Rhodium-catalyzed alkylthio exchange reaction of thioester and disulfide

The Wilkinson complex RhCl(PPh₃)₃ catalyzes equilibrating alkylthio exchange reaction of thioesters with disulfides. The treatment of a thioester and a dialkyl disulfide in refluxing diethyl ketone in the presence of RhCl(PPh₃)₃ (2.5 mol %) for 1.5 h gave an alkylthio exchanged thioester. The reaction of S-methyl ester was conducted shifting the equilibrium by removing volatile dimethyl disulfide.     

Colloidal aspects of protein digestion

The increase in food related health issues has sparked an interest in research on the digestion processes of the gastrointestinal tract. Because of the difficulty and expense of undertaking human trials or even animal experiments, much of the current research uses in vitro models that simulate various aspects of digestion. The results of this research indicate that the rate and extent of protein digestion is governed by accessibility of the cleavage sites to enzymes and local flexibility of the substrate molecule. However, results have also shown that digestion of an allergenic protein to small fragments does not necessarily mean that it will no longer be immunologically active. Other factors are also important. For example, adsorption to an interface increased rates of digestion as did the presence of bile acids. In fact, interaction with a range of physiological surfactants has been shown to be extremely important in protein digestion. When protein is adsorbed to an emulsified food it can be displaced by the surfactants in either the stomach or the small intestine. Lipid interaction with the protein in solution has been demonstrated to be important in effecting rates of proteolysis and phospholipids in particular have provided a protective effect for some milk proteins. Conversely the presence of specific proteins has been shown to affect rates of lipid digestion. The number of such colloidal interactions that we now know may play a role in protein digestion highlights the importance of this area to understanding how we can produce food that optimises nutrition for the consumer.     

Role of thiol‐disulfide exchange in episulfide polymerization

Episulfide polymerization offers a number of features that are uncommon in other ring‐opening anionic mechanisms. Besides the negligible sensitivity to water, the most distinctive and novel one is likely to be the role of disulfides, which may act both at the levels of chain transfer and end‐capping, producing polymers that feature both terminal and internal disulfides. In this article, we have qualitatively studied the kinetics of chain transfer and measured the thiolate–disulfide exchange equilibrium constants. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2233–2249, 2008     

Recombinant immobilized rhizopuspepsin as a new tool for protein digestion in hydrogen/deuterium exchange mass spectrometry

Hydrogen/deuterium (H/D) exchange coupled to mass spectrometry is nowadays routinely used to probe protein interactions or conformational changes. The method has many advantages, e.g. very low sample consumption, but offers limited spatial resolution. One way to higher resolution leads through the use of different proteases or their combinations. In the present work we describe recombinant production, purification and use of aspartic protease zymogen from Rhizopus chimensis, protease type XVIII (EC 3.4.23.6), commonly referred to as rhizopuspepsinogen (Rpg). The enzyme was expressed in Escherichia coli, refolded and purified to homogeneity. A typical yield was approximately 100 mg of pure enzyme per 1 L of original bacterial culture. The kinetics of protease activation, i.e. removal of the propeptide achieved by autolysis in an acidic environment, was followed by mass spectrometry. The digestion efficiency was tested for the protease in solution as well as for the immobilized enzyme. Apomyoglobin was successfully digested under all conditions tested and the protease displayed very low or no autodigestion. The results outperformed those obtained with commercial protease where the digestion of apomyoglobin was incomplete and accompanied by many contaminating peptides. Taken together, the recombinant protease type XVIII can be considered as a new and highly efficient tool for H/D exchange followed by mass spectrometry. Copyright © 2009 John Wiley & Sons, Ltd.     

