Planar ion trap geometry for microfabrication

We describe a novel high aspect ratio radiofrequency linear ion trap geometry that is amenable to modern microfabrication techniques. The ion trap electrode structure consists of a pair of stacked conducting cantilevers resulting in confining fields that take the form of fringe fields from parallel plate capacitors. The confining potentials are modeled both analytically and numerically. This ion trap geometry may form the basis for large scale quantum computers or parallel quadrupole mass spectrometers. PACS 39.25.+k; 03.67.Lx; 07.75.+h; 07.10+Cm     

Iminosugar glycosidase inhibitors: structural and thermodynamic dissection of the binding of isofagomine and 1-deoxynojirimycin to beta-glucosidases

The design and synthesis of transition-state mimics reflects the growing need both to understand enzymatic catalysis and to influence strategies for therapeutic intervention. Iminosugars are among the most potent inhibitors of glycosidases. Here, the binding of 1-deoxynojirimycin and (+)-isofagomine to the "family GH-1" beta-glucosidase of Thermotoga maritima is investigated by kinetic analysis, isothermal titration calorimetry, and X-ray crystallography. The binding of both of these iminosugar inhibitors is driven by a large and favorable enthalpy. The greater inhibitory power of isofagomine, relative to 1-deoxynojirimycin, however, resides in its significantly more favorable entropy; indeed the differing thermodynamic signatures of these inhibitors are further highlighted by the markedly different heat capacity values for binding. The pH dependence of catalysis and of inhibition suggests that the inhibitory species are protonated inhibitors bound to enzymes whose acid/base and nucleophile are ionized, while calorimetry indicates that one proton is released from the enzyme upon binding at the pH optimum of catalysis (pH 5.8). Given that these results contradict earlier proposals that the binding of racemic isofagomine to sweet almond beta-glucosidase was entropically driven (Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568), we reinvestigated the binding of 1-deoxynojirimycin and isofagomine to the sweet almond enzyme. Calorimetry confirms that the binding of isofagomine to sweet almond beta-glucosidases is, as observed for the T. maritima enzyme, driven by a large favorable enthalpy. The crystallographic structures of the native T. maritima beta-glucosidase, and its complexes with isofagomine and 1-deoxynojirimycin, all at approximately 2.1 A resolution, reveal that additional ordering of bound solvent may present an entropic penalty to 1-deoxynojirimycin binding that does not penalize isofagomine.     

Glycosidase inhibition: an assessment of the binding of 18 putative transition-state mimics

The inhibition of glycoside hydrolases, through transition-state mimicry, is important both as a probe of enzyme mechanism and in the continuing quest for new drugs, notably in the treatment of cancer, HIV, influenza, and diabetes. The high affinity with which these enzymes are known to bind the transition state provides a framework upon which to design potent inhibitors. Recent work [for example, Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568; Zechel, D. L. et al. J. Am. Chem. Soc. 2003, 125, 14313-14323] has revealed quite confusing and counter-intuitive patterns of inhibition for a number of glycosidase inhibitors. Here we describe a synergistic approach for analysis of inhibitors with a single enzyme 'model system', the Thermotoga maritima family 1 beta-glucosidase, TmGH1. The pH dependence of enzyme activity and inhibition has been determined, structures of inhibitor complexes have been solved by X-ray crystallography, with data up to 1.65 A resolution, and isothermal titration calorimetry was used to establish the thermodynamic signature. This has allowed the characterization of 18 compounds, all putative transition-state mimics, in order to build an 'inhibition profile' that provides an insight into what governs binding. In contrast to our preconceptions, there is little correlation of inhibitor chemistry with the calorimetric dissection of thermodynamics. The ensemble of inhibitors shows strong enthalpy-entropy compensation, and the random distribution of similar inhibitors across the plot of DeltaH degrees a vs TDeltaS degrees a likely reflects the enormous contribution of solvation and desolvation effects on ligand binding.     

An efficient, inexpensive, and shelf-stable diazotransfer reagent: imidazole-1-sulfonyl azide hydrochloride

The design and synthesis of a new diazotransfer reagent, imidazole-1-sulfonyl azide hydrochloride, are reported. This reagent has proven to equal triflyl azide in its ability to act as a "diazo donor" in the conversion of both primary amines into azides and activated methylene substrates into diazo compounds. Crucially, this reagent can be prepared in a one-pot reaction on a large scale from inexpensive materials, is shelf-stable, and is conveniently crystalline.     

The Chameleon of Retaining Glycoside Hydrolases and Retaining Glycosyl Transferases: The Catalytic Nucleophile

Summary.  This paper addresses the existence and role of a catalytic nucleophile in retaining glycoside hydrolases and retaining glycosyl transferases. Although the former has now been established beyond doubt, such is not the case with the latter. We report reliable procedures for the synthesis of various 2-deoxy-2-fluoro glycosyl nucleoside diphosphates, useful donor analogues for the study of the mechanism of action of retaining glycosyl transferases. Received October 16, 2001. Accepted November 7, 2001     

Quantum chromodynamics: Working group report

This is the report of the QCD working group at WHEPP-6. Discussions and work on heavy ion collisions, polarized scattering, and collider phenomenology are reported.     

Integration of fluorescence collection optics with?a?microfabricated surface electrode ion trap

We have successfully demonstrated an integrated optical system for collecting the fluorescence from a trapped ion. The system, consisting of an array of transmissive, dielectric micro-optics and an optical fiber array, has been intimately incorporated into the ion-trapping chip without negatively impacting trapping performance. Epoxies, vacuum feedthrough, and optical component materials were carefully chosen so that they did not degrade the vacuum environment, and we have demonstrated light detection as well as ion trapping and shuttling behavior comparable to trapping chips without integrated optics, with no modification to the control voltages of the trapping chip.     

α-L-Arabinofuranosylated pyrrolidines as arabinanase inhibitors

As part of continued efforts to understand the mechanisms of 1,5-α-l-arabinanases better, some arabinan-like iminosugar oligosaccharides were synthesized. An iminosugar analogue of arabinobiose was found to be a good inhibitor of the arabinanase Arb93A from Fusarium graminearum. Structures were determined for complexes of this inhibitor with wild-type Arb93A and a catalytically inactive mutant.