Optimized allosteric inhibition of engineered protein tyrosine phosphatases with an expanded palette of biarsenical small molecules

Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are important cell-signaling regulators, as well as potential drug targets for a range of human diseases. Chemical tools for selectively targeting the activities of individual PTPs would help to elucidate PTP signaling roles and potentially expedite the validation of PTPs as therapeutic targets. We have recently reported a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs, in which a tricysteine moiety is engineered within the PTP catalytic domain at a conserved location outside of the active site. Introduction of the tricysteine motif, which does not exist in any wild-type PTP, serves to sensitize target PTPs to inhibition by a biarsenical compound, providing a generalizable strategy for the generation of allosterically sensitized (as) PTPs. Here we show that the potency, selectivity, and kinetics of asPTP inhibition can be significantly improved by exploring the inhibitory action of a range of biarsenical compounds that differ in interarsenical distance, steric bulk, and electronic structure. By investigating the inhibitor sensitivities of five asPTPs from four different subfamilies, we have found that asPTP catalytic domains can be broadly divided into two groups: one that is most potently inhibited by biarsenical compounds with large interarsenical distances, such as AsCy3-EDT₂, and one that is most potently inhibited by compounds with relatively small interarsenical distances, such as FlAsH-EDT₂. Moreover, we show that a tetrachlorinated derivative of FlAsH-EDT₂, Cl4FlAsH-EDT₂, targets asPTPs significantly more potently than the parent compound, both in vitro and in asPTP-expressing cells. Our results show that biarsenicals with altered interarsenical distances and electronic properties are important tools for optimizing the control of asPTP activity and, more broadly, suggest that diversification of biarsenical libraries can serve to increase the efficacy of these compounds in targeted control of protein function.     

Antibodies to a Synthetic Peptide Corresponding to a Ser-40-Containing Segment of Tyrosine Hydroxylase: Activation and Immunohistochemical Localization of Tyrosine Hydroxylase

A peptide corresponding to position 32-47 in tyrosine hydroxylase was synthesized (TH-16) and polyclonal antibodies against this peptide were raised in rabbits (anti-TH-16). The effects of anti-TH-16 on modulation of tyrosine hydroxylase activity were investigated. Anti-TH-16 enhanced the enzymatic activity in a concentration-dependent manner, and the antigen TH-16 inhibited the stimulatory activity of the antiserum in a concentration-dependent manner. The activated enzyme had a lower Km app for the cofactor 2-amino-4-hydroxy-6-methyl-5,6,7,8-tetrahydropterin and a higher Vmax app than the nonactivated enzyme. Anti-TH-16 was characterized further by its ability to immunoprecipitate the enzyme activity by labeling tyrosine hydroxylase after Western blotting and by immunohistochemical labeling of catecholaminergic neurons. Anti-TH-16 did not block activation of tyrosine hydroxylase by phosphorylation catalyzed by cyclic AMP-dependent protein kinase. Exposure of the enzyme to anti-TH-16 and subsequent phosphorylation of the enzyme resulted in a greater activation of the enzyme than the sum of activation produced by these two treatments separately. However, the activation was less than additive when the enzyme was first phosphorylated and subsequently exposed to anti-TH-16. The present study demonstrates the utility of anti-TH-16 in investigating the molecular aspects of the enzyme activation.     

Physical crosslinking of lipase from Rhizomucor miehei immobilized on octyl agarose via coating with ionic polymers: Avoiding enzyme release from the support

Lipase from Rhizomucor miehei (RML) was immobilized on octyl-agarose (OC) at different loadings. Using low enzyme loadings (1/7 of the maximum loading), the incubation of the enzyme with polyethylenimine (PEI) increased the resistance to enzyme desorption in the presence of Triton X-100. However, more than 10% of the enzyme activity could be released from the OC-RML-PEI. The same treatment using fully loaded biocatalyst reduced the enzyme desorption to less than 5%. Further treatment with dextran sulfate (DS) of the PEI treaded immobilized enzyme fully avoids the enzyme desorption even in presence of a Triton X-100 concentration higher than that required for the complete enzyme release from OC-RML. This treatment produced a high stabilization of OC-RML in thermal or organic solvent inactivations, reducing the enzyme release under these drastic conditions. Nevertheless, the support could be recovered by incubation under adequate conditions, and reused in several adsorption/desorption cycles. Thus, the strategy permitted to avoid enzyme desorption, very likely by physical intermolecular crosslinking improving enzyme stability, while still maintaining the reversibility of the immobilization.     

