Homonuclear mixing sequences for perdeuterated proteins

We tested the performance of several (13)C homonuclear mixing sequences on perdeuterated microcrystalline ubiquitin. All sequences were applied without (1)H decoupling and at relatively low MAS frequencies. We found that RFDR gave the highest overall transfer efficiency and that DREAM performs surprisingly well under these conditions being twice as efficient in the aliphatic region of the spectrum than the other mixing sequences tested.     

Mechanistic investigations reveal that dibromobimane extrudes sulfur from biological sulfhydryl sources other than hydrogen sulfide

Hydrogen sulfide (H₂S) has emerged as an important biological signaling molecule in the last decade. During the growth of this field, significant controversy has arisen centered on the physiological concentrations of H₂S. Recently, a monobromobimane (mBB) method has been developed for the quantification of different biologically-relevant sulfide pools. Based on the prevalence of the mBB method for sulfide quantification, we expand on this method to report the use of dibromobimane (dBB) for sulfide quantification. Reaction of H₂S with dBB results in formation of highly-fluorescent bimane thioether (BTE), which is readily quantifiable by HPLC. Additionally, the reaction of sulfide with dBB to form BTE is significantly faster than the reaction of sulfide with mBB to form sulfide dibimane. Using the dBB method, BTE levels as low as 0.6 pM can be detected. Upon use of the dBB method in wild-type and CSE^–/– mice, however, dBB reports significantly higher sulfide levels than those measured using mBB. Further investigation revealed that dBB is able to extract sulfur from other sulfhydryl sources including thiols. Based on mechanistic studies, we demonstrate that dBB extracts sulfur from thiols with α- or β-hydrogens, thus leading to higher BTE formation than from sulfide alone. Taken together, the dBB method is a highly sensitive method for H₂S but is not compatible for use in studies in which other thiols are present.     

Bile UPLC-MS fingerprinting and bile acid fluxes during human liver transplantation

Bile flow restoration is a crucial step in the recovery process post transplantation of the liver. Here, metabolic trajectories based on changes in bile secretion - a known marker of functionality - have been utilised as an approach for discovering bile fluxes during transplantation. A total of ten liver transplants were monitored and from these 68 bile samples from both donors and recipients were collected and analysed using ultra-performance LC-MS in combination with multivariate statistical analysis. Based on the principal component scores constructed from the total bile fingerprint, differentiation of the bile acid concentrations before and after transplantation was detected. A trend was also observed, by constructing metabolic trajectories, whereby the post-transplant profiles approached the position of pre-transplant profiles within 30-60?min of the restoration of bile secretion function. The ten major conjugated bile acid salts were measured and a significant increase in concentrations of taurocholic acid and taurochenodeoxycholic acid were seen after transplantation. In addition, the ratios of secondary bile acids detected in gall bladder and hepatic bile were measured before and after transplantation. This study suggests that bile acid ratios in the donor liver at the pre-transplant and post-transplant stage may be important and that profiling of secreted bile after transplantation may aid clinical assessment and progress post-transplantation.     

Specific detection of Campylobacter jejuni using the bacteriophage NCTC 12673 receptor binding protein as a probe

Campylobacter jejuni is found in the intestines of poultry, cattle, swine, wild birds and pet animals and is the major cause of foodborne gastroenteritis in developed countries. We report the use of the receptor binding protein (RBP) of Campylobacter bacteriophage NCTC 12673 for the specific capture of Campylobacter jejuni bacteria using RBP-derivatized capturing surfaces. The Gp48 RBP was expressed as a glutathione S-transferase-Gp48 (GST-Gp48) fusion protein and immobilized onto surface plasmon resonance (SPR) surfaces using glutathione self-assembled monolayers (GSH SAM). Bovine serum albumin (BSA) was used to block any non-specific binding. Glutathione SAM leads to an oriented attachment of the protein, resulting in a two- to three-fold improvement of bacterial capture when compared to dithiobis(succinimidyl propionate) (DTSP) SAM-based unoriented attachment. The specificity of recognition was confirmed using Salmonella enterica subsp. enterica serovar Typhimurium as a negative control, which indeed showed negligible binding. The detection limit of the RBP-derivatized SPR surfaces was found to be 10(2) cfu/ml. Finally, GST-Gp48 was also immobilized onto magnetic beads that were successfully used to capture and pre-concentrate the host pathogen from suspension.     

Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes

Converting lead compounds into drug candidates is a crucial step in drug development, requiring early assessment of potency, selectivity, and off-target effects. We have utilized activity-based chemical proteomics to determine the potency and selectivity of deubiquitylating enzyme (DUB) inhibitors in cell culture models. Importantly, we characterized the small molecule PR-619 as a broad-range DUB inhibitor, and P22077 as a USP7 inhibitor with potential for further development as a chemotherapeutic agent in cancer therapy. A striking accumulation of polyubiquitylated proteins was observed after both selective and general inhibition of cellular DUB activity without direct impairment of proteasomal proteolysis. The repertoire of ubiquitylated substrates was analyzed by tandem mass spectrometry, identifying distinct subsets for general or specific inhibition of DUBs. This enabled identification of previously unknown functional links between USP7 and enzymes involved in DNA repair.     

Diffusion within a near-critical nanopore fluid

Results are presented for grand canonical Monte Carlo (GCMC) and both equilibrium and non-equilibrium molecular dynamics simulations (EMD and NEMD) conducted over a range of densities and temperatures that span the two-phase coexistence and supercritical regions for a pure fluid adsorbed within a model crystalline nanopore. The GCMC simulations provided the low temperature coexistence points for the open pore fluid and were used to locate the capillary critical temperature for the system. The equilibrium configurational states obtained from these simulations were then used as input data for the EMD simulations in which the self-diffusion coefficients were computed using the Einstein equation. NEMD colour diffusion simulations were also conducted to validate the use of a system averaged Einstein analysis for this inhomogeneous fluid. In all cases excellent agreement was observed between the equilibrium (linear response theory) predictions for the diffusivities and non-equilibrium colour diffusivities. The simulation results are also compared with a recently published quasi-hydrodynamic theory of Pozhar and Gubbins (Pozhar, L. A., and Gubbins, K. E., 1993, J. Chem. Phys., 99, 8970; 1997, Phys. Rev. E, 56, 5367.). The model fluid and the nature of the fluid wall interactions employed conform to the decomposition of the particle–particle interaction potential explicitly used by Pozhar and Gubbins. The local self-diffusivity was calculated from the local fluid–fluid and fluid wall hard core collision frequencies. While this theory provides reasonable results at moderate pore fluid densities, poor agreement is observed in the low density limit.     

Closeness of worlds

An objection is presented to Lewis’s analysis of counterfactual conditionals in terms of relative closeness of possible worlds. The objection depends on no special assumptions about the ‘closer-than’ relation. The argument also casts doubt on Lewis’s claim that Antecedent Strengthening fails for counterfactuals.     

High-power harmonic gyro-TWT's. II. Nonlinear theory and design

For pt.I, see ibid., vol.20, no.3, p.155-162 (1992). Based on an analytical study of the stability problems of gyrotron traveling wave amplifiers (gyro-TWTs), an extremely high power second-harmonic gyro-TWT has been designed, evaluated and optimized with a self-consistent nonlinear numerical simulation code. The design, which is based on the magnetron-injection-gun (MIG)-type beam, is presented. Using a 100 kV, 25 A MIG beam with α=1 and an axial velocity spread of 5%, nonlinear self-consistent analysis of a three-stage second-harmonic gyro-TWT amplifier predicts a peak output power of 533 kW, peak efficiency of 21.3% and a 7.4% saturated bandwidth, which verifies the theoretical predictions that a stable harmonic gyro-TWT can generate power levels an order of magnitude higher than those possible from a fundamental gyro-TWT. It is shown that the positioning of the electron beam is very important. A multistage structure is used to recover the loss in gain resulting from shortening the interaction sections to ensure stability     

Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin

High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D (13)C-(13)C correlation spectroscopy under magic angle spinning conditions. High-resolution (13)C spectra have been acquired from hydrated microcrystals of site-directed (13)C-enriched ubiquitin. Inter-residue carbon-carbon distance constraints defining the global protein structure have been evaluated from 'dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.     

Steepest-descent failure analysis

An extensive failure analysis of the steepest-descent optimization algorithm has been made. Each of the ways in which the algorithm can fail is discussed in terms of both the mathematical and numerical manifestations of a failure and the information which each type of failure provides about the formulation of the physical problem. Numerical tests for each of the various types of failure are described; several faulty problem formulations are presented, each of which illustrates a particular type of failure. A table is presented in which all failure modes are summarized and the corresponding numerical tests are exhibited.