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Hydrogen bond lifetime dynamics at the interface of a surfactant monolayer.

The dynamics of water near the polar headgroups of surfactants in a monolayer adsorbed at the air/water interface is likely to play a decisive role in determining the physical behavior of such organized assemblies. We have carried out an atomistic molecular dynamics (MD) simulation of a monolayer of the anionic surfactant sodium bis(2-ethyl-1-hexyl) sulfosuccinate (aerosol-OT or AOT) adsorbed at the air/water interface. The simulation is performed at room temperature with a surface coverage of that at the critical micelle concentration (78 Angstrom(2)/molecule). Detailed analyses of the lifetime dynamics of surfactant-water (SW) and water-water (WW) hydrogen bonds at the interface have been carried out. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the bound states at the interface and quantification of the dynamic equilibrium between bound and quasi-free water molecules, in terms of time-dependent relaxation rates. It is observed that the water molecules present in the first hydration layer form strong hydrogen bonds with the surfactant headgroups and hence have longer lifetimes. Importantly, it is found that the overall relaxation of the SW hydrogen bonds is faster for those water molecules which form two hydrogen bonds with the surfactant headgroups than those forming one such hydrogen bond. Equally interestingly, it is further noticed that water molecules beyond the first hydration layer form weaker hydrogen bonds than pure bulk water.

Journal Article↗

Microscopic modes and free energies of 3-phosphoinositide-dependent kinase-1 (PDK1) binding with celecoxib and other inhibitors.

Celecoxib, also known as Celebrex (approved by FDA in 1998) and remembered as the fastest-selling drug in history, was used as a cyclooxygenase-2 (COX-2) selective inhibitor having both anti-inflammatory and anticancer activities. Most recent studies have revealed that the apoptotic activity of celecoxib (and its derivatives) is actually independent of the COX-2 inhibitory activity and that celecoxib also inhibits the kinase activity of 3-phosphoinositide-dependent protein kinase-1 (PDK1), suggesting that the well-known anticancer activity of celecoxib is not due to the inhibition of COX-2, but possibly is due to the inhibition of PDK1. It is highly desirable to develop new celecoxib derivatives as PDK1-specifc inhibitors to avoid the side effects of COX-2 inhibitors. To understand how PDK1 binds with celecoxib and its derivatives, we have performed extensive molecular docking and combined molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on eight representative PDK1 inhibitors, leading to the finding of a new, more favorable binding mode which is remarkably different from the previously proposed binding mode. Based on the determined most stable binding structures, the calculated binding free energies are all in good agreement with the corresponding experimental data, and the biological activity data available for celecoxib and its derivatives can be better interpreted. The obtained new insights, concerning both the binding mode and computational protocol, will be valuable not only for future rational design of novel, more potent PDK1-specific inhibitors as promising anticancer therapeutics, but also for rational design of drugs targeting other proteins.

3-Phosphoinositide-Dependent Protein Kinases↗

Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study.

In the context of our detailed study of the chemical behavior of aquo- and ammine-Zn(II) complexes, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations were performed at the Hartree-Fock (HF) level for the zinc(II)-diamine complexes in aqueous solution. The initial structures of cis and trans isomers of the tetraaquodiamminezinc(II) complex were found to transform into the triaquodiamminezinc(II) complex by releasing one water ligand after approximately 6 and approximately 22 ps of simulation time, respectively. The structural and dynamical properties of these three zinc complexes, i.e., cis-[Zn(NH3)2(H2O)4]2+, trans-[Zn(NH3)2(H2O)4]2+, and [Zn(NH3)2(H2O)3]2+, were analyzed in terms of radial distribution functions (RDF), coordination number distributions (CND), angular distribution functions (ADF), tilt and theta angle distributions, ligands' mean residence times (MRTs), and ion-ligand stretching frequencies. One considerably elongated Zn-O bond of 2.43 A was observed in the case of the cis isomer for one of the water ligands located in the trans position to an ammonia ligand. In the trans isomer the average Zn-O bond length was observed to be 2.23 A, while in the triaquodiamminezinc(II) complex two distinct Zn-O bonds, namely 2.12 A for the ligands in the trigonal plane and 2.26 A for axial water molecules, were observed. As both of the octahedral isomers are transformed into the pentacoordinated structure within the picosecond range, they might be regarded as "metastable species or intermediates", while the triaquodiamminezinc(II) complex is the most stable species of the zinc(II)-diamine complex in aqueous solution.

