Liquid water confined in carbon nanochannels at high temperatures

Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex

KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.

Nucleation of Helium in Liquid Lithium at 843 K and High Pressures

Fusion energy stands out as a promising alternative for a future decarbonised energy system. In order to be sustainable, future fusion nuclear reactors will have to produce their own tritium. In the so-called breeding blanket of a reactor, the neutron bombardment of lithium will produce the desired tritium, but also helium, which can trigger nucleation mechanisms owing to the very low solubility of helium in liquid metals. An understanding of the underlying microscopic processes is important for improving the efficiency, sustainability and reliability of the fusion energy conversion process. The spontaneous creation of helium droplets or bubbles in the liquid metal used as breeding material in some designs may be a serious issue for the performance of the breeding blankets. This phenomenon has yet to be fully studied and understood. This work aims to provide some insight on the behaviour of lithium and helium mixtures at experimentally corresponding operating conditions (843 K and pressures between 108 and 1010 Pa). We report a microscopic study of the thermodynamic, structural and dynamical properties of lithium–helium mixtures, as a first step to the simulation of the environment in a nuclear fusion power plant. We introduce a new microscopic model devised to describe the formation of helium droplets in the thermodynamic range considered. Our model predicts the formation of helium droplets at pressures around 109 Pa, with radii between 1 and 2 Å. The diffusion coefficient of lithium (2 Å2/ps) is in excellent agreement with reference experimental data, whereas the diffusion coefficient of helium is in the range of 1 Å2/ps and tends to decrease as pressure increases.

In Silico Drug Design of Benzothiadiazine Derivatives Interacting with Phospholipid Cell Membranes

The use of drugs derived from benzothiadiazine, a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension, low blood sugar or the human immunodeficiency virus, among others. In this work we have investigated the interactions of benzothiadiazine and four of its derivatives designed in silico with model zwitterionic cell membranes formed by dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine and cholesterol at the liquid–crystal phase inside aqueous potassium chloride solution. We have elucidated the local structure of benzothiadiazine by means of microsecond molecular dynamics simulations of systems including a benzothiadiazine molecule or one of its derivatives. Such derivatives were obtained by the substitution of a single hydrogen site of benzothiadiazine by two different classes of chemical groups, one of them electron-donating groups (methyl and ethyl) and another one by electron-accepting groups (fluorine and trifluoromethyl). Our data have revealed that benzothiadiazine derivatives have a strong affinity to stay at the cell membrane interface although their solvation characteristics can vary significantly—they can be fully solvated by water in short periods of time or continuously attached to specific lipid sites during intervals of 10–70 ns. Furthermore, benzothiadiazines are able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of characteristic lengths between 1.6 and 2.1 Å.

Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10-20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10-7 cm2/s for the cholesterol-free and cholesterol-rich setups.

Influence of Cholesterol on the Orientation of the Farnesylated GTP-Bound KRas-4B Binding with Anionic Model Membranes

The Ras family of proteins is tethered to the inner leaflet of the cell membranes which plays an essential role in signal transduction pathways that promote cellular proliferation, survival, growth, and differentiation. KRas-4B, the most mutated Ras isoform in different cancers, has been under extensive study for more than two decades. Here we have focused our interest on the influence of cholesterol on the orientations that KRas-4B adopts with respect to the plane of the anionic model membranes. How cholesterol in the bilayer might modulate preferences for specific orientation states is far from clear. Herein, after analyzing data from in total 4000 ns-long molecular dynamics (MD) simulations for four KRas-4B systems, properties such as the area per lipid and thickness of the membrane as well as selected radial distribution functions, penetration of different moieties of KRas-4B, and internal conformational fluctuations of flexible moieties in KRas-4B have been calculated. It has been shown that high cholesterol content in the plasma membrane (PM) favors one orientation state (OS1), exposing the effector-binding loop for signal transduction in the cell from the atomic level. We confirm that high cholesterol in the PM helps KRas-4B mutant stay in its constitutively active state, which suggests that high cholesterol intake can increase mortality and may promote cancer progression for cancer patients. We propose that during the treatment of KRas-4B-related cancers, reducing the cholesterol level in the PM and sustaining cancer progression by controlling the plasma cholesterol intake might be taken into account in anti-cancer therapies.

