Direct observation of the protonation state of an imino sugar glycosidase inhibitor upon binding

Glycosidases are some of the most ubiquitous enzyme in nature. Their biological significance, coupled to their enormous catalytic prowess derived from tight binding of the transition state, is reflected in their importance as therapeutic targets. Many glycosidase inhibitors are known. Imino sugars are often potent inhibitors, yet many facets of their mode of action, such as their degree, if any, of transition-state "mimicry" and their protonation state when bound to the target glycosidase remain unclear. Atomic resolution analysis of the endoglucanase, Cel5A, in complex with a cellobio-derived isofagomine in conjunction with the pH dependence of Ki and kcat/KM reveals that this compound binds as a protonated sugar. Surprisingly, both the enzymatic nucleophile and the acid/base are unprotonated in the complex.     

Arsenocholine from anaerobic decomposition of a trimethylarsonioriboside

When subjected to conditions supporting anaerobic microbial activity, the naturally occurring trimethylarsonioriboside, (2′S)-2′-hydroxy-3′-(sulpho-oxy)propyl 5-deoxy-5-trimethylarsonio-β-D-riboside 4 was converted to arsenocholine 5 in virtually quantitative yield.     

Synthesis and use of mechanism-based protein-profiling probes for retaining beta-D-glucosaminidases facilitate identification of Pseudomonas aeruginosa NagZ

The NagZ class of retaining exo-glucosaminidases play a critical role in peptidoglycan recycling in Gram-negative bacteria and the induction of resistance to beta-lactams. Here we describe the concise synthesis of 2-azidoacetyl-2-deoxy-5-fluoro-beta-d-glucopyranosyl fluoride as an activity-based proteomics probe for profiling these exo-glycosidases. This active-site directed reagent covalently inactivates this class of retaining N-acetylglucosaminidases with exquisite selectivity by stabilizing the glycosyl-enzyme intermediate. Inactivated Vibrio cholerae NagZ can be elaborated with biotin or a FLAG-peptide epitope using the Staudinger ligation or the Sharpless-Meldal click reaction and detected at nanogram levels. This ABPP enabled the profiling of the Pseudomonas aeruginosa proteome and identification at endogenous levels of a tagged protein with properties consistent with those of PA3005. Cloning of the gene encoding this hypothetical protein and biochemical characterization enabled unambiguous assignment of this hypothetical protein as a NagZ. The identification and cloning of this NagZ may facilitate the development of strategies to circumvent resistance to beta-lactams in this human pathogen. As well, this general strategy, involving such 5-fluoro inactivators, may prove to be of general use for profiling proteomes and identifying glycoside hydrolases of medical importance or having desirable properties for biotechnology.     

Spherically symmetric inhomogeneous dust collapse in higher dimensional space-time and cosmic censorship hypothesis

We consider a collapsing spherically symmetric inhomogeneous dust cloud in higher dimensional space-time. We show that the central singularity of collapse can be a strong curvature or a weak curvature naked singularity depending on the initial density distribution.     

Distortion of a cellobio-derived isofagomine highlights the potential conformational itinerary of inverting beta-glucosidases

A cellobio-derived isofagomine glycosidase inhibitor (Ki approximately 400 nM) displays an unusual distorted 2,5B (boat) conformation upon binding to cellobiohydrolase Cel6A from Humicola insolens, highlighting the different conformational itineraries used by various glycosidases, with consequences for the design of therapeutic agents.     

Scattering by small defects in the neighbourhood of a fluid-solid interface

The scattering of incident plane elastic waves by a varietyof different defects that lie upon a fluid-solid interface isconsidered here using matched asymptotic expansions. The expansionscheme is developed in terms of a parameter , the ratio of typicaldefect length scale to a typical wavelength of the incidentfield, taken to be small. Three different canonical situations occur and these are illustratedvia three specific examples treated here: a rigid strut, anedge crack, and a rigid strip. In each case the leading-ordermatching is performed to identify the leading-order contributionof the defect to the acoustic field in the far field. In particular,each defect is identified with a source of dipole response ininterfacial stress of displacement. It is shown in the limit as s<<s1 that in the inner problemsthe fluid and solid pieces uncouple in a particularly convenientmanner allowing analytical solutions to be deduced. These arethen matched with appropriate outer solutions.     

Atomic qubit manipulations with an electro-optic modulator

We report new techniques for driving high-fidelity stimulated Raman transitions in trapped-ion qubits. An electro-optic modulator induces sidebands on an optical source, and interference between the sidebands allows coherent Rabi transitions to be efficiently driven between hyperfine ground states separated by 14.53 GHz in a single trapped 111Cd+ ion.     

A 1-acetamido derivative of 6-epi-valienamine: an inhibitor of a diverse group of beta-N-acetylglucosaminidases

The synthesis of an analogue of 6-epi-valienamine bearing an acetamido group and its characterisation as an inhibitor of beta-N-acetylglucosaminidases are described. The compound is a good inhibitor of both human O-GlcNAcase and human beta-hexosaminidase, as well as two bacterial beta-N-acetylglucosaminidases. A 3-D structure of the complex of Bacteroides thetaiotaomicron BtGH84 with the inhibitor shows the unsaturated ring is surprisingly distorted away from its favoured solution phase conformation and reveals potential for improved inhibitor potency.     

Heating rate and electrode charging measurements in a scalable, microfabricated, surface-electrode ion trap

We characterise the performance of a surface-electrode ion “chip” trap fabricated using established semiconductor integrated circuit and micro-electro-mechanical-system (MEMS) microfabrication processes, which are in principle scalable to much larger ion trap arrays, as proposed for implementing ion trap quantum information processing. We measure rf ion micromotion parallel and perpendicular to the plane of the trap electrodes, and find that on-package capacitors reduce this to ?10?nm in amplitude. We also measure ion trapping lifetime, charging effects due to laser light incident on the trap electrodes, and the heating rate for a single trapped ion. The performance of this trap is found to be comparable with others of the same size scale.