Analysis of the activation of acetylcholinesterase by carbon nanoparticles using a monolithic immobilized enzyme microreactor: role of the water molecules in the active site gorge

A biochromatographic system was used to study the direct effect of carbon nanoparticles (CNPs) on the acetylcholinesterase (AChE) activity. The AChE enzyme was covalently immobilized on a monolithic CIM-disk via its NH₂ residues. Our results showed an increase in the AChE activity in presence of CNPs. The catalytic constant (k_cat) was increased while the Michaelis constant (K_m) was slightly decreased. This indicated an increase in the enzyme efficiency with increase of the substrate affinity to the active site. The thermodynamic data of the activation mechanism of the enzyme, i.e. ΔH* and ΔS*, showed no change in the substrate interaction mechanism with the anionic binding site. The increase of the enthalpy (ΔH*) and the entropy (ΔS*) with decrease in the free energy of activation (Ea) was related to structural conformation change in the active site gorge. This affected the stability of water molecules in the active site gorge and facilitated water displacement by substrate for entering to the active site of the enzyme.     

Selective involvement of TIMP-2 in the second activational cleavage of pro-MMP-2: refinement of the pro-MMP-2 activation mechanism

A tissue inhibitor of metalloproteinases-2 (TIMP-2)-independent mechanism for generating the first activational cleavage of pro-matrix metalloproteinase-2 (MMP-2) was identified in membrane type-1 MMP (MT1-MMP)-transfected MCF-7 cells and confirmed in TIMP-2-deficient fibroblasts. In contrast, the second MMP-2-activational step was found to be TIMP-2 dependent in both systems. MMP-2 hemopexin C-terminal domain was found to be critical for the first step processing, confirming a need for membrane tethering. We propose that the intermediate species of MMP-2 forms the well-established trimolecular complex (MT1-MMP/TIMP-2/MMP-2) for further TIMP-2-dependent autocatalytic cleavage to the fully active species. This alternate mechanism may supplement the traditional TIMP-2-mediated first step mechanism.     

Molecular imprint of enzyme active site by camel nanobodies: rapid and efficient approach to produce abzymes with alliinase activity

Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach.     

Starches from different botanical sources I: Contribution of amylopectin fine structure to thermal properties and enzyme digestibility

Fifteen starches from different botanical sources were selected to study the influence of structural features on thermal properties and enzyme digestibility. Morphological appearance, X-ray diffraction pattern, apparent amylose content, unit-chain length distribution of amylopectin, thermal properties and enzyme digestibility of starch varied with botanical source. It was demonstrated that the distribution of unit-chains of amylopectin significantly correlated with functional properties of the starches. Gelatinization temperature of native and retrograded starches decreased and increased with a relative abundance of unit-chains with an approximate degree of polymerization (DP) of 8–12 and 16–26, respectively (P<0.01). Similar unit-chain lengths also affected the enzyme digestibility of starch granules (P<0.01).     

Ecophysiological studies on citrate-synthase: (I) enzyme regulation of selected crustaceans with regard to temperature adaptation

The characteristics and properties chromatographically purified citrate synthase from the euphausiids Euphausia superba (Antarctica) and Meganyctiphanes norvegica (Scandinavian Kattegat and Mediterranean Sea) and from the isopods Serolis polita (Antarctica) and Idotea baltica (Baltic Sea) were used to elucidate biochemical mechanisms of temperature adaptation. Additionally, maintenance experiments were carried out on the euphausiids to determine mechanisms of short term acclimation. Temperature optima (between 37 and 45°C) were unrelated to genotypic cold adaptation, but the activation energy of the Antarctic krill E. superba (10.9 kJ · mol^-1) was only a quarter of that in other species (41.8–45.1 kJ · mol^-1). The minima of apparent Michaelis constants (total range: 4–20 μmol · 1^-1 oxaloacetate; 7–45 μmol · 1^-1 acetyl-coenzyme A) showed no relation to natural conditions, and no distinct pH optimum occurred at ambient temperatures. In contrast, apparent Michaelis constants and specific enzyme activities were related to maintenance temperatures in M. norvegica, but not in E. superba. The differences between M. norvegica and E. superba can be interpreted as adaptations to the changes in ambient temperature with regard to the respective steno- and eurythermic tolerances of these crustaceans.     

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.     

An unusual course of thioglycoside activation with bromine: synthesis and crystal structure of 4-O-acetyl-2-bromo-2,3,6-trideoxy-3-C-methyl-3-trifluroacetamido-alpha-L-altropyranosyl bromide

Bromine activation of phenyl 4-O-acetyl-2,3,6-trideoxy-3-C-methyl-3-trifluoroacetamido-1-thio-alpha,beta-L-ribo-hexopyranoside and attempted coupling with an acceptor in the presence of silver silicate gave an unusual bicyclic product, 2-trifluoromethyl-(4-O-acetyl-2-bromo-2,3,6-trideoxy-3-C-methyl-alpha-L-altrohexopyrano)-[3,2,1-d,e]-2-oxazine, instead of the expected disaccharide. Detailed investigation supported by X-ray crystallographic analysis showed that a trans dibromide is an intermediate in this reaction and that the dibromide is likely formed from a glycal that is generated by elimination during the coupling step.     

