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Promoting drug delivery across the biological membrane is a common strategy to improve bioavailability. Inspired by the observation that carbonated alcoholic beverages can increase the absorption rate of ethanol, we speculate that carbon dioxide (CO2 ) molecules could also enhance membrane permeability to drugs. In the present work, we have investigated the effect of CO2 on the permeability of a model membrane formed by 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipids to three drug-like molecules, namely, ethanol, 2',3'-dideoxyadenosine, and trimethoprim. The free-energy and fractional-diffusivity profiles underlying membrane translocation were obtained from μs-timescale simulations and combined in the framework of the fractional solubility-diffusion model. We find that addition of CO2 in the lipid environment results in an increase of the membrane permeability to the three substrates. Further analysis of the permeation events reveals that CO2 expands and loosens the membrane, which, in turn, facilitates permeation of the drug-like molecules. © 2019 Wiley Periodicals, Inc.

In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extracellular loops of rhodopsin, the transmembrane photoreceptor protein responsible for the first steps in vision. Triggered by Ce6 deep-red light absorption, the retinal within rhodopsin can be isomerized thus starting the visual phototransduction cascade. Our data largely exclude previously hypothesized energy-transfer mechanisms while clearly lending credence to a retinal isomerization indirectly triggered by singlet oxygen, proposing an alternative mechanism to rationalize photosensitizer-mediated night vision.

B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.

Aromatic groups can engage in an interesting class of noncovalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins, and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect-the trend of nonpolar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Using DFT-CES, a mean-field QM/MM method recently developed by our group, we describe the benzene solute at a quantum-mechanical level. Full consideration of detailed solute-electron density enables an optimal description of the solute-solvent interactions, leading to an accurate prediction of hydration free energies. In π-stacking of benzene, we find an entropic stabilization associated with the shrinkage of the solvent-excluded volume, which agrees with the theory of hydrophobic effect at subnanoscales. However, at the equilibrium binding distance of the benzene dimer, we find that the entropic stabilization nearly cancels out due to the enthalpic cost required for dewetting the internal space. Such an enthalpy-entropy compensation leads the association free energy to be predominantly dictated by the solute-solute interaction enthalpy. The present work offers new insight into the mechanistic role of water and the primary thermodynamic driving force of hydrophobic association.

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International audience; The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.

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We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations. In particular, we determine the binding free energy for two competitive binding modes, minor groove binding and double insertion. Our results allow us to quantitatively resolve for the first time the mode of binding of this paradigmatic photosensitizer, indicating a marked preference for minor groove binding. Furthermore, we have settled a protocol allowing for the determination of binding energies in the case of non-covalent interaction with DNA, in particular, tackling the non-trivial problem of the strong reorganization of the DNA imposing extended statistical sampling. Our contribution paves the way to the systematic determination of the thermochemical properties of drugs or pollutants interacting with DNA.

International audience Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein–ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 102 s–1, which compares well with the experimental value.