Ammonia↗

Water at hydrophobic substrates: curvature, pressure, and temperature effects.

We studied the water density profile close to spherical and planar hydrophobic objects using molecular dynamics (MD) simulations. For normal pressure and room temperature, the depletion layer thickness of a planar substrate is approximately 2.5 Angstroms. Even for quite large spherical solutes with a radius of R = 18 Angstroms, the depletion layer thickness is reduced by 30%, which shows that substrate curvature and roughness is an experimentally important factor. Rising temperature leads to a substantial increase of the depletion layer thickness. The compressibility of the depletion layer is found to be surprisingly small and only approximately 5 times higher than that of bulk water. A high electrostatic surface potential of 0.5 V is found, which presumably plays an important role in the presence of charged solutes, since it can promote adsorption into the interfacial layer.

Journal Article↗

Self-diffusion of methane in single-walled carbon nanotubes at sub- and supercritical conditions.

The diffusivities of methane in single-walled carbon nanotubes (SWNTs) are investigated at various temperatures and pressures using classical molecular dynamics (MD) simulations complemented with grand canonical Monte Carlo (GCMC) simulations. The carbon atoms at the nanotubes are structured according to the (m, m) armchair arrangement and the interactions between each methane molecule and all atoms of the confining surface are explicitly considered. It is found that the parallel self-diffusion coefficient of methane in an infinitely long, defect-free SWNT decreases dramatically as the temperature falls, especially at subcritical temperatures and high loading of gas molecules when the adsorbed gas forms a solidlike structure. With the increase in pressure, the diffusion coefficient first declines rapidly and then exhibits a nonmonotonic behavior due to the layering transitions of the adsorbed gas molecules as seen in the equilibrium density profiles. At a subcritical temperature, the diffusion of methane in a fully loaded SWNT follows a solidlike behavior, and the value of the diffusion coefficient varies drastically with the nanotube diameter. At a supercritical temperature, however, the diffusion coefficient at high pressure reaches a plateau, with the limiting value essentially independent of the nanotube size. For SWNTs with the radius larger than approximately 2 nm, capillary condensation occurs when the temperature is sufficiently low, following the layer-by-layer adsorption of gas molecules on the nanotube surface. For SWNTs with a diameter less than about 2 nm, no condensation is observed because the system becomes essentially one-dimensional.

Journal Article↗

Structure and aggregation number of a lyotropic liquid crystal: a fluorescence quenching and molecular dynamics study.

The structure and aggregation number of a discotic lyotropic liquid crystal, prepared from tetradecyltrimethylammonium chloride (TDTMACl)/decanol (DeOH)/NaCl/H2O, have been examined using fluorescence quenching of pyrene by hexadecylpyridinium chloride and molecular dynamics (MD). The fluorescence method gives an aggregation number of 258 +/- 25 units (DeOH + TDTMACl). From the MD simulation, a lower limit for the aggregate dimension of 130 units of DeOH + TDTMACl is predicted. A stable oblate aggregate of 240 units was studied in detail. A strong polarization between the ammonium headgroups and chloride ions is observed from the calculated trajectory. DeOH headgroups are located, on average, 0.3 nm more to the interior of the aggregate than the TDTMACl headgroup and contribute to widening the interface by forming H-bonds with water. The radial distribution function of the ammonium headgroup shows that there are 16 water molecules in the first solvation sphere. The diagonal elements of the order parameter tensor of the tail atoms of both surfactants indicate that the interior of the micelle preserves about the same degree of order as at the interface, up to the last three atoms of the aliphatic chain, where the order starts to decrease.

Journal Article↗

Dynamics and density profile of water in nanotubes as one-dimensional fluid.

The transport and structural properties of water confined in nanotubes with different diameters were studied by molecular dynamics (MD) simulation. The effects of pore size, molecule-wall interaction, and the helicity of CNT on the diffusivity, thermal conductivity, and shear viscosity as well as density profile were analyzed. For diffusivity, in model NT > in armchair CNT > in zigzag CNT at similar conditions. However in contrast to the diffusivity, the thermal conductivity and the shear viscosity increase as the pore size decreases, in zigzag CNT > in armchair CNT > (or approximately ) in model NT. The ordered layer distribution of water molecules in nanotubes is clear. It suggests the structure of fluid in the zigzag CNTs is more ordered, and more solidlike. In the nanotubes, where the molecule and the pore dimensions are of similar order of magnitude, the nature of water-water and water-wall interactions, the confinement effect of space, and the helicity of CNT become more significant.

