Binding site opening by loop C shift and chloride ion-pore interaction in the GABAA receptor model.

GABAA receptors (GABAARs) are crucial in mediating inhibition in the adult mammalian brain. Although the kinetics of this receptor has been extensively studied, the molecular picture of interactions occurring at various channel conformations remains elusive. While electrophysiology combined with mutagenesis sheds light on the role of specific residues, ultrastructural studies reveal static structures which, in the case of GABAARs, are limited to the ß3 homomer. To take advantage of the newest crystal structures of cys-loop receptors, a homology model of α1ß2γ2 GABAAR in the unbound closed state was built using a template of the homomeric glycine receptor in the closed state. The template model contained strychnine molecules at the binding sites which were removed and molecular dynamics was used to study the system relaxation. The modeled GABAAR preserved the closed conformation. Two interfaces forming orthosteric binding sites (ß2/α1) exhibited opening due to the outward shift of loop C. Similar movement, although less pronounced, was observed at the α1/γ2 (modulatory) interface. In contrast, interfaces α1/ß2 and γ2/ß2 remained closed. The former one, due to interactions mediated mainly by loops C and F, affected the neighboring ß2/α1 interface leading to asymmetry between the orthosteric binding sites. Such interactions were not observed at the ß2/α1 interface preceded by a γ2 subunit. As expected, in the channel pore, the conserved leucine gate and selectivity filter were present. However, an additional constriction was found at the top of the pore which differed from a typical hydrophobic channel gate as it consisted of charged residues. Interestingly, this site showed a capacity to trap chloride ions and to undergo conformation transition-like expansion, suggesting an impact on pore properties. In conclusion, our homology model faithfully reproduced major features of heteromeric GABAARs offering insight into the underlying mechanisms of stabilizing the shut conformation and chloride ion interaction with the channel pore.

Selective condensation of DNA by aminoglycoside antibiotics.

The condensing effect of aminoglycoside antibiotics on the structure of double-stranded DNA was examined. The selective condensation of DNA by small molecules is an interesting approach in biotechnology. Here, we present the interaction between calf thymus DNA and three types of antibiotic molecules: tobramycin, kanamycin, and neomycin. Several techniques were applied to study this effect. Atomic force microscopy, transmission electron microscopy images, and nuclear magnetic resonance spectra showed that the interaction of tobramycin with double-stranded DNA caused the rod, toroid, and sphere formation and very strong condensation of DNA strands, which was not observed in the case of other aminoglycosides used in the experiment. Studies on the mechanisms by which small molecules interact with DNA are important in understanding their functioning in cells, in designing new and efficient drugs, or in minimizing their adverse side effects. Specific interactions between tobramycin and DNA double helix was modeled using molecular dynamics simulations. Simulation study shows the aminoglycoside specificity to bend DNA double helix, shedding light on the origins of toroid formation. This phenomenon may lighten the ototoxicity or nephrotoxicity issues, but also other adverse reactions of aminoglycoside antibiotics in the human body.

Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds.

Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based on quantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for the high flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies.

Experimental and simulation studies of unusual current blockade induced by translocation of small oxidized PEG through a single nanopore.

Detection of a single macromolecule based on the use of artificial nanopores is an attractive and promising field of research. In this work, we report a device based on a 5 nm single nanopore with a high length/diameter ratio, tailored by the track etching and atomic layer deposition techniques. The translocation of neutral polyethylene glycol (PEG) and charged polyethylene glycol-carboxylate (PEG-carboxylate) molecules of low molar masses (200 and 600 g mol(-1)) through this nanodevice was studied. It was shown that charged PEG-carboxylate molecules, which permeate through the pore, promote an unusual blockade of ionic current whereas the neutral PEG molecules do not show such behaviour. The molecular dynamics simulation shows that both neutral and charged PEGs permeate through the nanopore close to its inner surface. The main difference between the two macromolecules is the existence of a structured shell of cations around the charged PEG, which is likely to cause the observed unusual current blockade.

Determination of the shape and curvature of nonplanar lipid bilayers that are bent in a single plane in molecular dynamics simulations.

The curvature of biological membranes is known to be an important influence on important phenomena such as membrane fusion, endocytosis, and the functioning of integral membrane proteins. There is a growing demand for analytical tools that are able accommodate molecular dynamics trajectories of significantly curved lipid bilayers. In this work, an algorithm for determining the shape and curvature of a nonplanar lipid bilayer in molecular dynamics simulations is proposed. The algorithm calculates the coordinates of the midline and the curvature of the bilayer as well as the local normal to it at any point on the membrane, which is bent arbitrarily in a single plane and is topologically equivalent to an infinite bilayer. The algorithm is implemented as a C++ program and tested by exploring the molecular dynamic trajectories of a highly curved meander-like asymmetric lipid bilayer. The algorithm is general enough to allow it to be easily applied to other geometries of nonplanar membrane systems.

Theoretical study of amino derivatives and anticancer platinum drug grafted on various carbon nanostructures.

Density functional theory calculations with van der Waals approximation have been conducted to analyze the functionalization of various carbon-based nanostructures (fullerene, metallic, and semi-conducting nanotubes) with amino derivative groups. The results obtained with azomethine, show the formation of a five membered ring on fullerenes, and on nanotubes consistent with experimental observations. The attachment of an azomethine plus subsequent drug like a Pt(IV) complex does not perturb the cycloaddition process. Moreover, all theoretical results show that the length of different amino derivatives with subsequent Pt(IV) complex does not affect the complexed therapeutic agent when it is attached onto these carbon-based nanostructures.

Cholesterol induces uneven curvature of asymmetric lipid bilayers.

A remarkable flexibility is observed in biological membranes, which allows them to form the structures of different curvatures. We addressed the question of intrinsic ability of phospholipid membranes to form highly curved structures and the role of cholesterol in this process. The distribution of cholesterol in the highly curved asymmetric DOPC/DOPS lipid bilayer was investigated by the coarse-grained molecular dynamics simulations in the membrane patches with large aspect ratio. It is shown that cholesterol induces uneven membrane curvature promoting the formation of extended flattened regions of the membrane interleaved by sharp bends. It is shown that the affinity of cholesterol to anionic DOPS or neutral DOPC lipids is curvature dependent. The cholesterol prefers DOPS to DOPC in either planar or highly curved parts of the membrane. In contrast, in the narrow interval of moderate membrane curvatures this preference is inverted. Our data suggest that there is a complex self-consistent interplay between the membrane curvature and cholesterol distribution in the asymmetric lipid bilayers. The suggested new function of cholesterol may have a biological relevance.

Insertion kinetics of small nucleotides through single walled carbon nanotube.

We report molecular dynamic simulations showing that a DNA molecule constituted by five unique bases can be spontaneously inserted into single walled carbon nanotube (SWCNT) in normal conditions (P, T and water environment) depending on the tube radius value. The van der Waals and electrostatic interactions play a central role for the rapid insertion process. Our study shows also that the Guanine molecule inserts the fastest compared to thymine, adenine and cytosine bases, respectively. The differences of insertion time could be exploited for applications concerning for example DNA sequencing.