Evaluating substrate specificity of glutathione peroxidase mimic by molecular dynamics simulations and kinetics

The substrate specificities of glutathione peroxidase (GPX) mimic, 6,6′-ditellurobis(6-deoxy-β-cyclodextrin) (6-TeCD), for three hydroperoxides (ROOH), H₂O₂, tert-butyl hydroperoxide (t-BuOOH) and cumene hydroperoxide (CuOOH), are investigated through molecular dynamics (MD) simulations. The most stable conformations and the total interaction energies of complex of 6-TeCD with ROOH are used to evaluate the substrate specificity of 6-TeCD. The steady-state kinetics of 6-TeCD is studied and the Michaelis-Menten constant (K _m) and second-order rate constant k _max/K _ROOH show that 6-TeCD displays different affinity and specificity to ROOH. These results of experiments are well consistent with ones obtained by MD simulations, indicating that MD simulations could be applied to evaluation substrate specificity of small-molecule enzyme mimics.     

The phenomenon of water penetration into sodium octanoate micelles studied by molecular dynamics computer simulation

 In this publication we have studied the penetration process of water molecules into the hydrophobic core of a sodium octanoate micelle. The analysis of this phenomenon was based on a molecular dynamics computer simulation. We calculated the probability to find water molecules within a specific sphere which was adjusted in the center of the micelle. It turned out that the position of the micellar mass and geometry center was not too different, so that this reference point was well characterized. Water penetration was observed within the whole aggregate but if the radius is smaller than 300 pm, polar solvent molecules are very rarely observed. The results of our computer simulations suggest that significant water diffusion into the micelle occurs at larger distances from the micellar center with a lower threshold value of about 400 pm. In addition to these calculations, we used the Connolly algorithm in order to determine the solvent accessible surfaces of different micellar equilibrium structures. We observed large dynamical fluctuations with the formation of pores and channels. These structures are occasionally filled with water molecules. Received: 29 April 1998 Accepted: 27 May 1998     

Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane–water partition coefficients

The importance of membrane‐water partition coefficients led to the recent extension of the conductor‐like screening model for realistic solvation (COSMO‐RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO‐RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.     

Modeling,docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid–protein interactions, indicating some future applications of ns-LTP-mediated transport.     

Investigation of chiral recognition by molecular micelles with molecular dynamics simulations

Molecular dynamics simulations were used to characterize the binding of the chiral drugs chlorthalidone and lorazepam to the molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The project’s goal was to characterize the nature of chiral recognition in capillary electrophoresis separations that use molecular micelles as the chiral selector. The shapes and charge distributions of the chiral molecules investigated, their orientations within the molecular micelle chiral binding pockets, and the formation of stereoselective intermolecular hydrogen bonds with the molecular micelle were all found to play key roles in determining where and how lorazepam and chlorthalidone enantiomers interacted with the molecular micelle.     

Understanding the adsorption of branched polyamine on surface of gold nanoparticles by molecular dynamics simulations

Molecular dynamics simulations were conducted to characterize the adsorption behavior of branched polyethylenimine (br‐PEI) on the surface of gold nanoparticles (AuNPs). We observed the preferential adsorption of br‐PEI on the [111] surface of AuNPs. Furthermore, br‐PEI maintained a flat arrangement on the surface and wrapped the AuNPs in a stable manner, thereby blocking the adsorption of H₂O molecules and other free br‐PEI molecules. The model and computational results provide theoretical support for relevant experiments. Copyright © 2016 John Wiley & Sons, Ltd.     

