Validation of the 53A6 GROMOS force field

Molecular Dynamics Simulation Insight into Interfacial Stability and Fluidity Properties of Microemulsions

Although the interfacial properties of microemulsions have been extensively studied in both experimental and simulation research studies, the molecular mechanisms of stability and fluidity about microemulsion are still poorly understood. Herein, we report a molecular dynamics simulation study to elaborate the motion of an emulsion droplet involving dichain surfactant Aerosol OT (AOT) and its dynamics evolution at the oil-water interface. By varying the concentrations of AOT, we show that the interfacial thickness and emulsification rate display a piecewise change as the interfacial coverage increases and the W/O emulsion is more stable than the O/W one while O/W emulsion presents better fluidity. In addition, the dispersed system combined with water/AOT/n-heptane tends to form a W/O microemulsion instead of an O/W microemulsion due to the structural collapse of the latter. This work provides a molecular understanding of microemulsion interfacial stability and fluidity.

Stabilization of c-KIT G-Quadruplex DNA Structures by the RNA Polymerase I Inhibitors BMH-21 and BA-41

The stabilization of G-quadruplex DNA structures by small molecules with affinity to oncogene promoters has emerged as a promising anticancer strategy, due to a potential role in gene expression regulation. We explored the ability of BMH-21 (1) and its analogue BA-41 (2) to bind the G-quadruplex structure present in the c-KIT promoter by biophysical methods and molecular modeling. We provide evidence that both compounds interact with the c-KIT 21-mer sequence. The stable monomeric intramolecular parallel G-quadruplex obtained by the mutation of positions 12 and 21 allowed the precise determination of the binding mode by NMR and molecular dynamics studies. Both compounds form a complex characterized by one ligand molecule positioned over the tetrad at the 3′-end, stabilized by an extensive network of π–π interactions. The binding constants (Kb) obtained with fluorescence are similar for both complexes (around 10⁶ M⁻¹). Compound BA-41 (2) showed significant antiproliferative activity against a human lymphoma cell line, SU-DHL4, known to express substantial levels of c-KIT. However, the partial inhibition of c-KIT expression by Western blot analysis suggested that the interaction of compound 2 with the c-KIT promoter is not the primary event and that multiple effects provide a contribution as determinants of biological activity.

Molecular dynamics simulations of membrane properties affected by plasma ROS based on the GROMOS force field

Cold atmospheric plasma (CAP) has attracted substantial attention in the field of medical disinfection because its main components, reactive oxygen species (ROS), have a strong destructive effect on various cell components. The cell membrane plays an important role in maintaining proper cellular function by blocking harmful substances such as ROS. In this paper, we used molecular dynamics simulations to study the behaviour of different ROS at the membrane-water interface. The results showed that the cell membrane presented a weak barrier to hydrophobic ROS (O₂) but effectively prevented hydrophilic ROS (OH, HO₂, H₂O₂) from entering the cell. The plasma treatment significantly enhanced the permeability of the cell membrane to HO₂, while the energetic barrier to other types of ROS changed only slightly. O₂ very likely stopped in the centre of the lipid bilayer when crossing the membrane and there attacked the unsaturated region of the phospholipid. Cholesterol was most likely oxidized by HO₂, causing a condensing effect that destroyed the integrity and fluidity of the cell membrane. The study also found that large amounts of ROS decreased the thickness of the cell membrane, and the phospholipid arrangement became disordered.

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.

Insights into the binding mode and functional components of the analgesic-antitumour peptide from Buthus martensii Karsch to human voltage-gated sodium channel 1.7 based on dynamic simulation analysis

Voltage-gated sodium (Na_v) channels are transmembrane proteins composed of four homologous domains (DI-DIV) that play important roles in membrane excitability in neurons and muscles. Analgesic-antitumour peptide (AGAP) is a neurotoxin from the scorpion Buthus martensii Karsch, and has been shown to exert analgesic effect by binding on site 4 of human Na_v1.7 (hNa_v1.7). Mechanistic details about this binding, however, remain unclear. To address this issue, we compared the binding modes of AGAP/AGAP^W38G/AGAP^W38F and the hNa_v1.7 voltage-sensing domain on DII (VSD2^hNav1.7) using homology modeling, molecular docking, molecular dynamics simulation and steered molecular dynamics. Results revealed the key role of tryptophan at position 38 on the binding of AGAP to VSD2^hNav1.7. Pivotal roles are played also by residues on the β-turn and negatively charged residues at the C-terminal. We further show that electrostatic interaction is the main contributor to the binding free energy of the complex. Agreement between our computational simulation findings and prior experimental data supports the accuracy of the described mechanism. Accordingly, these results can provide valuable information for designing potent toxin analgesics targeting hNa_v1.7 with high affinity.Communicated by Ramaswamy H. Sarma.