Molecular Dynamics Simulation↗

Structure and mechanism of the deposition of multilayers of polyelectrolytes and nanoparticles.

MD simulation of the layer-by-layer assembly of polyelectrolytes (PEs) and nanoparticles (NPs) revealed that the assembly process is electrostatically driven with alternating charge reversal and an overcompensation mechanism. Layers were observed to grow in the lateral direction as well as in a direction normal to the surface. Weakly adsorbed PE molecules were observed to desorb from the flat and NP surfaces. Those molecules are attracted by suspended NPs in solution. PE molecules do not only pull NPs toward the surface but bridge NPs both in solution and on the surface, forming agglomerates and islands. The first double layer differs in structure from the second double layer as a result of strong adsorption of the PE molecules to the rigid surface.

Journal Article↗

Experimental and theoretical investigation of the micellar-assisted solubilization of ibuprofen in aqueous media.

Surfactants can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. In this article, the aqueous solubilization of the nonsteroidal, antiinflammatory drug ibuprofen is studied experimentally and theoretically in micellar solutions of anionic (sodium dodecyl sulfate, SDS), cationic (dodecyltrimethylammonium bromide, DTAB), and nonionic (dodecyl octa(ethylene oxide), C12E8) surfactants possessing the same hydrocarbon "tail" length but differing in their hydrophilic headgroups. We find that, for these three surfactants, the aqueous solubility of ibuprofen increases linearly with increasing surfactant concentration. In particular, we observed a 16-fold increase in the solubility of ibuprofen relative to that in the aqueous buffer upon the addition of 80 mM DTAB and 80 mM C12E8 but only a 5.5-fold solubility increase upon the addition of 80 mM SDS. The highest value of the molar solubilization capacity (chi) was obtained for DTAB (chi = 0.97), followed by C12E8 (chi = 0.72) and finally by SDS (chi = 0.23). A recently developed computer simulation/molecular-thermodynamic modeling approach was extended to predict theoretically the solubilization behavior of the three ibuprofen/surfactant mixtures considered. In this modeling approach, molecular-dynamics (MD) simulations were used to identify which portions of ibuprofen are exposed to water (hydrated) in a micellar environment by simulating a single ibuprofen molecule at an oil/water interface (modeling the micelle core/water interface). On the basis of this input, molecular-thermodynamic modeling was then implemented to predict (i) the micellar composition as a function of surfactant concentration, (ii) the aqueous solubility of ibuprofen as a function of surfactant concentration, and (iii) the molar solubilization capacity (chi). Our theoretical results on the solubility of ibuprofen in aqueous SDS and C12E8 surfactant solutions are in good agreement with the experimental data. The ibuprofen solubility in aqueous DTAB solutions was somewhat overpredicted because of challenges associated with accurately modeling the strong electrostatic interactions between the anionic ibuprofen and the cationic DTAB. Our results indicate that computer simulations of ibuprofen at a flat oil/water interface can be used to obtain accurate information about the hydrated and the unhydrated portions of ibuprofen in a micellar environment. This information can then be used as input to a molecular-thermodynamic model of self-assembly to successfully predict the aqueous solubilization behavior of ibuprofen in the three surfactant systems studied.

Ibuprofen↗

Perturbation of phospholipid bilayer properties by ethanol at a high concentration.

Atomistic molecular dynamics (MD) simulations have been carried out at 30 degrees C on a fully hydrated liquid crystalline lamellar phase of dimyrystoylphosphatidylcholine (DMPC) lipid bilayer with embedded ethanol molecules at 1:1 composition, as well as on the pure bilayer phase. The ethanol molecules are found to exhibit a preference to occupy regions near the upper part of the lipid acyl chains and the phosphocholine headgroups. The calculations revealed that the phosphocholine headgroup dipoles (P- --> N+) of the lipids prefer to orient more toward the aqueous layer in the presence of ethanol. It is noticed that the ethanol molecules modify the dynamic properties of both lipids as well as the water molecules in the hydration layer of the lipid headgroups. Both the in-plane "rattling" and out-of-plane "protrusion" motions of the lipids have been found to increase in the presence of ethanol. Most importantly, it is observed that the water molecules within the hydration layer of the lipid headgroups exhibit faster translational and rotational motions in the presence of ethanol. This arises due to faster dynamics of hydrogen bonds between lipid headgroups and water in the presence of ethanol.