A molecular dynamics simulation study of surface effects on gas permeation in free-standing polyimide membranes

A 141100-atom model of a glassy ODPA–ODA polyimide free-standing membrane, corresponding to a thickness of two average radii of gyration for the 40-mers chains, has been studied using molecular dynamics (MD) simulations. Due to the large-scale of the fully atomistic model, a parallelized particle-mesh technique using an iterative solution of the Poisson equation had to be implemented for the efficient evaluation of the electrostatic interactions. With flattened-chain configurations, the density was found to adjust itself naturally in the middle of the membrane to 95% of the ODPA–ODA experimental value. At the free-standing surfaces, the density profile became sigmoïdal, indicating surface roughness. For comparison, two isotropic bulk models, one at the “normal” density as obtained for ODPA–ODA under ambient conditions and the other one at 95% of the normal-density, were built. Small gas probes were inserted into all three models in order to investigate whether the interfacial structure of the glassy free-standing membrane can influence penetrant transport. Gas diffusion in the low-density part of the interface was found to be very fast. The limiting value for the gas diffusion coefficient D_membrane is only attained when the probes enter more dense regions in the membrane. Indeed, D_membrane compares well with D_bulk obtained for the 95%-density bulk system, i.e. about twice that in the normal-density bulk. Solubility is larger in the membrane than in both bulk models, thus suggesting an effect of chain flattening in addition to the density. Adsorption is particularly high at the free-standing interfaces.     

Force-field parametrization and molecular dynamics simulations of Congo red

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.     

Steady-state oxidation of cholesterol catalyzed by cholesterol oxidase in lipid bilayer membranes on platinum electrodes

Cholesterol oxidase is immobilized in electrode-supported lipid bilayer membranes. Platinum electrodes are initially modified with a self-assembled monolayer of thiolipid. A vesicle fusion method is used to deposit an outer leaflet of phospholipids onto the thiolipid monolayer forming a thiolipid/lipid bilayer membrane on the electrode surface. Cholesterol oxidase spontaneously inserts into the electrode-supported lipid bilayer membrane from solution and is consequently immobilized to the electrode surface. Cholesterol partitions into the membrane from buffer solutions containing cyclodextrin. Cholesterol oxidase catalyzes the oxidation of cholesterol by molecular oxygen, forming hydrogen peroxide as a product. Amperometric detection of hydrogen peroxide for continuous solution flow experiments are presented, where flow was alternated between cholesterol solution and buffer containing no cholesterol. Steady-state anodic currents were observed during exposures of cholesterol solutions ranging in concentration from 10 to 1000 μM. These data are consistent with the Michaelis-Menten kinetic model for oxidation of cholesterol as catalyzed by cholesterol oxidase immobilized in the lipid bilayer membrane. The cholesterol detection limit is below 1 μM for cholesterol solution prepared in buffered cyclodextrin. The response of the electrodes to low density lipoprotein solutions is increased upon addition of cyclodextrin. Evidence for adsorption of low density lipoprotein to the electrode surface is presented.     

Insight into the structural and transport properties of methyl and benzyl triphenyl phosphonium based deep eutectic solvents using molecular dynamics simulations

Molecular dynamics simulation of twelve phosphonium based DESs based on methyl triphenyl phosphonium bromide and benzyl triphenyl phosphonium chloride as hydrogen bond acceptors (HBA) with glycerol, ethylene glycol, triethylene glycol and trifluoroacetamide as hydrogen bond donors (HBDs) are carried out with the Generalized Amber Force Field between 25 °C and 95 °C at 1 atm pressure. Isobaric-isothermal ensemble is used for predicting the structural properties, namely, radial distribution function and coordination number. Further, time resolved trajectory data is correlated to predict the transport properties such as, self-diffusivity, binary-diffusivity, ionic conductivity and viscosity. The temperature dependence of predicted density is observed with 4.96 × 10⁻² absolute average deviations from experimental dataset. Further, the self-diffusivities are predicted using Einstein's approach and ionic conductivity is calculated from Nernst-Einstein equation as well as Green-Kubo formulation. Further, the viscosity is also predicted using the Green-Kubo formulation. The predicted ionic conductivities and viscosities are fitted in the Vogel-Fulcher-Tammann (VFT) equation to calculate the VFT parameters for the respective DESs.     

Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer

The phospholipid bilayer plays a central role in the lifecycle of the endogenous cannabinoid, N-arachidonoylethanolamine (anandamide, AEA). Therefore, the orientation and location of AEA in the phospholipid bilayer with respect to key membrane associated proteins, is a central issue in understanding the mechanism of endocannabinoid signaling. In this paper, we report a test of the hypothesis that a βXXβ motif (formed by beta branching amino acids, V6.43 and I6.46) on the lipid face of the cannabinoid CB1 receptor in its inactive state may serve as an initial CB1 interaction site for AEA. Eight 6 ns NAMD2 molecular dynamics simulations of AEA were conducted in a model system composed of CB1 transmembrane helix 6 (TMH6) in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer. In addition, eight 6 ns NAMD2 molecular dynamics simulations of a low CB1 affinity (20:2, n−6) analog of AEA were conducted in the same model system. AEA was found to exhibit a higher incidence of V6.43/I6.46 groove insertion than did the (20:2, n−6) analog. In certain cases, AEA established a high energy of interaction with TMH6 by first associating with the V6.43/I6.46 groove and then molding itself to the lipid face of TMH6 to establish a hydrogen bonding interaction with the exposed backbone carbonyl of P6.50. Based upon these results, we propose that the formation of this hydrogen bonded AEA/TMH6 complex may be the initial step in CB1 recognition of AEA in the lipid bilayer.     

The effect of corrugation of pore wall on the thermal diffusion in nanopores by molecular dynamics simulations

In this work we have studied the effect of corrugation on the thermal diffusion (soret effect) in isotopic and non-isotopic fluid mixtures confined in a slit pore. We used a boundary driven non-equilibrium molecular dynamics to simulate thermal diffusion in Lennard–Jones (LJ) binary mixtures confined in structureless Steele 10-4-3 and atomistic Lennard–Jones pore walls. The results showed that for the isotopic mixture thermal diffusion factor for both wall types agrees and the corrugation of the LJ wall has no effect in isotopic mixture. However, for non-isotopic mixture confined in atomistic LJ pore the component with stronger attraction adsorbs more to the wall than the structureless Steele wall. The effect of corrugation of pore wall on the thermal diffusion is noticeable in narrow slit pore and mixture with large difference in molecular attraction parameter of components.     

Solubilization of supported lipid membranes by octyl glucoside observed by time-lapse atomic force microscopy

Detergents are very useful for the purification of membrane proteins. A good detergent for protein extraction has to prevent denaturation by unfolding, and to avoid aggregation. Therefore, gaining access to the mechanism of biomembranes’ solubilization by detergents is crucial in biochemical research. Among the wide range of detergents used to purify membrane proteins, n-octyl β-d-glucopyranoside (OG) is one of the most important as it can be easily removed from final protein extracts.

Here, we used real-time atomic force microscopy (AFM) imaging to visualize the behavior of a model supported lipid bilayer in the presence of OG. Two kinds of supported model membranes were prepared by fusion of unilamellar vesicles: with an equimolar mixing of dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DOPC/DPPC) or with DPPC alone. Time-lapse AFM experiments evidenced that below its critical micelle concentration (CMC), OG was not able to solubilize the bilayer but the gel DPPC domains were instantly dissolved into the DOPC matrix. This result was interpreted as a disorganization of the DPPC molecular packing induced by OG. When membranes were incubated with OG at concentrations higher than CMC, the detergent immediately provoked the complete and immediate desorption of the whole bilayer for both compositions: DPPC and DOPC/DPPC. After a while, some patches appeared onto the bare mica surface. This redeposition activity, together with fusion events, progressively led to the recovery of a continuous bilayer. These results provide a new insight on the unique properties of OG employed in membrane reconstitution protocols.     

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation

Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.     