Alpha-hemolysin nanopore allows discrimination of the microcystins variants

Microcystins (MCs) are a class of cyclic heptapeptides with more than 100 variants produced by cyanobacteria present in surface waters. MCs are potent hepatotoxic agents responsible for fatal poisoning in animals and humans. Several techniques are employed in the detection of MCs, however, there is a shortage of methods capable of discriminating variants of MCs. In this work we demonstrate that the α-hemolysin (αHL) nanopore can detect and discriminate the variants (LR, YR and RR) of MCs in aqueous solution. The discrimination process is based on the analysis of the residence times of each variant of MCs within the unitary nanopore, as well as, on the amplitudes of the blockages in the ionic current flowing through it. Simulations of molecular dynamics and calculation of the electrostatic potential revealed that the variants of MCs present different charge distribution and correlated with the three patterns on the amplitudes of the blockages in the ionic current. Additionally, molecular docking analysis indicates different patterns of interaction of the variants of MCs with two specific regions of the nanopore. We conclude that αHL nanopore can discriminate variants of microcystins by a mechanism based mainly on electrostatic interaction. Finally, we propose the use of nanopore-based technology as a promising method for analyzing microcystins in aqueous solutions.

Investigation of reverse ionic diffusion in forward-osmosis-aided dewatering of microalgae: A molecular dynamics study

This study aimed to investigate the transport mechanisms of ions during forward-osmosis-driven (FO-driven) dewatering of microalgae using molecular dynamics (MD) simulations. The dynamical and structural properties of ions in FO systems of varying NaCl or MgCl₂ draw solution (DS) concentrations were calculated and correlated. Results indicate that FO systems with higher DS concentration caused ions to have lower hydration numbers and higher coordination numbers leading to lower diffusion coefficients. The higher hydration number of Mg²⁺ ions resulted in significantly lower ionic permeability as compared to Na⁺ ions at all concentrations (p = 0.002). The simulations also revealed that higher DS concentrations led to higher accumulation of ions in the membrane. This study provides insights on the proper selection of DS for FO systems.

Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes

Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized with respect to atomistic reference simulations. Our simulations provide detailed insights in the thylakoid lipid fingerprint of LHCII which compares well with experimental data from membrane protein purification. Comparing the monomer and trimeric LHCII reveals a stabilizing effect of trimerization on the chromophores as well as the protein. Moreover, the average chromophore distance shortens in the trimer leading to stronger excitonic couplings. When changing the native thylakoid environment to a model membrane the protein flexibility remains constant, whereas the chromophore flexibility is reduced. Overall, the presented LHCII model lays the foundation to investigate the μs dynamics of this key antenna protein of plants.

Conformational Dynamics and Responsiveness of Weak and Strong Polyelectrolyte Brushes: Atomistic Simulations of Poly(dimethyl aminoethyl methacrylate) and Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride)

The complex solution behavior of polymer brushes is key to control their properties, including for biomedical applications and catalysis. The swelling behavior of poly(dimethyl aminoethyl methacrylate) (PDMAEMA) and poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) (PMETAC) in response to changes in pH, solvent, and salt types has been investigated using atomistic molecular dynamics simulations. PDMAEMA and PMETAC have been selected as canonical models for weak and strong polyelectrolytes whose complex conformational behavior is particularly challenging for the development and validation of atomistic models. The GROMOS-derived atomic parameters reproduce the experimental swelling coefficients obtained from ellipsometry measurements for brushes of 5-15 nm thickness. The present atomistic models capture the protonated morphology of PDMAEMA, the swollen and collapsed conformations of PDMAEMA and PMETAC in good and bad solvents, and the salt-selective response of PMETAC. The modular nature of the molecular models allows for the simple extension of atomic parameters to a variety of polymers or copolymers.