International audience; We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the Ϸ1.5-nm ␣-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3-threaded DNA or 5 DNA differ by Ϸ30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5 end, assuming an asymmetric conformation. As a result, the bases of a 5-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore. asymmetry ͉ DNA translocation ͉ DNA hairpin T he transport of biomolecules across cell walls is a ubiquitous process in biology, controlled by membrane proteins that act as selective channels and transporters (1, 2). These processes usually involve the passage of a biopolymer through a narrow proteinic confinement that, in the case of polynucleic acids, can result in temporary structural deformations of the molecules. The ability of membrane proteins to sort single molecules, and in particular polynucleic acids, is also of great interest in bioengineering. In the past few years membrane channels like the bacterial ␣-hemolysin (␣-HL) have been adapted as in vitro devices for rapid, single-molecule nucleic acid characterization (3-7). In these experiments the negatively charged single-stranded DNA (ssDNA) or RNA molecules were electrophoreti-cally driven through a single, membrane-embedded pore having dimensions that are only slightly larger than the size of a nucleotide (8). The passage time of each individual molecule was measured by monitoring the residual ion current f lowing through the pore during the transport of the biopolymer. One of the important findings has been that the translocation dynamics is dominated by the nucleic acid interactions with the pore walls, and that these interactions are substantially stronger for purine-rich DNA sequences as compared with pyrimidine-rich molecules (5, 9). However, the microscopic source for this sequence selectivity as well as the exact shape of the interaction potential between the DNA and the pore have not yet been resolved. In particular, it was unclear whether the asymmetric structure of ␣-HL (8) coupled with the directionality of ssDNA can lead to asymmetric polynucleotide dynamics, with and without an external biasing potential. To address these questions, we have carried out extensive DNA translocation experiments, which take advantage of the finding that ssDNA can enter the trans membrane pore of the ␣-HL, but double-stranded DNA cannot (8, 10-12). Thus, DNA hairpin molecules with a long single-stranded overhang only enter the ␣-HL pore with the single-stranded part, either the 3Ј or the 5Ј end, depending on the DNA construct. As a result, the blockade currents and the DNA transport resulting from either 3Ј or 5Ј entries can be unambiguously discriminated and characterized. Moreover, by taking advantage of the dynamic voltage control method (13), the escape dynamics of molecules from the pore can be measured at a finite voltage level, as well as at V ϭ 0. Previous DNA translocation experiments have revealed two peaks in the translocation time distribution (3) as well as in the blockade current histogram (5, 7, 13) comprised of several hundred translocation events from identical molecules. The two peaks have been associated with the direction of polynucleotide translocation, either 3Ј or 5Ј end first (5, 7, 14). However, it remained unclear which of the two orientations produce the shorter blockade times and the lower blockade current. Here, we show that 3Ј end DNA entries induce a larger current blockade as compared with the 5Ј end threading, and measure the fundamental, voltage-free diffusion constants associated with either 3Ј or 5Ј threading of ssDNA through the pore. Remarkably , we found that the voltage-free dynamics of the 3Ј-threaded molecules (entering and exiting from the same side of the pore) is two times slower than the corresponding diffusion of the 5Ј threading. To delineate the underlying mechanism responsible for the observed dynamics, we carried out all-atom molecular dynamics (MD) simulations, using the known structures of the ␣-HL pore and the DNA. The MD simulations independently confirmed the experimental results, indicating that the 3Ј threading blocks the ion current more effectively and will result in stronger interactions. Moreover, the MD data allow us to pinpoint a mechanistic explanation for the observed asymmetry in DNA dynamics based on a microscopic picture. We find that the confinement of the ssDNA in the ␣-HL pore results in straightening of the DNA backbone and, consequently, in a collective tilt of the bases with respect to the DNA backbone in the direction of the 5Ј end of the molecule, and that this tilt can create an asymmetric DNA-pore interaction. Noteworthy is the fact that the MD simulations were performed without any a priori knowledge of the experimental data (i.e., which orientation is faster or causes larger ion current blockade). Our results agree with a theoretical model that describes the DNA-pore interactions by using a different asymmetric sawtooth potential for each orientation (14). These potentials yield asymmetric dynamics of the threaded DNA even at zero applied voltage, as observed in our experiments. Methods Experiments. PAGE-purified ssDNA and DNA hairpins (Euro-gentec, San Diego) were buffered in 10 mM Tris͞1 mM EDTA (pH 8.5) solution. Before each measurement the samples were heated to 75°C for 10 min and then quenched to 4°C. The hairpins are constituted of a single-stranded overhang of 50

We study the octahedron relation (also known as the $A_{\infty}$ $T$-system), obeyed in particular by the partition function for dimer coverings of the Aztec Diamond graph. For a suitable class of doubly periodic initial conditions, we find exact solutions with a particularly simple factorized form. For these, we show that the density function that measures the average dimer occupation of a face of the Aztec graph, obeys a system of linear recursion relations with periodic coefficients. This allows us to explore the thermodynamic limit of the corresponding dimer models and to derive exact "arctic" curves separating the various phases of the system., Comment: 39 pages, 21 figures; typos fixed, four references and an appendix added