Chemistry, Physical↗

Hydrogen bonded dimers of triurea derivatives of triphenylmethanes.

Tri-(2-alkoxy-5-ureido-phenyl)methanes represent a novel self-complementary motif forming hydrogen bonded homo- and heterodimers in nonpolar, aprotic solvents as evidenced by 1H NMR and ESI-mass spectra and by the formation of heterodimers. MD simulations suggest the formation of hydrogen bonds of different strength in agreement with NMR data. The dimerization does not interfere with that of tetraurea calix[4]arenes. A combination of both motifs may be used therefore to build up larger structures via self-assembly processes. [structure: see text]

Journal Article↗

Conformational properties of amphotericin B amide derivatives--impact on selective toxicity.

Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (phi,psi)=(290 degrees,180 degrees) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model.

Amides↗

Glycosylations versus conformational preferences of cancer associated mucin core.

Synthetic oligosaccharide vaccines based on core STn (sialyl alpha2-6 GalNAc) carbohydrate epitopes are being evaluated by a number of biopharmaceutical firms as potential immunotherapeutics in the treatment of mucin-expressing adenocarcinomas. The STn carbohydrate epitopes exist as discontinuous clusters, O-linked to proximal serine and threonine residues within the mucin sequence. In an effort to probe the structure and dynamics of STn carbohydrate clusters as they may exist on the cancer-associated mucin, we have used NMR spectroscopy and MD simulations to study the effect of O-glycosylation of adjacent serine residues in a repeating (Ser)n sequence. Three model peptides/glyco-peptides were studied: a serine trimer containing no carbohydrate groups ((Ser)3 trimer); a serine trimer containing three Tn (GalNAc) carbohydrates alpha-linked to the hydroxyls of adjacent serine sidechains ((Ser.Tn)3 trimer); and a serine trimer containing three STn carbohydrates alpha-linked to the hydroxyls of adjacent serine sidechains ((Ser.STn)3 trimer). Our results demonstrate that clustering of carbohydrates shifts the conformational equilibrium of the underlying peptide backbone into a more extended and rigid state, an arrangement that could function to optimally present the clustered carbohydrate antigen to the immune system. Steric effects appear to drive these changes since an increase in the size of the attached carbohydrate (STn versus Tn) is accompanied by a stronger shift in the equilibrium toward the extended state. In addition, NMR evidence points to the formation of hydrogen bonds between the peptide backbone NH protons and the proximal GalNAc groups in the (Ser.Tn)3 and (Ser.STn)3 trimers. The putative peptide-sugar hydrogen bonds may also play a role in influencing the conformation of the underlying peptide backbone, as well as the orientation of the O-linked carbohydrate. The significance of these results will be discussed within the framework of developing clustered STn-based vaccines, capable of targeting the clustered STn epitopes on the cancer-associated mucin.

Adenocarcinoma↗

Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues.

In the present study experimentally determined ligand selectivity of three methylated buspirone analogues (denoted as MM2, MM5 and P55) towards 5-HT1A and 5-HT2A serotonin receptors was theoretically investigated on a molecular level. The relationships between the ligand structure and 5-HT1A and 5-HT2A receptor affinities were studied and the results were found to be in agreement with the available site-directed mutagenesis and binding affinity data. Molecular dynamics (MD) simulations of ligand-receptor complexes were performed for each investigated analogue, docked twice into the central cavity of 5-HT1A/5-HT2A, each time in a different orientation. Present results were compared with our previous theoretical results, obtained for buspirone and its non-methylated analogues. It was found that due to the presence of the methyl group in the piperazine ring the ligand position alters and the structure of the ligand-receptor complex is modified. Further, the positions of derivatives with pyrimidinyl aromatic moiety and quinolinyl moiety are significantly different at the 5-HT2A receptor. Thus, methylation of such derivatives alters the 3D structures of ligand-receptor complexes in different ways. The ligand-induced changes of the receptor structures were also analysed. The obtained results suggest, that helical domains of both receptors have different dynamical behaviour. Moreover, both location and topography of putative binding sites for buspirone analogues are different at 5-HT1A and 5-HT2A receptors.