Atomistic evidence of how force dynamically regulates thiol/disulfide exchange

The intricate coupling of mechanical force and chemical reactivity has been increasingly revealed in recent years by force spectroscopy experiments on the thiol/disulfide exchange reaction. We here aimed at elucidating the underlying dynamic effects of force on the reaction center for the case of disulfide bond reduction by dithiothreitol at forces of 200-2000 pN, by combining transition path sampling and quantum/classical mechanical simulations. Reaction rates and their dependence on force as quantified by Δx(r), the distance between reactant and transition state, are in good agreement with experiments but indicate a shift of the transition state structure at high forces. Indeed, while an associate S(N)2 mechanism prevails, force causes a move of the transition state to a longer length of the cleaving bond and a shorter length of the forming disulfide bond. Our results highlight the distribution of force into various degrees of freedom, which implies that care must be taken when correlating Δx(r) with a single order parameter of the reaction.     

Probing protein dynamics and function under native and mildly denaturing conditions with hydrogen exchange and mass spectrometry

A combination of hydrogen exchange and mass spectrometry emerged in recent years as a powerful experimental tool capable of probing both structural and dynamic features of proteins. Although its concept is very simple, the interpretation of experimental data is not always straightforward, as a combination of chemical reactions (isotope exchange) and dynamic processes within protein molecules give rise to convoluted exchange patterns. This paper provides a historical background of this technique, candid assessment of its current state and limitations and a discussion of promising recent developments that can result in tremendous improvements and a dramatic expansion of the scope of its applications.     

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.     

Tailoring orthogonal proteomic routines to understand protein separation during ion exchange chromatography

Surface charge, molecular weight, and folding state are known to influence protein chromatographic behaviour onto ion exchangers. Experimentally, information related to such factors can be gathered via 2-DE methods. The application of 2-D PAGE under denaturing/reducing conditions was already shown to reveal separation trends within a large protein population from cell extracts. However, ion-exchange chromatography normally runs under native conditions. A tailored protocol consisting in a first separation based on IEF on Immobiline strips under native conditions followed by a second dimension SDS-PAGE run was adopted. The chromatographic versus electrophoretic separation behaviours of two model proteins, thaumatin (TAU) and BSA, were compared to better understand which proteomic routine would be better suited to anticipate IEX chromatographic separations. It was observed that the information contained in the pI value obtained with the adapted 2-DE protocol showed better correlation with the IEX chromatographic behaviour. On the other hand, chromatographic separations performed in the presence of urea as a denaturant have demonstrated the potential influence of hydrodynamic radius/conformation on protein separation. Moreover, the information provided by such 2-D system correlated well with the chromatographic behaviour of an additional set of pure proteins. An initial prediction of protein ion-exchange chromatographic behaviour could be possible utilizing an experimental approach based on 2-DE running under milder chemical conditions. This technique provides information that more closely resembles the separation behaviour observed with a complex biotechnological feedstock.     

Molecular aspects of boundary lubrication by human lubricin: effect of disulfide bonds and enzymatic digestion

Lubricin (LUB) is a glycoprotein of the synovial cavity of human articular joints, where it serves as an antiadhesive, boundary lubricant, and regulating factor for the cartilage surface. It has been proposed that these properties are related to the presence of a long, extended, heavily glycosylated and highly hydrated mucinous domain in the central part of the LUB molecule. In this work, we show that LUB has a contour length of 220 +/- 30 nm and a persistence length of < or =10 nm. LUB molecules aggregate in oligomers where the protein extremities are linked by disulfide bonds. We have studied the effect of proteolytic digestion by chymotrypsin and removal of the disulfide bonds, both of which mainly affect the N- and C- terminals of the protein, on the adsorption, normal forces, friction (lubrication) forces, and wear of LUB layers adsorbed on smooth, negatively charged mica surfaces, where the protein naturally forms lubricating polymer brush-like layers. After in situ digestion, the surface coverage was drastically reduced, the normal forces were altered, and both the coefficient of friction and the wear were dramatically increased (the COF increased to mu = 1.1-1.9), indicating that the mucinous domain was removed from the surface. Removal of disulfide bonds did not change the surface coverage or the overall features of the normal forces; however, we find an increase in the friction coefficient from mu = 0.02-0.04 to mu = 0.13-1.17 in the pressure regime below 6 atm, which we attribute to a higher affinity of the protein terminals for the surface. The necessary condition for LUB to be a good lubricant is that the protein be adsorbed to the surface via its terminals, leaving the central mucin domain free to form a low-friction, surface-protecting layer. Our results suggest that this "end-anchoring" has to be strong enough to impart the layer a sufficient resistance to shear, but without excessively restricting the conformational freedom of the adsorbed proteins.     