Hemin-mediated para-hydroxylation of aniline: A potential model for oxygen activation and insertion reactions of mixed function oxidases

The activation of molecular oxygen by alkaline hemin (ferriprotoporphyrin IX) has been studied. In the presence of reductant nicotineamide adenine dinucleotide (NADH) or nicotineamide adenine dinucleotide phosphate (NADPH) and organic substrate, aniline, hemin activates oxygen to the hydroperoxide anion (HO₂^?) and subsequently mediates insertion of active oxygen into the benzene ring of the substrate to form p-aminophenol, with a high degree of regiospecificity. Oxygen activation does not occur in the absence of aniline. Stoichiometry of the reaction indicates that two electrons are required per molecule of oxygen activated or atom of oxygen inserted into the substrate aromatic ring system. Direct measurements of H₂O₂ and of the pK_a for maximum rate of p-aminophenol formation (11.7 ± 0.1) indicate participation of the hydroperoxide anion as the active oxygen species in the rate-determining step of the insertion reaction. Powerful scavengers of the hydroxyl radical (OH′) have little effect on the formation of H₂O₂ or p-aminophenol by the system. Superoxide dismutase (10^?7 mol dm^?3) inhibited both p-aminophenol and H₂O₂ formation, when added to the system immediately prior to initiation of the reaction. Studies involving N-phenylhydroxylamine indicate that aromatic ring hydroxylation is occurring directly and not by rearrangement of an N-hydroxylated intermediate. Implications of hemin-mediated hydroxylation reactions for those of enzymatic mixed function oxidase activity are discussed.     

Ecophysiological studies on citrate synthase: (II) enzyme regulation of selected crustaceans with regard to life-style and the climatic zone

Citrate synthase is a regulatory enzyme of the energy metabolism pathway controlling the citric acid cycle. It was studied in order to determine modes of enzyme regulation with regard to the life-style of the investigated species. Citrate synthase from crustaceans with different life-styles were compared: the pelagic euphausiids Euphausia superba from the Antarctic and Meganyctiphanes norvegica from the Scandinavian Kattegat and the Mediterranean were compared to the benthic isopods Serolis polita from the Antarctic and Idotea baltica from the Baltic. Citrate synthase was partly purified chromatographically and the influence of adenosine 5′-triphosphate on enzyme activity was examined. Mechanisms of inhibition and inhibitor constants were determined. Two different mechanisms of enzyme regulation by ATP were found. Citrate synthase from isopods was only competitively inhibited, while citrate synthase from euphausiids showed not only competitive inhibition but also activation by low concentrations of ATP. This activation is equivalent to the reversed methanism of uncompetitive inhibition. The ecophysiological relevances of the coupling of these mechanisms are discussed. The degree of competitive inhibition was different in the two groups of investigated crustaceans. Inhibitor constants were similar within the euphausiids but not in isopods, which showed higher or lower inhibition depending on the climatic zone: the colder the ambient temperature the lower the ATP inhibition. A possible mechanism of temperature adaptation through effects of varying inhibition constants is concluded.     

Cooperative mechanisms of thin filament activation and their contribution to the myocardial contractile function: Assessment in a mathematical model

A mathematical model was used for comparative analysis of the contribution to the myocardial mechanical activity of two potentially possible variants of the cooperative influence of myosin cross-bridges on calcium activation of sarcomere actin filaments. One of these variants implies that the cooperative action of the cross-bridge on the affinity of troponin C for calcium is localized within the functional group A₇TmTn (seven adjacent globular actin monomers, tropomyosin, and one troponin complex TnC + TnI + TnT) where this bridge is attached. The second variant is based on the assumption that cross-bridges may influence the troponin C affinity for calcium also in neighboring A₇TmTn groups (and the closer the group is positioned relative to the bridge, the stronger is the influence on the CaTnC complex affinity in this group). The contribution of each of these two variants to the active mechanical behavior of the cardiac muscle in the contraction-relaxation cycle was assessed. It turned out that adequate simulation of the muscle mechanical activity is provided only by the second variant. Thus, the results of modeling argue in favor of the existence of just this variant of cooperativity.     

