Fully automated molecular mechanics based induced fit protein-ligand docking method

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by a protein side-chain refinement stage that models protein flexibility. The final step of the process is an energy minimization of the ligand pose in the presence of the rigid receptor. Thus the algorithm models flexibility of the protein at two stages, before and after ligand placement. We validated this method by performing docking and cross docking studies of eight protein systems for which crystal structures were available for at least two bound ligands. The resulting rmsd values of the 21 docked protein-ligand complexes showed values of 2 A or less for all but one of the systems examined. The method has two critical benefits for high throughput virtual screening studies. First, no user intervention is required in the docking once the initial binding site selection has been made in the protein. Second, the initial protein conformation generation needs to be performed only once for a given binding region. Also, the method may be customized in various ways depending on the particular scenario in which dockings are being performed. Each of the individual steps of the method is fully independent making it straightforward to explore different variants of the high level workflow to further improve accuracy and performance.     

Green microfluidic devices made of corn proteins

An alternative green microfluidic device made of zein, a prolamin of corn, can be utilized as a disposable environmentally friendly microchip especially in agriculture applications. Using standard soft lithography and stereo lithography techniques, we fabricated thin zein films with microfluidic chambers and channels. These were bonded to both a glass slide and another zein film. The zein film with microfluidic features bonds irreversibly with other surfaces by vapor-deposition of ethanol to create an adhesive layer resulting in very little or no trapped air and small shape distortion. Zein-zein and zein-glass microfluidic devices demonstrated sufficient strength to facilitate fluid flow in a complex microfluidic design that showed no leakage under high hydraulic pressure. Zein-glass microfluidic devices with serpentine mixing design showed successful fluid manipulation as a concentration gradient of Rhodamine B solution was generated. The ease of fabrication and bonding and the flexibility and moldability of zein offer attractive possibilities for microfluidic device design and manufacturing. These devices can include several unit operations with mixing being one of the most commonly used. The zein-based microfluidic devices, made entirely from a biopolymer from agricultural origin, offer alternative environmentally friendly material choices that are less dependent on limited petroleum based polymer resources.     

Bacterial Spores Survive Electrospray Charging and Desolvation

The survivability of Bacillus subtilis spores and vegetative Escherichia coli cells after electrospray from aqueous suspension was tested using mobility experiments at atmospheric pressure. E. coli did not survive electrospray charging and desolvation, but B. subtilis did. Experimental conditions ensured that any surviving bacteria were de-agglomerated, desolvated, and electrically charged. Based on mobility measurements, B. subtilis spores survived even with 2,000–20,000 positive charges. B. subtilis was also found to survive introduction into vacuum after either positive or negative electrospray. Attempts to measure the charge distribution of viable B. subtilis spores using electrostatic deflection in vacuum were inconclusive; however, viable spores with low charge states (less than 42 positive or less than 26 negative charges) were observed.

Assessment of the ageing of triterpenoid paint varnishes using fluorescence,Raman and FTIR spectroscopy

The assessment of the influence of natural and artificial ageing on the spectrofluorescence of triterpenoid varnishes dammar and mastic is the focus of this work. Both Fourier transform infrared (FTIR) microscopy using attenuated total reflectance and Raman spectroscopy have been employed for complementary molecular analysis of samples. Synchronous fluorescence spectroscopy, excitation emission spectroscopy, and statistical analysis of data have been used to monitor changes in the optical properties of varnish samples. Assessment of naturally and artificially aged samples using excitation emission spectroscopy suggests that extensive exposure to visible light does not lead to easily appreciable differences in the fluorescence of mastic and dammar; cluster analysis has been used to assess changes, which occur with artificial ageing under visible light, indicating that differences in the fluorescence spectra of aged triterpenoids may be insufficient for their discrimination. The results highlight significant differences between the initial fluorescence of films of dammar and mastic and the fluorescence, which develops with ageing and oxidation, and specific markers, which change with ageing in FTIR and Raman spectra, have been identified.     

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.     

Encapsulated clay particles in polystyrene by RAFT mediated miniemulsion polymerization

RAFT grafted montmorillonite (MMT) clays [i.e., N,N‐dimethyl‐N‐(4‐(((phenylcarbonothioyl)thio)methyl)benzyl)ethanammonium‐MMT (PCDBAB‐MMT) and N‐(4‐((((dodecylthio)carbonothioyl)thio)methyl)benzyl)‐N,N‐dimethylethanammo‐nium‐MMT (DCTBAB‐MMT)] of various loadings were dispersed in styrene (S) monomer and the resultant mixtures emulsified and sonicated in the presence of a hydrophobe (hexadecane) into miniemulsions. The stable miniemulsions thus obtained were polymerized to yield encapsulated polystyrene‐clay nanocomposites (PS‐CNs). The molar mass and polydispersity index (PDI) of the PS‐CNs depended on the amount of RAFT agent in the system, in accordance with the features of the RAFT process. The morphology of the PS‐CNs ranged from partially exfoliated to an intercalated morphology, depending on the percentage clay loading. The thermomechanical properties of the PS‐CNs were better than those of the neat PS polymer, and were dependent on the molar mass, PS‐CN morphology and clay loading. The similarities and differences of the PS‐CNs prepared here by miniemulsion polymerization were compared to those prepared using the same RAFT agents and polymer system by bulk polymerization (as reported by us in a previous article). © Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7114–7126, 2008     

Conformational landscape of platinum(II)-tetraamine complexes: DFT and NBO studies

The potential energy surfaces of chiral tetraamine Pt(II) coordination complexes were computed at the B3LYP/LANL2DZ level of theory by a systematic variation of two dihedral angles: C12–C15–C34–C37 (θ) and C24–C17–C31–C48 (ψ) employing a grid resolution of 30°. Potential energy surfaces calculated using density functional theory methods and Boltzmann-derived populations revealed strong preference for one diasteromer of each series studied. In addition, natural bond orbital analysis show that the minima are stabilized predominantly by a combination of electronic interactions between two phenyl groups, the phenyl groups and the Pt²⁺ ion, as well as with the amine groups. Additional experimental characterization of the diasteroisomers studied here is in progress and will permit further molecular modeling studies with the appropriate stereochemistry.     

On connected dominating sets of restricted diameter

A connected dominating set (CDS) is commonly used to model a virtual backbone of a wireless network. To bound the distance that information must travel through the network, we explicitly restrict the diameter of a CDS to be no more than s leading to the concept of a dominating s-club. We prove that for any fixed positive integer s it is NP-complete to determine if a graph has a dominating s  -club, even when the graph has diameter s+1$s+1$. As a special case it is NP-complete to determine if a graph of diameter two has a dominating clique. We then propose a compact integer programming formulation for the related minimization problem, enhance the approach with variable fixing rules and valid inequalities, and present computational results.     

An efficient and scalable synthesis of substituted phenanthrenequinones by intramolecular Friedel-Crafts reaction of imidazolides

An efficient synthesis of 9,10-phenanthrenequinones is described. The two carbonyl groups were introduced by an orthoselective intermolecular Friedel-Crafts reaction of 3-methoxyphenol with ethyl chlorooxoacetate. The formation of a biaryl bond by Suzuki-Miyaura coupling reaction, followed by the hydrolysis of the ester, gave a biaryloxoacetic acid. Treatment of this acid with CDI gave the corresponding imidazolide. The ring closure to the desired phenanthrenequinone was accomplished by intramolecular Friedel-Crafts reaction of the imidazolide promoted by TiCl(4).