Solid state differentiation of plasma thiols using a centrifugally activated mercaptobenzothiazole disulfide exchange indicator

The solid state interaction of mono and macromolecular thiols at a disulfide heterocycle is shown to provide a versatile pathway for their speciation.     

Expanding diversity in dynamic combinatorial libraries: simultaneous exchange of disulfide and thioester linkages

Dynamic combinatorial libraries have been prepared which feature two simultaneous covalent exchange reactions in aqueous solution at neutral pH. This allows for diversity, not only of the subunits that are linked, but also of the linkage itself.     

Engineering the HER catalytic behavior of heteroatom-doped molybdenum disulfide via versatile partial cation exchange

正Water electrolysis is regarded as an environmental friendly and effective technique for large-scale hydrogen (H2) production [1,2].To date, Pt-based electrocatalysts are still the most efficient HER catalysts [3]. However, the prohibitive cost and scarcity of precious metal catalysts have restricted its large-scale applications. Thus,finding an earth-abundant and effective alternative electrocatalysts     

Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion

Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins. Graphical Abstract

Sequence logos of four cleavage site types with different kinetics (very fast, fast, slow, and very slow sites)     

Redox-dependent formation of disulfide bonds in human replication protein A

Human replication protein A (RPA) is a single-stranded DNA (ssDNA)-binding protein with three subunits. The largest subunit, p70, contains a conserved (cysteine)(4)-type zinc-finger motif that has been implicated in the regulation of DNA replication and repair. Previous studies indicated that the ssDNA-binding activity of RPA could be redox-regulated via reversible oxidation of cysteines in the zinc-finger motif. We exposed recombinant human RPA to hydrogen peroxide and characterized the oxidized protein by liquid chromatography/tandem mass spectrometric (LC/MS/MS) analyses. Our results demonstrated that, upon H(2)O(2) treatment, four cysteines, which reside at the zinc-finger motif of the p70 subunit, could result in the formation of two pairs of intramolecular disulfides, Cys481-Cys486 and Cys500-Cys503; no cysteine sulfinic acid or cysteine sulfonic acid could be found. Moreover, the other 11 cysteines in this protein remained intact. The results demonstrated that the formation of disulfide bonds at the zinc-finger site was responsible for the redox regulation of the DNA-binding activity of RPA.     

Post-functionalization of ATRP polymers using both thiol/ene and thiol/disulfide exchange chemistry

In this communication, we report on a new route to the functionalization of ATRP polymers exploiting their halide end-groups, which were converted successfully into reactive disulfide end-groups, using sodium methanethiosulfonate. The resultant disulfide-terminated polymers could then be reacted with different functional thiols to yield functional polymers exploiting either thiol/disulfide exchange chemistry or thiol/ene "click" reactions.     

Use of self assembled magnetic beads for on-chip protein digestion

The use of grafted trypsin magnetic beads in a microchip for performing protein digestion is described. The PDMS device uses strong magnets to create a magnetic field parallel to the flow with a strong gradient pointing through the center of the chip channel. This allows for the formation of a low-hydrodynamic resistance plug of magnetic trypsin beads that serves as a matrix for protein digestion. This device represents an inexpensive way of fabricating a multi open-tubular-like column with an appropriate pore size for proteins. Kinetics studies of the hydrolysis of a model peptide show a 100-fold increase in digestion speed obtained by the microsystem when compared to a batch wise system. This system also offers the great advantage of easy replacement, as the bead matrix is easily washed out and replaced. High performance and reproducibility for digesting recombinant human growth hormone are confirmed by analysing the digest products in both CE and MALDI-TOF MS. Similar sequence coverage (of about 44%) is obtained from MS analysis of products after 10 minutes on-chip and 4 h with soluble trypsin in bulk.