Molecular Sponge: pH-Driven Reversible Squeezing of Stimuli-Sensitive Peptide Monolayers

The cyclic change of structure, thickness, and density, with pH switching from acidic (pH = 3) to basic (pH = 11) condition, has been revealed for chemisorbed monolayers of the peptide Lipo-Aib-Lys-Leu-Aib-Lys-Lys-Leu-Aib-Lys-Ile-Lol, a trichogin GA IV-analogue carrying Lys residues instead of Gly ones at positions 2, 5, 6, and 9, while a homologous peptide not containing Lys residues does not show any response to pH changes. Experimental and theoretical results, obtained by means of quartz crystal microbalance with dissipation monitoring, surface plasmon resonance, nanoplasmonic sensing technique, Fourier transform infrared-reflection attenuated spectroscopy and dynamic force spectroscopy, and molecular dynamics simulations provide detailed information on the overall monolayer structure changes with pH, including the analysis of the intra- and interchain peptide dynamics, the structure of the peptide layer/water/solid interface, as well as the position and role of solvation and nonsolvation water. The observed stimuli-responsive behavior of L1 peptide monolayers is accounted in terms of the occurrence of a pH-induced wetting/dewetting process, due to the pH-induced switching of the hydrophilic character of charged lysine groups to hydrophobic one of the same uncharged groups, along the peptide chain. This behavior in turn promotes the collective change of the aggregation state of the peptide chains. The present results may pave the way to critically reexamine the mechanism of stimuli-responsive systems.

Identification, description and structural analysis of beta phospholipase A2 inhibitors (sbβPLIs) from Latin American pit vipers indicate a binding site region for basic snake venom phospholipases A2

Several snake species possess, in their circulating blood, endogenous PLA₂ inhibitors (sbPLIs) with the primary function of natural protection against toxic enzymes from homologous and heterologous venoms. Among the three structural classes of sbPLIs – named α, β, and γ − the β class (sbβPLIs) is the least known with only four identified sequences, so far. The last class of inhibitors encompass molecules with leucine rich repeats (LRRs) motifs containing repeating amino acid segments. In the present study, we identified and characterized putative sbβPLIs from the liver and venom glands of six Latin American pit vipers belonging to Bothrops and Crotalus genera. The inhibitor from Crotalus durissus terrificus snakes (CdtsbβPLI) was chosen as a reference for the construction of the first in silico structural model for this class of inhibitors, using molecular modeling and molecular dynamics simulations. Detailed analyses of the electrostatic surface of the CdtsbβPLI model and protein-protein docking with crotoxin B from homologous venoms predict the interacting surface between these proteins.

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Transcripts of phospholipases A₂ inhibitors from the β-class (sbβPLIs) were identified in Latin American pit vipers.

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Structural features of sbβPLIs were compared and discussed, including their characteristic leucine-rich repeats (LRRs).

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One sbβPLI (CdtsbβPLI) was chosen for the in silico construction of the first structural model of a sbβPLI.

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A possible mechanism of interaction between sbβPLIs and basic snake venom PLA₂s was suggested.

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Docking predictions between CdtsbβPLI and crotoxin B highlighted the amino acids residues at the interaction surfaces.

Tailoring carbon nitride properties and photoactivity by interfacial engineering of hydrogen-bonded frameworks

The rational synthesis of carbon nitride materials, ranging from polymeric carbon nitride to nitrogen-doped carbon, by supramolecular preorganization of their monomers is a powerful tool for the design of their morphology and photophysical and catalytic activities. Here we show a new facile and scalable approach for the synthesis of ordered CN materials with excellent photoactivity, which consists of supramolecular interfacial preorganization of CN monomers at the interface of two non-miscible solvents. Molecular dynamic simulations supported by experimental results reveal that an appropriate choice of monomers and solvents leads to the formation of a supramolecular assembly solely at the interface of the solvents. As a proof of concept, we show that the properties of the CN materials after thermal condensation can be tuned by adding an additional monomer to one solvent only. The advantages of the new method are demonstrated here through the tunable morphologies and surface area, the formation of new electronic junctions and high activity as a photocatalyst for hydrogen evolution and pollutant degradation of the CN materials.

Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints

The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.

Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning

The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing Gaucher disease, an autosomal recessive disorder that displays profound genotype-phenotype nonconcordance. More than 250 disease-causing mutations in GBA1, the gene encoding GCase, have been discovered, although only one of these, N370S, causes 70% of disease. Here, we have used a knowledge-based docking protocol that considers experimental data of protein-protein binding to generate a complex between GCase and its known facilitator protein saposin C (SAPC). Multiscale molecular-dynamics simulations were used to study lipid self-assembly, membrane insertion, and the dynamics of the interactions between different components of the complex. Deep learning was applied to propose a model that explains the mechanism of GCase activation, which requires SAPC. Notably, we find that conformational changes in the loops at the entrance of the substrate-binding site are stabilized by direct interactions with SAPC and that the loss of such interactions induced by N370S and another common mutation, L444P, result in destabilization of the complex and reduced GCase activation. Our findings provide an atomistic-level explanation for GCase activation and the precise mechanism through which N370S and L444P cause Gaucher disease.

