the C-Laurdan marker can considerably extend the capabilities of fluorescent solvent relaxation method.

International audience; ensity functional theory calculations with van der Waals approximation have been conducted to analyze the functionalization of various carbon-based nanostructures (fullerene, metallic, and semi-conducting nanotubes) with amino derivative groups. The results obtained with azomethine, show the formation of a five membered ring on fullerenes, and on nanotubes consistent with experimental observations. The attachment of an azomethine plus subsequent drug like a Pt(IV) complex does not perturb the cycloaddition process. Moreover, all theoretical results show that the length of different amino derivatives with subsequent Pt(IV) complex does not affect the complexed therapeutic agent when it is attached onto these carbon-based nanostructures.

The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues.

Carbon nanotubes have been proposed to be efficient nanovectors able to deliver genetic or therapeutic cargo into living cells. However, a direct evidence of the molecular mechanism of their translocation across cell membranes is still needed. Here, we report on an extensive computational study of short (5 nm length) pristine and functionalized single-walled carbon nanotubes uptake by phospholipid bilayer models using all-atom molecular dynamics simulations. Our data support the hypothesis of a direct translocation of the nanotubes through the phospholipid membrane. We find that insertion of neat nanotubes within the bilayer is a "nanoneedle" like process, which can often be divided in three consecutive steps: landing and floating, penetration of the lipid headgroup area and finally sliding into the membrane core. The presence of functional groups at moderate concentrations does not modify the overall scheme of diffusion mechanism, provided that their deprotonated state favors translocation through the lipid bilayer. journal article research support, non-u.s. gov't 2012 2012 07 16 imported

International audience; A hybrid nanoporous membrane made of a solid-state polymeric thin film in which an ion channel is confined is realized. The primary and extremely encouraging results obtained by confocal fluorescence spectroscopy and ion diffusion measurement demonstrate respectively that (i) the considered ion channel, that is, Gramicidin-A, can be confined selectively inside the nanopores and (ii) the ionic permeability of the membrane is enhanced. Atomistic molecular simulations are also reported and fruitfully compared to the experimental findings.

The charge profile of K+ and Na+ ions moving in a single file across the filter of the KcsA channel is determined using both molecular dynamics simulations and ab initio calculations. We show a strong correlation between the charge variation and the ion location resulting in a saw-tooth profile, which provides additional information on the influence of charge transfer on the permeation and selectivity of the channel.

KcsA potassium channel belongs to a wide family of allosteric proteins that switch between closed and open states conformations in response to a stimulus, and act as a regulator of cation activity in living cells. The gating mechanism and cation selectivity of such channels have been extensively studied in the literature, with a revival emphasis these latter years, due to the publication of the crystallized structure of KcsA. Despite the increasing number of research and review papers on these topics, quantitative interpretation of these processes at the atomic scale is far from achieved. On the basis of available experimental and theoretical data, and by including our recent results, we review the progresses in this field of activity and discuss the weaknesses that should be corrected. In this spirit, we partition the channel into the filter, cavity, extra and intracellular media, in order to analyze separately the specificity of each region. Special emphasis is brought to the study of an open state for the channel and to the different properties generated by the opening. The influence of water as a structural and dynamical component of the channel properties in closed and open states, as well as in the sequential motions of the cations, is analyzed using molecular dynamics simulations and ab initio calculations. The polarization and charge transfer effects on the ions’ dynamics and kinetics are discussed in terms of partial charge models.

International audience; Specific separations of protons and cations are usually performed by electromembrane processes, which require external electric energy. An easier process would be using a membrane able to separate both entities by passive diffusion. Presently, such synthetic nanoporous membranes do not exist. Here, we report the production of a robust hybrid biological/artificial solid-state membrane, which allows selective permeation of alkali metal cations without competing or concurrent permeation of protons. This membrane is simple to prepare and is based on the hydrophobic nature of the polymeric pore walls, and the confined gramicidin A molecules within. This work opens a new route for separation in the domain of nanobiofiltration, especially for tunable nanodevices based on differential ion conduction, with a fundamental understanding of the confinement mechanism.

International audience; The secondary, ternary and quaternary structures of the biological ion channel Gramicidin-A are investigated by means of UV-visible and fluorescence spectroscopies, and by computational simulations in water/methanol solvent with various molar ratios. Both experiments and molecular dynamics calculations show that the two considered conformations, i.e. the head-to-head and double-stranded β-helix dimers, behave differently with regard to their stability as a function of the methanol content in the water/methanol mixture. To sum-up, calculations show that the double-stranded dimer is stabilized by methanol, even at low content, while the head-to-head dimer conformation breaks into two monomers which remain however coupled whatever the water/methanol mixture. In pure water and low methanol content, the resulting single β-helix structure is maintained due to the stabilization of the channel by water molecules and cations.

Since the pioneering work of Zhou et al. (Y. Zhou, J. H. Morais-Cabral, A. Kaufman and R. MacKinnon, Nature, 2001, 414, 43-48) it is now well established that the streptomyces lividans potassium channel (KcsA) can accommodate more than one ion, namely between 2 and 3. As a result, it is usually assumed that the conduction of ions proceeds through a barrier-less knock-on mechanism. This one is an alternation of two sequences containing either 2 or 3 ions which have nearly the same energies. However, the origin of such knock-on mechanism is not clearly known. The entry and the exit of ion in or out of the selectivity filter are suspected to be due to the repulsive interactions between ions. In this work, molecular dynamics simulations running over nanoseconds have been done in order to identify such events. Two specific situations, namely (S(1), S(3)) containing 2 ions and (S(2), S(4)) containing 3 ions, have been investigated regarding the different locations that ions can occupy during their diffusion through the selectivity filter of KcsA. We show that contractions of the (S(1), S(3)) file and dilation of the (S(2), S(4)) file are at the origin of the passage from one sequence to the other. The comparison between the experimentally observed diffusion rate and the occurrence's frequency of such contractions or dilation confirm the importance of such events. Ab initio calculations have also been conducted in order to examine the effect of ion polarization in the filter of KcsA. During the contraction of the ion/water file, one charge at the extra-cellular mouth of the channel strongly deviates from the others. This behavior could guide the diffusion direction to a certain extent since the contraction of the (S(1), S(3)) is favored.

Fluorescence methods are widely used in studies of biological and model membranes. The dynamics of membrane fluorescent markers in their ground and excited electronic states and correlations with their molecular surrounding within the fully hydrated phospholipid bilayer are still not well understood. In the present work, Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations are used to characterize location and interactions of two membrane polarity probes (Prodan; 6-propionyl-2-dimethylaminonaphthalene and its derivative Laurdan; 2-dimethylamino-6-lauroylnaphthalene) with the dioleoylphosphatidylcholine (DOPC) lipid bilayer model. MD simulations with fluorophores in ground and excited states are found to be a useful tool to analyze the fluorescent dye dynamics and their immediate vicinity. The results of QM calculations and MD simulations are in excellent agreement with available experimental data. The calculation shows that the two amphiphilic dyes initially placed in bulk water diffuse within 10ns towards their final location in the lipid bilayer. Analysis of solvent relaxation process in the aqueous phase occurs on the picoseconds timescale whereas it takes nanoseconds at the lipid/water interface. Four different relaxation time constants, corresponding to different relaxation processes, where observed when the dyes were embedded into the membrane.