Long-lasting Salt Bridges Provide the Anchoring Mechanism of Oncogenic Kirsten Rat Sarcoma Proteins at Cell Membranes

RAS proteins work as GDP-GTP binary switches and regulate cytoplasmic signaling networks that are able to control several cellular processes, playing an essential role in signal transduction pathways involved in cell growth, differentiation, and survival, so that overacting RAS signaling can lead to cancer. One of the hardest challenges to face is the design of mutation-selective therapeutic strategies. In this work, a G12D-mutated farnesylated GTP-bound Kirsten RAt sarcoma (KRAS) protein has been simulated at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane. A specific long-lasting salt bridge connection between farnesyl and the hypervariable region of the protein has been identified as the main mechanism responsible for the binding of oncogenic farnesylated KRAS-4B to the cell membrane. Free-energy landscapes allowed us to characterize local and global minima of KRAS-4B binding to the cell membrane, revealing the main pathways between anchored and released states.

Probing the effects of 2D confinement on hydrogen dynamics in water and ice adsorbed in graphene oxide sponges

We studied the single particle dynamics of water and ice adsorbed in graphene oxide (GO) sponges at T = 293 K and T = 20 K. We used Deep Inelastic Neutron Scattering (DINS) at the ISIS neutron and muon spallation source to derive the hydrogen mean kinetic energy, 〈EK〉, and momentum distribution, n(p). The goal of this work was to study the hydrogen dynamics under 2D confinement and the potential energy surface, fingerprinting the hydrogen interaction with the layered structure of the GO sponge. The observed scattering is interpreted within the framework of the impulse approximation. Samples of both water and ice adsorbed in GO show n(p) functions with almost harmonic and anisotropic line shapes and 〈EK〉 values in excess of the values found at the corresponding temperatures in the bulk. The hydrogen dynamics are discussed in the context of the interaction between the interfacial water and ice and the confining hydrophilic surface of the GO sponge.

Size effects on water adsorbed on hydrophobic probes at the nanometric scale

Molecular dynamics simulations of liquid water at ambient conditions, adsorbed at the external walls of (n,n) single-walled armchair carbon nanotubes have been performed for n = 5, 9, 12. The comparison with the case of water adsorbed on graphene has also been included. The analysis of Helmholtz free energies reveals qualitatively different ranges of thermodynamical stability, eventually starting at a given threshold surface density. We observed that, in the framework of the force field considered here, water does not wet graphene nor (12,12) tubes, but it can coat thinner tubes such as (9,9) and (5,5), which indicates that the width of the carbon nanotube plays a role on wetting. On the other hand, density profiles, orientational distributions of water, and hydrogen-bond populations indicate significant changes of structure of water for the different surfaces. Further, we computed self-diffusion of water and spectral densities of water and carbon molecules, which again revealed different qualitative behavior of interfacial water depending on the size of the nanotube. The crossover size corresponds to tube diameters of around 1 nm.

Aqueous NaCl and CsCl solutions confined in crystalline slit-shaped silica nanopores of varying degree of protonation

All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion-surface, water-ion, and only in some cases ion-ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl(-) ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na(+) or Cs(+) ions are present in the systems considered). The cations show significant ion-specific behavior. Na(+) ions occupy different positions within the pore as the degree of protonation changes, while Cs(+) ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs(+) is always greater than that of Na(+) ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.

Wetting and prewetting of water on top of a single sheet of hexagonal boron nitride

Wetting of a single hexagonal boron nitride sheet by liquid water has been investigated by molecular dynamics simulations within a temperature range between 278 and 373 K. The wetting temperature was found to be ~310 K, while the onset of prewetting happens around the much higher temperature of 354 K. The static (hydrogen-bond populations, density profiles, energy per molecule) and dynamic (diffusion coefficients) properties of water in the stable phases in this temperature range were also studied and compared to those of water on graphene. The results indicate that hydrophobicity of boron nitride is milder than that of graphene.