Reversible Solubilization of Pyrene by a Gas Switchable Surfactant Investigated by Molecular Dynamics Simulation

The reversible solubilization behavior of pyrene by a CO₂/N₂ switchable surfactant (named N'-dodecyl- N, N-dimethylacetamidinium bicarbonate (DDAB)) was investigated with molecular dynamics (MD) simulations. We first individually simulated the aggregation of the inactive surfactant N'-dodecyl- N, N-dimethylacetamidines (DDA) and effective surfactant DDAB in water. Detailed structural properties analysis showed that DDAB molecules aggregated into a micelle, while the aggregation of DDA molecules was considered to be an oil droplet that was separated from the water phase. MD simulations revealed that pyrene molecule was solubilized in the interior hydrophobic region of the micelle as expected. Pyrene was adsorbed on the surface of the oil droplet which is due to the dense packing of DDA molecules inside the oil droplet. The simulated release process showed that the solubilized pyrene in the interior was squeezed out when the micelle was changed to an oil droplet. Reduced density gradient (RDG) function was used to study the weak interactions and explore the molecular driving force behind the reversible solubilization. The results demonstrated that repulsion effects of water molecules on the DDA headgroups play an important role on the pyrene release. Because of the persistent molecular motion of DDA molecules into the droplet center, pyrene was finally repelled out of the oil droplet. Our study provided a molecular mechanism into the reversible solubilization of a gas-controlled switchable surfactant. This is expected to be useful for surfactant-enhanced remediation (SER) experiments.

Small Molecule Inhibitor that Stabilizes the Autoinhibited Conformation of the Oncogenic Tyrosine Phosphatase SHP2

Genetic mutations in the phosphatase PTPN11 (SHP2) are associated with childhood leukemias. These mutations cause hyperactivation of SHP2 due to the disruption of the autoinhibitory conformation. By targeting the activation-associated protein conformational change, we have identified an SHP2 inhibitor ( E)-1-(1-(5-(3-(2,4-dichlorophenyl)acryloyl)-2-ethoxy-4-hydroxybenzyl)-1,2,5,6-tetrahydropyridin-3-yl)-1 H-benzo[ d]imidazol-2(3 H)-one (LY6, 1) using computer-aided drug design database screening combined with cell-based assays. This compound inhibited SHP2 with an IC₅₀ value of 9.8 μM, 7-fold more selective for SHP2 than the highly related SHP1. Fluorescence titration, thermal shift, and microscale thermophoresis quantitative binding assays confirmed its direct binding to SHP2. This compound was further verified to effectively inhibit SHP2-mediated cell signaling and proliferation. Furthermore, mouse and patient leukemia cells with PTPN11 activating mutations were more sensitive to this inhibitor than wild-type cells. This small molecule SHP2 inhibitor has a potential to serve as a lead compound for further optimization studies to develop novel anti-SHP2 therapeutic agents.

Structural Ordering in SWCNT-Polyimide Nanocomposites and Its Influence on Their Mechanical Properties

Using fully-atomistic models, tens-microseconds-long molecular-dynamic modelling was carried out for the first time to simulate the kinetics of polyimides ordering induced by the presence of single-walled carbon nanotube (SWCNT) nanofillers. Three polyimides (PI) were considered with different dianhydride fragments, namely 3,3',4,4'-biphenyltetracarboxylic dianhydride (BPDA), 2,3',3,4'-biphenyltetracarboxylic dianhydride (aBPDA), and 3,3',4,4'-oxidiphthalic dianhydride (ODPA) and same diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (diamine P3). Both crystallizable PI BPDA-P3 and two amorphous polyimides ODPA-P3 and aBPDA-P3 reinforced by SWCNTs were studied. The structural properties of the nanocomposites at temperature close to the bulk polymer melting point were studied. The mechanical properties were determined for the nanocomposites cooled down to the glassy state. It was found that the SWCNT nanofiller initiates' structural ordering not only in the crystallizable BPDA-P3 but also in the amorphous ODPA-P3 samples were in agreement with previously obtained experimental results. Two stages of the structural ordering were detected in the presence of SWCNTs, namely the orientation of the planar moieties followed by the elongation of whole polymer chains. The first type of local ordering was observed on the microsecond time scale and did not lead to the change of the mechanical properties of a polymer binder in considered nanocomposites. At the end of the second stage, both BPDA-P3 and ODPA-P3 PI chains extended completely along the SWCNT surface, which in turn led to enhanced mechanical characteristics in their glassy state.

