A robust micro-electrospray ionization technique for high-throughput liquid chromatography/mass spectrometry proteomics using a sanded metal needle as an emitter

A 60 microm internal diameter (i.d.) stainless-steel needle was adapted to the orthogonal ESI probe ( microESI) of a commercial ion trap mass spectrometer, and used for capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS) protein identification experiments. The modification allows for the use of nitrogen sheath gas which helps in the nebulization at LC flow rates exceeding 500 nL/min and eliminates problems caused by liquid junctions commonly used to initiate nanospray ionization (NSI). A comparison is made between the performance of a 75 microm i.d. column with a 15 microm pulled glass tip using a liquid junction, and that of a 150 microm i.d. column using the new microESI device. The combination of the 150 microm i.d. column and microESI gave sensitivity close to that of NSI (250 attomoles horse heart myoglobin digest on column), and proved to be more robust than the standard pulled glass tips of similar i.d. No evidence of metal needle catalyzed oxidation of methionine was observed during analysis of the tetrapeptide MRFA under a range of test conditions. Phosphorylated peptides in a beta-casein tryptic digest were also successfully identified using the microESI interface with a steel needle. In addition it was found that a mild sanding of the metal needle tip improved spray performance.     

De novo design of strand-swapped beta-hairpin hydrogels

De novo designed peptides, capable of undergoing a thermally triggered beta-strand-swapped self-assembly event leading to hydrogel formation were prepared. Strand-swapping peptide 1 (SSP1) incorporates an exchangeable beta-strand domain composed of eight residues appended to a nonexchangeable beta-hairpin domain. CD shows that, at pH 9 and temperatures less than 35 degrees C, this peptide adopts a random coil conformation, rendering it soluble in aqueous solution. On heating to 37 degrees C or greater, SSP1 adopts a beta-hairpin that displays an exchangeable beta-strand region. The exchangeable strand domain participates in swapping with the exchangeable domain of another peptide, affording a strand-swapped dimer. These dimers further assemble into fibrils that define the hydrogel. A second peptide (SSP2) containing an exchangeable strand composed of only four residues was also studied. Microscopy and scattering data show that the length of the exchangeable domain directly influences the fibril nanostructure and can be used as a design element to construct either twisted (SSP1) or nontwisted (SSP2) fibril morphologies. CD, FTIR, and WAXS confirm that both peptides adopt beta-sheet secondary structure when assembled into fibrils. Fibril dimensions, as measured by TEM, AFM, and SANS indicate a fibril diameter of 6.4 nm, a height of 6.0 nm, and a pitch of 50.4 nm for the twisted SSP1 fibrils. The nontwisted SSP2 fibrils are 6.2 nm in diameter and 2.5 nm in height. Oscillatory rheology, used to measure bulk hydrogel rigidity, showed that the gel composed of the nontwisted fibrils is more mechanically rigid (517 Pa at 6 rad/s) than the gel composed of twisted fibrils (367 Pa at 6 rad/s). This work demonstrates that beta-strand-swapping can be used to fabricate biomaterials with tunable fibril nanostructure and bulk hydrogel rheological properties.     

Deubiquitylating enzymes and disease

Abstract

Deubiquitylating enzymes (DUBs) can hydrolyze a peptide, amide, ester or thiolester bond at the C-terminus of UBIQ (ubiquitin), including the post-translationally formed branched peptide bonds in mono- or multi-ubiquitylated conjugates. DUBs thus have the potential to regulate any UBIQ-mediated cellular process, the two best characterized being proteolysis and protein trafficking. Mammals contain some 80–90 DUBs in five different subfamilies, only a handful of which have been characterized with respect to the proteins that they interact with and deubiquitylate. Several other DUBs have been implicated in various disease processes in which they are changed by mutation, have altered expression levels, and/or form part of regulatory complexes. Specific examples of DUB involvement in various diseases are presented. While no specific drugs targeting DUBs have yet been described, sufficient functional and structural information has accumulated in some cases to allow their rapid development.

Publication history

Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).

     

Beryllium bonding with noble gas atoms

Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be₃ ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be₃ complexes. The Be atoms in the Be₃ moiety are chemically bonded to one another, with the Be Be bond dissociation energy being ~125 kJ mol⁻¹. The Be₃ ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be₃ ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.     

Fluorescence based strategies for genetic analysis

Synthetic chemistry has been central to the design of modern methods of genetic analysis. In this article, we discuss the underlying chemistry and biophysical principles that have been used in the development of robust methods for the analysis of DNA in the diagnostic laboratory.     

Design of a silicon-based field-effect electro-optic modulator with enhanced light-charge interaction

A new design for an all-silicon field-effect optical modulator in a ring resonator geometry is proposed and modeled by means of finite-element method simulations. It is shown that the optimal relative placement of the ultrathin field-effect-generated charge layers and the optical mode in the strong-confinement waveguides leads to more than an order-of-magnitude enhancement in the light-charge interaction compared with the recent predictions in the literature. We show that such an enhancement could provide optical modulation with a >7 dB extinction-ratio using a voltage swing of only 2 V, thus making our design compatible with complementary metal-oxide semiconductor technology.     

Modelling and sensitivity analysis for design of phononic crystals

The two-scale homogenization is employed to study the band gaps in strongly heterogeneous periodic elastic media – the phononic crystals. It was observed that wave propagation can be suppressed for certain frequency intervals. Moreover, the gap distribution w.r.t. the incident frequencies can be modified by changing the shape of inclusions embedded in the matrix. The sensitivity analysis formulae were derived and implemented to obtain optimized microstructures of the phononic crystals. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Design,synthesis and spectroscopic characterisation of a focused library based on the polyandrocarpamine natural product scaffold

A focused library based on the marine natural products polyandrocarpamines A ( 1 ) and B ( 2 ) has been designed and synthesised using parallel solution‐phase chemistry. In silico physicochemical property calculations were performed on synthetic candidates in order to optimise the library for drug discovery and chemical biology. A library of ten 2‐aminoimidazolone products ( 3–12 ) was prepared by coupling glycocyamidine and a variety of aldehydes using a one‐step stereoselective aldol condensation reaction under microwave conditions. All analogues were characterised by NMR, UV, IR and MS. The library was evaluated for cytotoxicity towards the prostate cancer cell lines, LNCaP, PC‐3 and 22Rv1. Copyright © 2013 John Wiley & Sons, Ltd.     

Error propagation in normalization of stable isotope data: a Monte Carlo analysis

A higher analytical precision of a stable isotope ratio mass spectrometer does not automatically guarantee accurate determination of the true isotope composition (δ‐value) of samples, since estimates of true δ‐values are obtained from the normalization of raw isotope data. We performed both Monte Carlo simulations and laboratory experiments to investigate aspects of error propagation during the normalization of carbon stable isotope data. We found that increasing both the number of different reference standards and the number of repetitions of each of these standards reduces the normalization error. A 50% reduction in the normalization error can be achieved over the two‐point normalization by either analyzing two standards four times each, or four standards two times each. If the true δ‐value of a sample is approximately known a priori, the normalization error may then be reduced through a targeted choice of locally optimal standards. However, the difference in improvement is minimal and, therefore, a more practical strategy is to use two or more standards covering the whole stable isotope scale. The selection of different sets of standards by different laboratories or for different batches of samples in the same laboratory may lead to significant differences in the normalized δ‐values of the same samples, leading to inconsistent results. Hence, the same set of standards should always be used for a particular element and a particular stable isotope analytical technique. Copyright © 2010 John Wiley & Sons, Ltd.