Second SH3 domain of ponsin solved from powder diffraction

Determination of protein crystal structures is dependent on the growth of high-quality single crystals, a process that is not always successful. Optimum crystallization conditions must be systematically sought for, and microcrystalline powders are frequently obtained in failed attempts to grow the desired crystal. In materials science, structures of samples ranging from ceramics, pharmaceuticals, zeolites, etc., can nowadays be solved, almost routinely, from powdered samples, and there seems to be no fundamental reason, except the sheer size and complexity of the structures involved, why powder diffraction should not be employed to solve structures of small proteins. Indeed, recent work has shown that the high-quality powder diffraction data can be used in the study of protein crystal structures. We report the solution, model building, and refinement of a 67-residue protein domain crystal structure, with a cell volume of 64 879 A3, from powder diffraction. The second SH3 domain of ponsin, a protein of high biological significance due to its role in cellular processes, is determined and refined to resolution limits comparable to single-crystal techniques. Our results demonstrate the power and future applicability of the powder technique in structural biology.     

Controlling relative fundamental crystal growth rates in silicalite: AFM observation

A detailed atomic force microscopy study has been performed on the open-framework, microporous material silicalite. Emphasis has been placed on determining the effect of supersaturation on the crystal growth process. The relative rates of fundamental crystal growth processes can be substantially altered by tuning the supersaturation. In this manner, it is possible to, for instance, switch on and off surface nucleation while retaining terrace spreading. This offers a potential mechanism by which it might be possible to control important crystal aspects such as defect density and intergrowths.     

Evaluation of monolithic and sub 2 microm particle packed columns for the rapid screening for illicit drugs--application to the determination of drug contamination on Irish euro banknotes

A study comparing recently available 100 x 3 mm id, 200 x 3 mm id monolithic reversed-phase columns with a 50 x 2.1 mm id, 1.8 microm particle packed reversed-phase columns was carried out to determine the most efficient approach (using traditional van Deemter analysis and a modern kinetic plot approach) for the rapid screening of samples for 16 illicit drugs and associated metabolites. A plot of column backpressure versus plate number (N) showed a significant advantage of using the monolithic phases, with the 20 cm monolithic column exhibiting a maximum 15,000 plates at a column backpressure of approximately 70 bar, compared to approximately 7000 plates at 150 bar for the 5 cm 1.8 microm particle packed column. Optimum linear velocities were found to be 0.40 mm s(-1), 0.52 mm s(-1) and 0.98 mm s(-1) for the three above columns, respectively. The 20 cm monolithic column was subsequently applied to the separation and determination of illicit drug contamination on Irish euro banknotes, using methanol extraction followed by LC-MS/MS. Method performance data showed that the new LC-MS/MS method was significantly more sensitive than previous GC-MS/MS based methods for this application, with detection limits in the pg note(-1) region, based upon a 20 microL standard injection. All of the notes examined tested positive for trace quantities of cocaine, with benzoylecgonine detected on 12 of the 45 notes sampled. Traces of heroin were also detected on three of the 45 notes.     

Classification of water molecules in protein binding sites

Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.     

Direct immobilization of Fab' in nanocapillaries for manipulating mass-limited samples

Interfacing nanoscale elements into a microfluidic device enables a new range of fluidic manipulations. Nanocapillary array membranes (NCAMs), consisting of thin (5 microm < d < 20 microm) membranes containing arrays of nanometer diameter (10 nm < a < 500 nm) pores, are a convenient method of interfacing vertically separated microchannels in microfluidic devices that allow the external control of analyte transport between microfluidic channels. To add functionality to these nanopores beyond simple fluid transport, here we incorporate an antibody-based molecular recognition element onto the pore surface that allows selective capture, purification, and release of specific analytes from a mixture. The pores are fabricated by electroless plating of gold into the nanopores of an NCAM (Au-NCAM). An antibody is then immobilized on the Au-NCAM via gold-thiol chemistry as a thiolated fragment of antigen-binding (Fab') prepared by direct digestion of the antibody followed by reduction of the disulfide linkage on the hinge region. The successful immobilization and biological activity of the resultant Fab' through this protocol is verified on planar gold by fluorescence microscopy, scanning electron microscopy, and atomic force microscopy. Selective capture and release of human insulin is verified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The relative mass spectral peak intensities for insulin versus nonantigenic peptides increase more than 20-fold after passing through the Fab'-Au-NCAM relative to the control Au-NCAM. The affinity-tagged Au-NCAM can be incorporated into microfluidic devices to allow the concentration, capture, and characterization of analytes in complex mixtures with high specificity.