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

The accurate sequencing of DNA using nanopores requires control over the speed of DNA translocation through the pores and also of the DNA conformation. Our studies show that ssDNA translocates through hourglass-shaped pores with hydrophobic constriction regions when an electric field is applied. The constriction provides a barrier to translocation and thereby slows down DNA movement through the pore compared with pores without the constriction. We show that ssDNA moves through these hydrophobic pores in an extended conformation and therefore does not form undesirable secondary structures that may affect the accuracy of partial current blockages for DNA sequencing.

Elucidating the bactericidal mechanism of action of the linear antimicrobial tetrapeptide BRBR-NH2

Linear antimicrobial peptides, with their rapid bactericidal mode of action, are well-suited for development as topical antibacterial drugs. We recently designed a synthetic linear 4-residue peptide, BRBR-NH₂, with potent bactericidal activity against Staphylococcus aureus (MIC 6.25 μM), the main causative pathogen of human skin infections with an unknown mechanism of action. Herein, we describe a series of experiments conducted to gain further insights into its mechanism of action involving electron microscopy, artificial membrane dye leakage, solution- and solid-state NMR spectroscopy followed by molecular dynamics simulations. Experimental results point towards a SMART (Soft Membranes Adapt and Respond, also Transiently) mechanism of action, suggesting that the peptide can be developed as a topical antibacterial agent for treating drug-resistant Staphylococcus aureus infections.

Enhanced delivery of fixed-dose combination of synergistic antichagasic agents posaconazole-benznidazole based on amorphous solid dispersions

Posaconazole (PCZ) and benznidazole (BNZ) are known to show synergetic effect in treating the acute and chronic phases of Chagas disease, a neglected parasitic disease. However, as both compounds are poorly water soluble, the development of amorphous solid dispersions (ASDs) of a PCZ/BNZ fixed-dose combination in a water-soluble polymer becomes an attractive option to increase their apparent solubility and dissolution rate, potentially improving their oral bioavailability. The initial approach was to explore solvent evaporated solid dispertion (SD) systems for a PCZ/BNZ 50:50 (wt%) combination at several total drug loading levels (from SD with 10% to 50% drug loading) in water-soluble carriers, including polyvinylpyrrolidone (PVP K-30) and vinylpyrrolidone-vinyl acetate copolymer (PVPVA 64). Based on comparison of non-sink in vitro dissolution performance, ASD systems based on PVPVA was identified as the most effective carrier for a 50:50 (w/w %) fixed-dose combination of PCZ/BNZ to increase their apparent solubility and dissolution rate, mainly at 10% drug loading, which shows more expressive values of area under the curve (AUC) (7336.04 ± 3.77 min.μL/mL for PCZ and 15,795.02 ± 7.29 min.μL/mL for BNZ). Further characterization with polarized microscopy, powder X-ray diffraction, and thermal analysis reveals that there exists a threshold drug loading level at about 30% PCZ/BNZ, below which ASDs are obtained and above which a certain degree of crystallinity tends to result. Moreover, infrared spectroscopic analysis reveals the lack of hydrogen bonding interactions between the drugs (PCZ and BNZ) and the polymer (PVPVA) in the ASD, this is also confirmed through molecular dynamics simulations. The molecular modeling results further show that even in the absence of meaningful hydrogen bonding interactions, there is a greater tendency for PVPVA to interact preferentially with PCZ and BNZ through electrostatic interactions thereby contributing to the stability of the system. Thus, the present SD system has the advantage of presenting a fixed-dese combination of two synergistic antichagasic agents PCZ and BNZ together in amorphous form stabilized in the PVPVA matrix with enhanced dissolution, potentially improving their bioavailability and therapeutic activity in treating Chagas disease.

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and χ-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states, 3 J-coupling, nuclear Overhauser effect, and residual dipolar coupling data were compared with NMR results. Starting from a totally unstacked/unfolding state, the rCAAU tetranucleotide was folded into A-form-like structures during ∼1 μs molecular dynamics simulations.