Binding Sites↗

Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.

The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calculations that include Ca2+ ions and explicit solvent molecules. Four parallel sets of MD refinements were run to provide accurate comparisons of structures produced in vacuo, in vacuo with Ca2+ ions, and with two different protocols in a solvent bath with Ca2+ ions. The structural ensembles were analyzed in terms of structural definition, molecular energies, packing density, solvent-accessible surface, hydrogen bonds, and the coordination of calcium ions in the two binding loops. Refinement including Ca2+ ions and explicit solvent results in significant improvements in the precision and accuracy of the structure, particularly in the binding loops. These results are consistent with results previously obtained in free MD simulations of proteins in solution and show that the rMD refined NMR-derived solution structures of proteins, especially metalloproteins, can be significantly improved by these strategies.

Calbindins↗

Solvent effect on the synthesis of clarithromycin: a molecular dynamics study.

Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4"-[O-bis(TMS)]erythromycin A 9-[O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the 'O-' of the anions. At distances shorter than 5 A, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.

Clarithromycin↗

Correlation times and adiabatic barriers for methyl rotation in SNase.

The relation of rotational correlation times to adiabatic rotational barriers for alanine methyl groups in staphylococcal nuclease (SNase) is investigated. The hypothesis that methyl rotational barriers may be useful probes of local packing in proteins is supported by an analysis of ten X-ray crystal structures of SNase mutants. The barrier heights are consistent across a set of ten structures of a native SNase and mutants containing single-point mutations or single or double insertions, most in a ternary SNase complex. The barriers for different methyls have a range of 7.5 kcal/mol, which at 300 K would correspond to a five-order-of-magnitude range in correlation time. It is demonstrated that adiabatic rotational barriers can fluctuate significantly during an MD simulation of hydrated SNase, but that a Boltzmann weighted average is predictive of rotational correlation times determined from correlation functions. Even if a given methyl is on average quite sterically hindered, infrequently sampled low-barrier conformations may dominate the Boltzmann distribution. This result is consistent with the observed uniformity of NMR correlation times for (13)C-labeled methyls. The methyl barriers in simulation fluctuate on multiple time scales, which can make the precise relationship between methyl rotational correlation time and methyl rotation barriers complicated. The implications of these issues for the interpretation of correlation times determined from NMR and simulation are discussed.

Alanine↗

[Interaction of cardiotoxin A5 with a membrane: role of conformational heterogeneity and hydrophilic properties].

The hypothesis that local conformational differences of snake venom cardiotoxins (cytotoxins, CTs) may play a significant role in their interaction with membrane was tested by molecular modeling of the behavior of the CT A5 from the venom of Naja atra in water and at the water-membrane interface. Two models of the CT A5 spatial structure are known: the first was obtained by X-ray analysis and the second, by NMR studies in solution. A molecular dynamics (MD) analysis demonstrated that loop II of the toxin has a fixed omega-like shape in water, which does not depend on its initial structure. Interaction of the experimentally derived (X-ray and NMR) conformations and MD-simulated conformations of CT A5 with the lipid bilayer was studied by the Monte Carlo method using the previously developed model of the implicit membrane. The following was found: (1) Unlike the previously studied CT2 from the venom of cobra Naja oxiana, CT A5 has only loops I and II bound to the membrane, with the involvement of a lesser number of hydrophobic residues. (2) A long hydrophobic area is formed on the surface of CT A5 due to the omega-like shape of loop II and the arrangement of loop I in proximity to loop II. This hydrophobic area favors the toxin embedding into the lipid bilayer. (3) The toxin retains its conformation upon interaction with the membrane. (4). The CT A5 molecule has close values of the potential energy in the membrane and in an aqueous environment, which suggests a dynamic character of the binding. The results of the molecular modeling indicate a definite configuration of loops I and II and, consequently, a specific character of distribution of polar and apolar properties on the toxin surface, which turns out to be the most energetically favorable. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol. 29, no. 6; see also http://www.maik.ru.

Amino Acid Sequence↗