The solution structure of adenosylcobalamin and adenosylcobinamide determined by nOe-restrained molecular dynamics simulations

The solution structure of coenzyme B₁₂ (5′-deoxyadenosylcobalamin, AdoCbl) and the corresponding cobinamide, AdoCbi⁺, in which the axial nucleotide has been chemically removed, have been investigated using NMR-restrained molecular dynamics (MD) and simulated annealing (SA) calculations. The nOe cross peaks in the ROESY spectrum of both AdoCbl and AdoCbi⁺ are consistent with the presence of at least two principal conformations for each compound in solution. In the first, termed the southern conformation, the adenosyl (Ado) ligand is over the C ring of the molecule, the structure observed in the solid state. In the second, the Ado ligand has undergone an anticlockwise rotation and is over C10 in the eastern quadrant of the molecule. A two-state MD/SA simulation was used omitting nOes that arise only from the eastern conformation and that arise only from the southern conformation, respectively. Consensus structures were obtained by averaging the coordinates of 25 annealed structures of the southern and eastern conformations, respectively, of AdoCbl and AdoCbi⁺, followed by energy minimization. The consensus structure of the southern conformation of AdoCbl agrees well with the solid-state structure and has a very similar corrin fold angle. Several observations show that AdoCbl is considerably more rigid than AdoCbi⁺, and indeed is one of the most rigid cobalt corrinoids studied by these methods to date: the variability in the conformations of the corrin ring between the family of 25 annealed structure and the consensus structure is much smaller for AdoCbl than for AdoCbi⁺; during MD simulations, the previously demonstrated flexibility of the corrin ring as gauged by the corrin ruf angle (C5–Co–C15) is preserved for AdoCbi⁺ but is considerably diminished in AdoCbl because of a decrease in the maximum fold angle and an increase in the minimum fold angle achieved in the latter; the range of values of the Co–C bond length experienced in AdoCbi⁺ is substantially larger than in AdoCbl; the Ado ligand visits many more orientations relative to the corrin ring in AdoCbi⁺ than in AdoCbl; the pyrrole rings in AdoCbl undergo smaller deformations than in AdoCbi⁺; and the “breathing motion” of the corrin ring in which C5, C10 and C15 oscillate from above to below the mean corrin plane is much less pronounced in AdoCbl than in AdoCbi⁺. This rigidity is attributed to the presence of two bulky ligands in AdoCbl, the Ado ligand in the upper (β) axial position and the 5,6-dimethylbenzimidazole (bzm) ligand in the lower () axial ligand position, in contrast to the other structures which have only one or other of these two bulky ligands. The corrin fold angle in AdoCbl is significantly larger than that in AdoCbi⁺, a finding that is in agreement with a previous observation that CH₃Cbl has a larger fold angle than CH₃Cbi⁺; this implies that base-on corrins are under steric strain.     

A comparative study of 5- fluorouracil,doxorubicin, methotrexate,paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations

The new corona virus (nCoV) is aetiological agent responsible for the viral pneumonia epidemic. Three is no specific therapeutic medicines available for the treatment of this condition and also effective treatment choices are few. In this work, authors tried to investigate few potential of repurposing drugs (5- fluorouracil, doxorubicin, methotrexate and paclitaxel) against the main protease (Mpro) of nCoV by the computational tools. Molecular docking was performed to screen out the best compound and doxorubicin was found to have minimum binding energy ?121.89 kcal/mol. To further study, molecular dynamics (MD) simulations were performed at 300 K and the result successfully corroborate the energy obtained by molecular docking. Further, temperature dependent MD simulations of the best molecule, that is, doxorubicin based on results of docking, was performed to check the variation in structural changes in Mpro of nCoV at 290 K, 310 K, 320 K and 325 K. It is found that doxorubicin binds effectively with Mpro of nCoV at 290 K. Further, ADME properties of the 5- fluorouracil, doxorubicin, methotrexate and paclitaxel were also evaluated to understand the bioavailability.