Extension of the GROMOS 56a6CARBO/CARBO_R Force Field for Charged, Protonated, and Esterified Uronates

An extension of the GROMOS 56a6_{CARBO/CARBO_R} force field for hexopyranose-based carbohydrates is presented. The additional parameters describe the conformational properties of uronate residues. The three distinct chemical states of the carboxyl group are considered: deprotonated (negatively charged), protonated (neutral), and esterified (neutral). The parametrization procedure was based on quantum-chemical calculations, and the resulting parameters were tested in the context of (i) flexibility of the pyranose rings under different pH conditions, (ii) conformation of the glycosidic linkage of the (1 → 4)-type for uronates with different chemical states of carboxyl moieties, (iii) conformation of the exocyclic (i.e., carboxylate and lactol) moieties, and (iv) structure of the Ca²⁺-linked chain-chain complexes of uronates. The presently proposed parameters in combination with the 56a6_{CARBO/CARBO_R} set can be used to describe the naturally occurring polyuronates, composed either of homogeneous (e.g., glucuronans) or heterogeneous (e.g., pectins, alginates) segments. The results of simulations relying on the new set of parameters indicate that the conformation of glycosidic linkage is nearly unaffected by the chemical state of the carboxyl group, in contrary to the ring conformational equilibria. The calculations for the poly(α-d-galacturonate)-Ca²⁺ and poly(α-l-guluronate)-Ca²⁺ complexes show that both parallel and anitiparallel arrangements of uronate chains are possible but differ in several structural aspects.

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase

[NiFe] hydrogenases catalyze the reversible splitting of H₂ into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O₂, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O₂ to water. This O₂ tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O₂ attack. Here, the O₂ accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O₂ molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O₂ concentrations used for MBH crystal derivatization. The examination of the O₂-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O₂ tolerance of the enzyme.

LeadOp+R: Structure-Based Lead Optimization With Synthetic Accessibility

We previously described a structure-based fragment hopping for lead optimization using a pre-docked fragment database, “LeadOp,” that conceptually replaced “bad” fragments of a ligand with “good” fragments while leaving the core of the ligand intact thus improving the compound's activity. LeadOp was proven to optimize the query molecules and systematically developed improved analogs for each of our example systems. However, even with the fragment-based design from common building blocks, it is still a challenge for synthesis. In this work, “LeadOp+R” was developed based on 198 classical chemical reactions to consider the synthetic accessibility while optimizing leads. LeadOp+R first allows user to identify a preserved space defined by the volume occupied by a fragment of the query molecule to be preserved. Then LeadOp+R searches for building blocks with the same preserved space as initial reactants and grows molecules toward the preferred receptor-ligand interactions according to reaction rules from reaction database in LeadOp+R. Multiple conformers of each intermediate product were considered and evaluated at each step. The conformer with the best group efficiency score would be selected as the initial conformer of the next building block until the program finished optimization for all selected receptor-ligand interactions. The LeadOp+R method was tested with two biomolecular systems: Tie-2 kinase and human 5-lipoxygenase. The LeadOp+R methodology was able to optimize the query molecules and systematically developed improved analogs for each of our example systems. The suggested synthetic routes for compounds proposed by LeadOp+R were the same as the published synthetic routes devised by the synthetic/organic chemists.

Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin-like protein 1

Toxoplasma and Plasmodium are the parasitic agents of toxoplasmosis and malaria, respectively, and use perforin-like proteins (PLPs) to invade host organisms and complete their life cycles. The Toxoplasma gondii PLP1 (TgPLP1) is required for efficient exit from parasitophorous vacuoles in which proliferation occurs. We report structures of the membrane attack complex/perforin (MACPF) and Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains of TgPLP1. The MACPF domain forms hexameric assemblies, with ring and helix geometries, and the APCβ domain has a novel β-prism fold joined to the MACPF domain by a short linker. Molecular dynamics simulations suggest that the helical MACPF oligomer preserves a biologically important interface, whereas the APCβ domain binds preferentially through a hydrophobic loop to membrane phosphatidylethanolamine, enhanced by the additional presence of inositol phosphate lipids. This mode of membrane binding is supported by site-directed mutagenesis data from a liposome-based assay. Together, these structural and biophysical findings provide insights into the molecular mechanism of membrane targeting by TgPLP1.

