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.     

Ion trap mass spectrometry on a comet nucleus: the Ptolemy instrument and the Rosetta space mission

In May 2014, the Rosetta spacecraft is scheduled to rendezvous with the comet Churyumov-Gerasimenko ('67P'). One of the instruments on board the 'Lander' which will descend on to the surface of the comet is a miniaturised GC/MS system that incorporates an ion trap mass spectrometer, specially developed for isotope ratio analysis. This article describes the development and optimisation of the ion trap for this unique application, and presents a summary of the range of pre-programmed experiments that will contribute to the characterisation of the solid and volatile cometary materials.     

Copper and iron interactions with angiotensin-converting enzyme inhibitors. A study by fast-atom bombardment tandem mass spectrometry

Fast atom bombardment, combined with high-energy collision-induced tandem mass spectrometry, has been used to investigate gas-phase metal-ion interactions with captopril, enalaprilat and lisinopril, all angiotensin-converting enzyme inhibitors.Suggestions for the location of metal-binding sites are presented. For captopril, metal binding occurs most likely at both the sulphur and the nitrogen atom. For enalaprilat and lisinopril, binding preferably occurs at the amine nitrogen. Copyright 1999 John Wiley & Sons, Ltd.     

Submicron streptavidin patterns for protein assembly

Micron and submicron-scale features of aldehyde functionality were fabricated in polymer films by photolithography to develop a platform for protein immobilization and assembly at a biologically relevant scale. Films containing the pH-reactive polymer poly(3,3'-diethoxypropyl methacrylate) and a photoacid generator (PAG) were patterned from 500 nm to 40 mum by exposure to 365 nm (i-line) light. Upon PAG activation and hydrolysis of acetals, aldehyde groups formed. After the films were incubated with a biotinylated aldehyde reactive probe, the X-ray photoelectron spectroscopy results were consistent with biotin being attached to the surface. The background was subsequently passivated by flood exposure and incubation with an aminooxy-terminated poly(ethylene glycol), resulting in a 98% reduction in nonspecific protein adsorption. Protein patterning and assembly was demonstrated using streptavidin, biotinylated anthrax toxin receptor-1, and the protective antigen moiety of anthrax toxin and confirmed by fluorescence microscopy and atomic force microscopy (AFM). AFM demonstrated that 500 nm protein features were achieved. Because of the abundance of biotinylated proteins, this methodology provides a platform for protein immobilization and assembly for various applications in biotechnology.     

Underwater measurement of narrowband sound power and directivity using Supersonic Intensity in Reverberant Environments

A laboratory underwater acoustic measurement technique, Supersonic Intensity in Reverberant Environments (SIRE), is developed analytically and validated experimentally and numerically. Unlike standard free or diffuse field techniques, SIRE enables the measurement of narrowband sound power and directivity in an environment with inexact field conditions. The technique takes advantage of underwater vector sensors, measuring only acoustic pressure and the normal component of particle velocity/acceleration, and supersonic wavenumber filtering in the near field of a source. The result is outward-propagating acoustic waves separated from interfering incoming and/or evanescent waves. The SIRE technique was experimentally applied to monopole and dipole sources and the results are compared with theory and standard methods. SIRE is shown to accurately measure radiated sound power to within the limits of ANSI S12.51 and to accurately measure the directivity indices of simple sources to within ±3 dB. A coupled finite element/boundary element model of a point-driven, thin-walled cylinder is also developed to establish the limitations of the SIRE technique. The model results show that the measurement standoff distance should be less than the reciprocal of the largest wavenumber in the frequency band of interest. Furthermore, the maximum measurement grid spacing must be less than twice the standoff distance.     

Group 14 Metal Terminal Phosphides: Correlating Structure with |J(MP)|

A series of heavier group 14 element, terminal phosphide complexes, M(BDI)(PR(2)) (M = Ge, Sn, Pb; BDI = CH{(CH(3))CN-2,6-iPr(2)C(6)H(3)}(2); R = Ph, Cy, SiMe(3)) have been synthesized. Two different conformations (endo and exo) are observed in the solid-state; the complexes with an endo conformation have a planar coordination geometry at phosphorus (M = Ge, Sn; R = SiMe(3)) whereas the complexes possessing an exo conformation have a pyramidal geometry at phosphorus. Solution-state NMR studies reveal through-space scalar coupling between the tin and the isopropyl groups on the N-aryl moiety of the BDI ligand, with endo and exo exhibiting different J(SnC) values. The magnitudes of the tin-phosphorus and lead-phosphorus coupling constants, |J(SnP)| and |J(PbP)|, differ significantly depending upon the hybridization of the phosphorus atom. For Sn(BDI)(P{SiMe(3)}(2)), |J(SnP)| is the largest reported in the literature, surpassing values attributed to compounds with tin-phosphorus multiple-bonds. Low temperature NMR studies of Pb(BDI)(P{SiMe(3)}(2)) show two species with vastly different |J(PbP)| values, interpreted as belonging to the endo and exo conformations, with sp(2)- and sp(3)-hybridized phosphorus, respectively.