Web server to identify similarity of amino acid motifs to compounds (SAAMCO)

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which protein-protein interactions derive substantial affinity from short linear peptide sequences, or motifs, we can develop search algorithms for peptidomimetic compounds that resemble the short peptide's structure but are not compromised by poor pharmacological properties. SAAMCO is a Web service ( http://bioware.ucd.ie/ approximately saamco) that facilitates the screening of motifs with known structures against bioactive compound databases. It is built on an algorithm that defines compound similarity based on the presence of appropriate amino acid side chain fragments and a favorable Root Mean Squared Deviation (RMSD) between compound and motif structure. The methodology is efficient as the available compound databases are preprocessed and fast regular expression searches filter potential matches before time-intensive 3D superposition is performed. The required input information is minimal, and the compound databases have been selected to maximize the availability of information on biological activity. "Hits" are accompanied with a visualization window and links to source database entries. Motif matching can be defined on partial or full similarity which will increase or reduce respectively the number of potential mimetic compounds. The Web server provides the functionality for rapid screening of known or putative interaction motifs against prepared compound libraries using a novel search algorithm. The tabulated results can be analyzed by linking to appropriate databases and by visualization.     

Hydration of OCS with one to four water molecules in atmospheric and laboratory conditions

Carbonyl sulfide is the most abundant sulfur gas in the atmosphere. We have used MP2 and CCSD(T) theory to study the structures and thermochemistries of carbonyl sulfide interacting with one to four water molecules. We have completed an extensive search for clusters of OCS(H2O)n , where n = 1-4. We located three dimers, two trimers, five tetramers, and four pentamers with the MP2/aug-cc-pVDZ method. In each of the complexes with two or more waters, OCS preferentially interacts with low-energy water clusters. Our results match current theoretical and experimental literature, showing correlation with available geometries and frequencies for the OCS(H2O) species. The CCSD(T)/aug-cc-pVTZ thermochemical values combined with the average amount of OCS and the saturated concentration of H2O in the troposphere, lead to the prediction of 10(6) OCS(H2O) clusters x cm(-3) and 10(2) OCS(H2O)2 clusters x cm(-3) at 298 K. We predict the structures of OCS(H2O)n , n = 1-4 that should predominate in a low-temperature molecular beam and identify specific infrared vibrations that can be used to identify these different clusters.     

Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (alpha, phi, psi) and (beta, phi, psi), whereas for three-bond linkages, there are 54 possible regions that can be defined by (alpha, phi, psi, omega) and (beta, phi, psi, omega). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.     

Phase diversity with undersampled systems via superresolution preprocessing

Phase diversity algorithms allow a wavefront to be reconstructed from through-focus measurements of a point source or extended scene. These algorithms have traditionally been limited to systems that are Nyquist sampled. Many optical systems for remote sensing applications are designed to be undersampled, however. One approach to phase diversity with undersampled systems is to employ superresolution techniques to first create properly sampled scenes. This is demonstrated experimentally for a point object, but is applicable to extended scenes as well.     

Time-resolved studies of single quantum dots in magnetic fields

We present time-resolved and time-integrated spectroscopy of single InAs quantum dots grown in a GaAs matrix. We observe a number of interesting features in the spectra, including the zero field splitting of exciton and biexciton lines due to quantum dot asymmetry. By the application of an in-plane magnetic field, the normally optically active and inactive exciton states become mixed, enabling us to optically probe the normally inaccessible ‘dark’ states. Time resolved measurements on the mixed states show decay times several times longer than the exciton lifetime at zero field, which we show to be consistent with a dark exciton lifetime orders of magnitude longer than that for bright exciton.     

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy-metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.     

Catalytic activity of water molecules in gas-phase glycine dimerization

The dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known as cis and trans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas-phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of the cis transition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm-based configurational sampling, density functional theory geometries, and domain-based local pair natural orbital coupled-cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concerted cis mechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.     

Carbenoxolone induced depression of rhythmogenesis in the pre-Bötzinger Complex

Background

Carbenoxolone (CBX), a gap junction uncoupler, alters the functioning of the pre-Bötzinger Complex (preBötC), a central pattern generating neuronal network important for the production of respiratory rhythm in mammals. Even when isolated in a 1/2 mm-thick slice of medulla oblongata from neonatal mouse the preBötC continues producing periodic bursts of action potentials, termed population bursts that are thought to be important in generating various patterns of inspiration, in vivo. Whether gap junction communication contributes to preBötC rhythmogenesis remains unresolved, largely because existing gap junction uncouplers exert numerous non-specific effects (e.g., inhibition of active transport, alteration of membrane conductances). Here, we determined whether CBX alters preBötC rhythmogenesis by altering membrane properties including input resistance (R_in), voltage-gated Na⁺ current (I_Na), and/or voltage-gated K⁺ current (I_K), rather than by blocking gap junction communication. To do so we used a medullary slice preparation, network-level recordings, whole-cell voltage clamp, and glycyrrhizic acid (GZA; a substance used as a control for CBX, since it is similar in structure and does not block gap junctions).

Results

Whereas neither of the control treatments [artificial cerebrospinal fluid (aCSF) or GZA (50 μM)] noticeably affected preBötC rhythmogenesis, CBX (50 μM) decreased the frequency, area and amplitude of population bursts, eventually terminating population burst production after 45–60 min. Both CBX and GZA decreased neuronal R_in and induced an outward holding current. Although neither agent altered the steady state component of I_K evoked by depolarizing voltage steps, CBX, but not GZA, increased peak I_Na.

Conclusion

The data presented herein are consistent with the notion that gap junction communication is important for preBötC rhythmogenesis. By comparing the effects of CBX and GZA on membrane properties our data a) demonstrate that depression of preBötC rhythmogenesis by CBX results from actions on another variable or other variables; and b) show that this comparative approach can be used to evaluate the potential contribution of other non-specific actions (e.g., Ca⁺⁺ conductances or active transport) of CBX, or other uncouplers, in their alteration of preBötC rhythmogenesis, or the functioning of other networks.