Molecular Dynamics Simulation of the pH-Induced Structural Transitions in CTAB/NaSal Solution

We performed molecular dynamics simulations to study the pH-induced structural transitions for aqueous mixtures of a cationic surfactant (cetyltrimethylammonium bromide, CTAB) and a hydrotrope (sodium salicylate, NaSal). We obtained rigid cylindrical, spherical, and flexible cylindrical micelles at pH 7, 2, and 0, respectively, which agrees well with the experimental results of Umeasiegbu et al. (Langmuir 2016, 32, 655). By analyzing the different micellar structural properties, including distribution and molecular orientation of CTA⁺ and Sal^- inside the micelle, we found that the binding form of the protonated salicylate molecules with CTA⁺ is different from that of Sal^- ions. Because of the protonation of salicylate molecules with reduction in pH, their hydrogen bonding interactions with water molecules strengthened and the electrostatic interactions with CTA⁺ headgroups weakened. Thus, the repulsion of the CTA⁺ headgroups led to the breakage of the cylindrical micelle into spherical ones. At pH 0, the H-bond-strengthened cation-π interactions between salicylate and CTA⁺ were verified. We concluded that the penetration of salicylate molecules inside the micelle and the strong association of Cl^- ions on the micellar surface play a key role in the formation of a flexible cylindrical micelle. This work provides an atomic-level insight into the mechanism of pH-induced shape transitions in the CTAB/NaSal systems, which is expected to be helpful to understand the aggregate behavior of cationic surfactant-hydrotrope solution.

PRODAN differentially influences its local environment

PRODAN influences its local environment at the nanoscale differently between ordered and disordered phases as shown by MD simulations.

c-MYC G-quadruplex binding by the RNA polymerase I inhibitor BMH-21 and analogues revealed by a combined NMR and biochemical Approach

BACKGROUND

Pyridoquinazolinecarboxamides have been reported as RNA polymerase I inhibitors and represent a novel class of potential antitumor agents. BMH-21, was reported to intercalate with GC-rich rDNA, resulting in nucleolar stress as a primary mechanism of cytotoxicity.

METHODS

The interaction of BMH-21 and analogues with DNA G-quadruplex structures was studied by NMR and molecular modelling. The cellular response was investigated in a panel of human tumor cell lines and protein expression was examined by Western Blot analysis.

RESULTS AND CONCLUSIONS

We explored the ability of BMH-21 and its analogue 2 to bind to G-quadruplex present in the c-MYC promoter, by NMR and molecular modelling studies. We provide evidence that both compounds are not typical DNA intercalators but are effective binders of the tested G-quadruplex. The interaction with c-MYC G-quadruplex was reflected in down-regulation of c-Myc expression in human tumor cells. The inhibitory effect was almost complete in lymphoma cells SUDHL4 characterized by overexpression of c-Myc protein. This downregulation reflected an early and persistent modulation of cMyc mRNA. Given the relevance of c-MYC in regulation of ribosome biogenesis, it is conceivable that the inhibition of c-MYC contributes to the perturbation of nuclear functions and RNA polymerase I activity. Similar experiments with CX-5461, another RNA polymerase I transcription inhibitor, indicate the same behaviour in G-quadruplex stabilization.

GENERAL SIGNIFICANCE

Our results support the hypothesis that BMH-21 and analogue compounds share the same mechanism, i.e. G-quadruplex binding as a primary event of a cascade leading to inhibition of RNA polymerase I and apoptosis.

Development and characterization of an α-l-rhamnosidase mutant with improved thermostability and a higher efficiency for debittering orange juice

The glycoside hydrolase, α-l-rhamnosidase, could remove the bitter taste of naringin from citrus juices. However, most α-l-rhamnosidases are easily deactivated at high temperatures, limiting the practice in debittering citrus juices. The V529A mutant of the α-l-rhamnosidase r-Rha1 from Aspergillus niger JMU-TS528 was developed with improved thermostability using directed evolution technology and site-directed mutagenesis. The enzyme mutant had a half-live of thermal inactivation T_(1/2) of 1.92 h, 25.00 min, and 2 min at 60, 65, and 70 °C, respectively. In addition, it had improved substrate affinity and better resistance to the inhibition of glucose. The improved substrate affinity was related to its lowered binding energy. Most significantly, the naringin content was reduced to below the bitter taste threshold by treatment with 75 U/mL of the mutant during the preheating process of orange juice production. The comprehensive results indicate that thermostability improvement could promote the practical value of α-l-rhamnosidase in citrus juice processing.

