Suicide inactivation of dioldehydratase by glycolaldehyde and chloroacetaldehyde: an examination of the reaction mechanism

High-level ab initio calculations have been used to study the mechanism for the inactivation of diol dehydratase (DDH) by glycolaldehyde or 2-chloroacetaldehyde. As in the case of the catalytic substrates of DDH, e.g., ethane-1,2-diol, the 5'-deoxyadenosyl radical (Ado*) is able to abstract a hydrogen atom from both substrate analogues in the initial step on the reaction pathway, as evidenced by comparable energy barriers. However, in subsequent step(s), each substrate analogue produces the highly stable glycolaldehyde radical. The barrier for hydrogen atom reabstraction by the glycolaldehyde radical is calculated to be too high ( approximately 110 kJ mol-1) to allow Ado* to be regenerated and recombine with the cob(II)alamin radical, the latter therefore remaining tightly bound to DDH. As a consequence, the catalytic pathway is disrupted, and DDH becomes an impotent enzyme. Interconversion of equivalent structures of the glycolaldehyde radical via the symmetrical cis-ethanesemidione radical is calculated to require 38 kJ mol-1. EPR indications of a symmetrical cis-ethanesemidione structure are likely to be the result of formation of an equilibrium mixture of glycolaldehyde radical structures, this equilibration being facilitated by partial deprotonation of the glycolaldehyde radical by the carboxylate of an amino acid residue within the active site of DDH.     

Chemical analysis and cellular imaging with quantum dots

Quantum dots are tiny light-emitting particles on the nanometer scale. They are emerging as a new class of biological labels with properties and applications that are not available with traditional organic dyes and fluorescent proteins. Their novel properties such as improved brightness, resistance against photobleaching, and multicolor light emission, have opened new possibilities for ultrasensitive chemical analysis and cellular imaging. In this Research Highlight article , we discuss the unique optical properties of semiconductor quantum dots, surface chemistry and bioconjugation, current applications in bioanalytical chemistry and cell biology, and future research directions.     

Assembly of large simple 1D and rare polycatenated 3D molecular ladders from T-shaped building blocks containing a new, long N,N'-bidentate ligand

Molecular ladders [Co(2)(nbpy4)(3)(NO(3))(4)]*solvents and [Cd(2)(nbpy4)(3)(NO(3))(4)](nbpy4 =N,N'-bis-(4-pyridinylmethylene)-1,5-naphthalenediamine) were synthesized via self-assembly; the former is a large, simple, noninterpenetrated 1D ladder that contains guest solvent molecules between the rungs, while the latter exists as 1D ladders in a rare four-fold interlocked 3D structure.     

Asymmetric synthesis of the cis- and trans-stereoisomers of 4-aminopyrrolidine-3-carboxylic acid and 4-aminotetrahydrofuran-3-carboxylic acid

The diastereoselective conjugate addition of lithium (S)-N-benzyl-N-[small alpha]-methylbenzylamide has been successfully applied to the first asymmetric syntheses of cis-(3S,4R)- and trans-(3R,4R)-4-aminotetrahydrofuran-3-carboxylic acids (26% and 25% overall yield respectively, >98% d.e. and >97% e.e. in each case). Furthermore, the most efficient asymmetric synthesis to date of cis-(3R,4R)- and trans-(3R,4S)-4-aminopyrrolidine carboxylic acids is delineated: for cis-(3R,4R), four steps, >98% d.e., 52% overall yield; for trans-(3R,4S), five steps, >98% d.e., 50% overall yield.     

Functionalized nanoparticles for liquid atmospheric pressure matrix-assisted laser desorption/ionization peptide analysis

Nanoparticles for the extraction of peptides and subsequent analysis using atmospheric pressure matrix-assisted laser desorption/ionization (APMALDI) have been evaluated. The atmospheric pressure source allows for particles to be directly introduced in the liquid matrix, minimizing sample loss and analysis time. Described in this work are two sample preparation procedures for liquid APMALDI analysis: a C18 functionalized silica nanoparticle for hydrophobic extractions, and an aptamer functionalized magnetite core nanoparticle for rapid, affinity extractions. The C18 particles provide a non-selective support for rapid profiling applications, while the aptamer particles are directed towards reducing the complexity in biological samples. The aptamer functionalized particles provide a more selective analyte-nanoparticle interaction whereby the tertiary structure of the analyte becomes more critical to the extraction. In both cases, the liquid APMALDI matrix provides a support for ionization, and acts as the releasing agent for the analyte-particle interaction. Additionally, analyte enrichment was possible due to the large surface-to-volume ratio of the particles. The experiments conducted with functionalized nanoparticles, in an atmospheric pressure liquid matrix, present a basis for further methodologies and utilities of silica nanoparticles to be developed.     

General one-pot, three-step methodology leading to an extended class of N-heterocyclic cations: spontaneous nucleophilic addition, cyclization, and hydride loss

A new class of phenanthridinium derivative has been isolated from the reaction of 2-bromoethyl-phenanthridinium bromide with a range of primary amines in excellent yields. The reaction pathway is unprecedented and proceeds via three cascade steps: nucleophilic attack of a primary amine on the iminium moiety of a heteroaromatic ring system and cyclization to form a five-membered ring, followed by hydride loss to yield a rearomatized dihydro-1H-imidazo[1,2-f]phenanthridinium derivative. A range of NMR phase transfer experiments were carried out to elucidate the mechanistic pathway, and the methodology has been further developed by means of a biphasic system using N-bromosuccinimide as a co-oxidizing agent. The method has also been extended to other N-heterocyclic cation derivatives such as quinolinium and quinazolinium.     

Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element

The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1'-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable.     

Effect of the counterion on the rate of electron transfer in dendrimer films

The electrochemical behavior of a film composed of a redox-active dendrimer was studied as a function of the type of counterion available during its reduction and reoxidation. The rate of permeation/migration of counterions into the film appeared to be the bottleneck to electron transfer through the film. Because the dendrimer is rather hydrophobic, increasing the hydrophobicity of the counterion increased the rate and extent of electron hopping within the films.     

Quantum dot nanocrystals for in vivo molecular and cellular imaging

Semiconductor quantum dots (QD) are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. In comparison with organic dyes and fluorescent proteins, QD are emerging as a new class of fluorescent labels with improved brightness, resistance against photobleaching and multicolor fluorescence emission. These properties could improve the sensitivity of biological detection and imaging by at least 10- to 100-fold. Further development in high-quality near-infrared-emitting QD should allow ultrasensitive and multicolor imaging of molecular targets in deep tissue and living animals. Here, we discuss recent developments in QD synthesis and bioconjugation, applications in molecular and cellular imaging as well as promising directions for future research.     

Preferential hydration and the exclusion of cosolvents from protein surfaces

Protein stability is enhanced by the addition of osmolytes, such as sugars and polyols and inert crowders, such as polyethylene glycols. This stability enhancement has been quantified by the preferential hydration parameter which can be determined by experiments. To understand the mechanism of protein stability enhancement, we present a statistical mechanical analysis of the preferential hydration parameter based upon Kirkwood-Buff theory. Previously, the preferential hydration parameter was interpreted in terms of the number of hydration waters, as well as the cosolvent exclusion volume. It was not clear how accurate these interpretations were, nor what the relationship is between the two. By using the Kirkwood-Buff theory and experimental data, we conclude that the contribution from the cosolvent exclusion dominantly determines the preferential hydration parameters for crowders. For osmolytes, although the cosolvent exclusion largely determines the preferential hydration parameters, the contribution from hydration may not be negligible.