An analysis of the role of actin during pollen activation leading to germination in pear (Pyrus communis L.): treatment with cytochalasin D

Summary Major stages of actin organization during activation leading to germination of pear (Pyrus communis L.) pollen were disrupted by treatment with 5 g/ml cytochalasin D (CD), and the effects of the drug were monitored with rhodamine-phalloidin staining. CD induced the formation of granules or short rods in the place of the filamentous arrays that occur in normally developing pollen. Filamentous arrays, however, returned upon removal of CD. Pollen incubated directly in CD showed a gradual disappearance of circular actin profiles and their replacement by either granules or, less frequently, short rods. These granules and rods initially had a random distribution in the cell, but with time in CD they became localized at one of the three germination apertures. Pollen was also allowed to reach three stages of microfilament (MF) organization (initial fibrillar arrays, interapertural MFs, and MFs confined beneath a single aperture) prior to being continously exposed to CD. After CD treatment, germination was blocked and the number of cells containing short rods increased, but movement of actin to a single aperture continued. Finally, when pollen at different stages of MF organization was treated with a CD pulse and then transferred to drug-free medium, germination was delayed regardless of the stage of MF organization at the time of treatment. The results indicate that an uninterrupted progression of actin organization is essential for pollen germination, but that movement of actin in the cell is CD-insensitive.     

Control of the nitrile-hydrolyzing enzyme activity in Rhodococcus rhodochrous IFO 15564: preferential action of nitrile hydratase and amidase depending on the reaction condition factors and its application to the one-pot preparation of amides from aldehydes

The reaction conditions towards the preferential action of either nitrile hydratase or amidase in the harvested whole cells of Rhodococcus rhodochrous IFO 15564 were elaborated. The amidase showed higher heat tolerance than the nitrile hydratase and, at 45 °C the amidase worked exclusively. DMSO assisted the preferential action of nitrile hydratase, however, at more than 30% (v/v) addition of DMF, the nitrile hydratase activity was completely lost and only amidase worked. A one-pot chemo-enzymatic conversion of aldehydes to amides [(1) aq. NH₃, I₂, DMSO; (2) Na₂S₂O₃; (3) harvested cells of R. rhodochrous] was established. Under these reaction conditions, most of the amidase was lost, and the incubation of the firstly formed intermediates, nitriles in aq. NH₃ was responsible for the selective inhibition of amidase. The freezing of harvested cells in an exhaustively deionized environment provided a long-term preservable “ready to use” for the organic chemist.     

Enzymatic activity of Lecithin:retinol acyltransferase: A thermostable and highly active enzyme with a likely mode of interfacial activation

Lecithin:retinol acyltransferase (LRAT) plays a major role in the vertebrate visual cycle. Indeed, it is responsible for the esterification of all-trans retinol into all-trans retinyl esters, which can then be stored in microsomes or further metabolized to produce the chromophore of rhodopsin. In the present study, a detailed characterization of the enzymatic properties of truncated LRAT (tLRAT) has been achieved using in vitro assay conditions. A much larger tLRAT activity has been obtained compared to previous reports and to an enzyme with a similar activity. In addition, tLRAT is able to hydrolyze phospholipids bearing different chain lengths with a preference for micellar aggregated substrates. It therefore presents an interfacial activation property, which is typical of classical phospholipases. Furthermore, given that stability is a very important quality of an enzyme, the influence of different parameters on the activity and stability of tLRAT has thus been studied in detail. For example, storage buffer has a strong effect on tLRAT activity and high enzyme stability has been observed at room temperature. The thermostability of tLRAT has also been investigated using circular dichroism and infrared spectroscopy. A decrease in the activity of tLRAT was observed beyond 70 °C, accompanied by a modification of its secondary structure, i.e. a decrease of its α-helical content and the appearance of unordered structures and aggregated β-sheets. Nevertheless, residual activity could still be observed after heating tLRAT up to 100 °C. The results of this study highly improved our understanding of this enzyme.     

The effects of exposure to night shift work on liver function: A cross-sectional study with emphasis of alkaline phosphatase enzyme

ABSTRACT

Background: Previous studies have demonstrated that shift work can be significantly associated with adverse effects on liver function. However, the association between shift work and alkaline phosphatase (ALP) enzyme as a well-known biomarker of liver disease has been undefined. Methods: This cross-sectional study was conducted on a total number of 6,475 eligible oil refinery workers. According to shift work schedules, the participants divided to the following groups: 12-hr rotating night (n = 2,630) and 12-hr fixed day (n = 3845). The Spearman’s correlation and logistic regression were applied to assess the association between shift work and ALP. Results: We found significantly higher levels of ALP in 12-hr rotating night compared to 12-hr fixed-day shift work groups (196.2 ± 52.1 versus 191.5 ± 53.4). According to quartile (Q) logistic regression adjusted by significant variables between study group (age, body mass index, fasting blood sugar, and total cholesterol), the odds ratio and 95% confidence interval of high (Q2–<Q3 versus <Q1) and severe (≥Q3 versus <Q1) levels of ALP in 12-hr rotating night group in comparison to 12-hr fixed-day group were estimated as 1.26 (1.08–1.45) and 1.26 (1.09–1.45), respectively. Conclusions: This study indicated that 12-hr rotating night shift work may be associated with higher levels of ALP. More studies are needed to confirm our findings.