Structural and kinetic considerations on the catalysis of deoxyarbutin by tyrosinase

Deoxyarbutin, a potent inhibitor of tyrosinase, could act as substrate of the enzyme. Oxytyrosinase is able to hydroxylate deoxyarbutin and finishes the catalytic cycle by oxidizing the formed o-diphenol to quinone, while the enzyme becomes deoxytyrosinase, which evolves to oxytyrosinase in the presence of oxygen. This compound is the only one described that does not release o-diphenol after the hydroxylation step. Oxytyrosinase hydroxylates the deoxyarbutin in ortho position of the phenolic hydroxyl group by means of an aromatic electrophilic substitution. As the oxygen orbitals and the copper atoms are not coplanar, but in axial/equatorial position, the concerted oxidation/reduction cannot occur and the release of a copper atom to bind again in coplanar position, enabling the oxidation/reduction or release of the o-diphenol from the active site to the medium. In the case of deoxyarbutin, the o-diphenol formed is repulsed by the water due to its hydrophobicity, and so can bind correctly and be oxidized to a quinone before being released. Deoxyarbutin has been characterized with: [Formula: see text] = 1.95 ± 0.06 s-1 and [Formula: see text] = 33 ± 4 μM. Computational simulations of the interaction of β-arbutin, deoxyarbutin and their o-diphenol products with tyrosinase show how these ligands bind at the copper centre of tyrosinase. The presence of an energy barrier in the release of the o-diphenol product of deoxyarbutin, which is not present in the case of β-arbutin, together with the differences in polarity and, consequently differences in their interaction with water help understand the differences in the kinetic behaviour of both compounds. Therefore, it is proposed that the release of the o-diphenol product of deoxyarbutin from the active site might be slower than in the case of β-arbutin, contributing to its oxidation to a quinone before being released from the protein into the water phase.

Atomistic Molecular Dynamics Simulations of the Initial Crystallization Stage in an SWCNT-Polyetherimide Nanocomposite

Crystallization of all-aromatic heterocyclic polymers typically results in an improvement of their thermo-mechanical properties. Nucleation agents may be used to promote crystallization, and it is well known that the incorporation of nanoparticles, and in particular carbon-based nanofillers, may induce or accelerate crystallization through nucleation. The present study addresses the structural properties of polyetherimide-based nanocomposites and the initial stages of polyetherimide crystallization as a result of single-walled carbon nanotube (SWCNT) incorporation. We selected two amorphous thermoplastic polyetherimides ODPA-P3 and aBPDA-P3 based on 3,3′,4,4′-oxydiphthalic dianhydride (ODPA), 2,3′,3,4′-biphenyltetracarboxylic dianhydride (aBPDA) and diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (P3) and simulated the onset of crystallization in the presence of SWCNTs using atomistic molecular dynamics. For ODPA-P3, we found that the planar phthalimide and phenylene moieties show pronounced ordering near the CNT (carbon nanotube) surface, which can be regarded as the initial stage of crystallization. We will discuss two possible mechanisms for ODPA-P3 crystallization in the presence of SWCNTs: the spatial confinement caused by the CNTs and π–π interactions at the CNT-polymer matrix interface. Based on our simulation results, we propose that ODPA-P3 crystallization is most likely initiated by favorable π–π interactions between the carbon nanofiller surface and the planar ODPA-P3 phthalimide and phenylene moieties.

Investigating Ebola virus pathogenicity using molecular dynamics

BACKGROUND

Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5.

RESULTS

As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling.

CONCLUSION

Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation

Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water.

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers. The N-terminal domains were embedded in an asymmetric model of the outer membrane, with lipopolysaccharide molecules in the outer leaflet and phospholipids in the inner leaflet. Our results reveal a large dimerization interface within the membrane environment, ensuring that the dimer is stable over the course of the simulations. The linker is flexible, expanding and contracting to pull the globular C-terminal domain up toward the membrane or push it down toward the periplasm, suggesting a possible mechanism for providing mechanical stability to the cell. The external loops were more stabilized than was observed in previous studies due to the extensive dimerization interface and presence of lipopolysaccharide molecules in our outer-membrane model, which may have functional consequences in terms of OmpA adhesion to host cells. In addition, the pore-gating behavior of the protein was modulated compared with previous observations, suggesting a possible role for dimerization in channel regulation.