Water on graphene surfaces

In this paper, we summarize the main results obtained in our group about the behavior of water confined inside or close to different graphene surfaces by means of molecular dynamics simulations. These include the inside and outside of carbon nanotubes, and the confinement inside a slit pore or a single graphene sheet. We paid special attention to some thermodynamical (binding energies), structural (hydrogen-bond distributions) and dynamic (infrared spectra) properties, and their comparison to their bulk counterparts.

Ion-specific effects under confinement: the role of interfacial water

All-atom molecular dynamics simulations were employed for the study of the structure and dynamics of aqueous electrolyte solutions within slit-shaped silica nanopores with a width of 10.67 A at ambient temperature. All simulations were conducted for 250 ns to capture the dynamics of ion adsorption and to obtain the equilibrium distribution of multiple ionic species (Na+, Cs+, and Cl(-)) within the pores. The results clearly support the existence of ion-specific effects under confinement, which can be explained by the properties of interfacial water. Cl(-) strongly adsorbs onto the silica surface. Although neither Na+ nor Cs+ is in contact with the solid surface, they show ion-specific behavior. The differences between the density distributions of cations within the pore are primarily due to size effects through their interaction with confined water molecules. The majority of Na+ ions appear within one water layer in close proximity to the silica surface, whereas Cs+ is excluded from well-defined water layers. As a consequence of this preferential distribution, we observe enhanced in-plane mobility for Cs+ ions, found near the center of the pore, compared to that for Na+ ions, closer to the solid substrate. These observations illustrate the key role of interfacial water in determining ion-specific effects under confinement and have practical importance in several fields, from geology to biology.

Molecular dynamics simulations of supercritical water confined within a carbon-slit pore

We report the results of a series of molecular dynamics simulations of water inside a carbon-slit pore at supercritical conditions. A range of densities corresponding from liquid (0.66gcm;{-3}) to gas environments (0.08gcm;{-3}) at the supercritical temperature of 673K were considered. Our findings are compared with previous studies of liquid water confined in graphene nanochannels at ambient and high temperatures, and indicate that the microscopic structure of water evolves from hydrogen bond networks characteristic of hot dense liquids to looser arrangements where the dominant units are water monomers and dimers. Water permittivity was found to be very small at low densities, with a tendency to grow with density and to reach typical values of unconfined supercritical water at 0.66gcm;{-3}) . In supercritical conditions, the residence time of water at interfaces is roughly similar to that of water in the central regions of the slabs, if the size of the considered region is taken into account. That time span is long enough to compute dynamical properties such as diffusion or spectral densities. Water diffusion in supercritical states is much faster at low densities, and it is produced in such a way that, at interfaces, translational diffusion is mainly produced along planes parallel to the carbon walls. Spectral frequency shifts depend on several factors, being temperature and density effects the most relevant. However, we can observe corrections due to confinement, important both at the graphene interface and in the central region of the water slab.

Dynamical properties of confined water nanoclusters: Simulation study of hydrated zeolite NaA: structural and vibrational properties

Water nanoclusters confined to zeolitic cavities have been extensively investigated by various experimental techniques. We report a series of molecular dynamics simulations at different temperatures and for water nanoclusters of different sizes in order to attempt an atomistic interpretation of the properties of these systems. The cavities of zeolite NaA are spherical in shape and about 1 nm in diameter and can host nanoclusters of water containing nearly up to 24 water molecules. A modified interaction potential, yielding a better reproduction of experimental hydration energy and water diffusivity across a number of different zeolites, is proposed. Molecular dynamics simulations reproduce the known experimental structural features obtained by X-ray diffraction. Variations of simulated vibrational IR and IINS spectra with temperature and size of nanoclusters are in good agreement with experiment. The simulated water nanoclusters in zeolite NaA are found to be too small to crystallize and, at low temperature, behave as amorphous ice, in agreement with recent experimental results for similar water nanoclusters in reverse micelles.