Different Enzymatic Processing of γ‐Phosphoramidate and γ‐Phosphoester‐Modified ATP Analogues

Monitoring the activity of ATP‐consuming enzymes provides the basis for elucidating their modes of action and regulation. Although a number of ATP analogues have been developed for this, their scope is restricted because of the limited acceptance by respective enzymes. In order to clarify which kind of phosphate‐modified ATP analogues are accepted by the α‐β‐phosphoanhydride‐cleaving ubiquitin‐activating enzyme 1 (UBA1) and the β‐γ‐phosphoanhydride‐cleaving focal adhesion kinase (FAK), we tested phosphoramidate‐ and phosphoester‐modified ATP analogues. UBA1 and FAK were able to convert phosphoramidate‐modified ATP analogues, even with a bulky modification like biotin. In contrast, a phosphoester‐modified analogue was poorly accepted. These results demonstrate that minor variations in the design of ATP analogues for monitoring ATP utilization have a significant impact on enzymatic acceptance.     

Small‐Molecule Inhibitors of the Tumor Suppressor Fhit

The tumor suppressor Fhit and its substrate diadenosine triphosphate (Ap₃A) are important factors in cancer development and progression. Fhit has Ap₃A hydrolase activity and cleaves Ap₃A into adenosine monophosphate (AMP) and adenosine diphosphate (ADP); this is believed to terminate Fhit‐mediated signaling. How the catalytic activity of Fhit is regulated and how the Fhit ? Ap₃A complex might exert its growth‐suppressive function remain to be discovered. Small‐molecule inhibitors of the enzymatic activity of Fhit would provide valuable tools for the elucidation of its tumor‐suppressive functions. Here we describe the development of a high‐throughput screen for the identification of such small‐molecule inhibitors of Fhit. Two clusters of inhibitors that decreased the activity of Fhit by at least 90 % were identified. Several derivatives were synthesized and exhibited in vitro IC₅₀ values in the nanomolar range.     

Metal Organic Frameworks for Natural Gas Storage in Vehicles

With the increasing demand for alternative fuels the storage of natural gas (NG) in adsorbents like metal organic frameworks (MOFs) will become more important. In order to use MOFs as storage media in fuel delivery systems, the optimization of mass and energy transfer of the system is crucial. For rapid NG filling of a tank, molecules need to reach the adsorption sites within a reasonable time while the heat of adsorption should be dissipated to the environment. In this article, mass transfer in shaped bodies of MOFs was determined by permeability measurements and pulsed field gradient (PFG) NMR spectroscopy. The heat dissipation was also experimentally measured and both data sets were used to set up a theoretical density function theory model to predict the behavior of MOFs for NG storage.     

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

A Study of the Electrode Potential of Nickel in Accelerated Corrosion Test Media

Potential measurements are reported on bright, semi-bright and Watts-type nickel electrodeposits in a number of electrolytes simulating accelerated corrosion test media, both on open circuit and when anodically polarized. The changes in the potentials with time have been recorded in some cases over a period of several days. The appearance of the deposits has been found to alter with polarization. In some cases, the value of the potential has been found to depend in a surprising manner on agitation, and tentative deductions are made from this phenomenon. Results obtained with different deposits and electrolytes are compared.     

CD73 Overexpression in Podocytes: A Novel Marker of Podocyte Injury in Human Kidney Disease

The CD73 pathway is an important anti-inflammatory mechanism in various disease settings. Observations in mouse models suggested that CD73 might have a protective role in kidney damage; however, no direct evidence of its role in human kidney disease has been described to date. Here, we hypothesized that podocyte injury in human kidney diseases alters CD73 expression that may facilitate the diagnosis of podocytopathies. We assessed the expression of CD73 and one of its functionally important targets, the C-C chemokine receptor type 2 (CCR2), in podocytes from kidney biopsies of 39 patients with podocytopathy (including focal segmental glomerulosclerosis (FSGS), minimal change disease (MCD), membranous glomerulonephritis (MGN) and amyloidosis) and a control group. Podocyte CD73 expression in each of the disease groups was significantly increased in comparison to controls (p < 0.001–p < 0.0001). Moreover, there was a marked negative correlation between CD73 and CCR2 expression, as confirmed by immunohistochemistry and immunofluorescence (Pearson r = −0.5068, p = 0.0031; Pearson r = −0.4705, p = 0.0313, respectively), thus suggesting a protective role of CD73 in kidney injury. Finally, we identify CD73 as a novel potential diagnostic marker of human podocytopathies, particularly of MCD that has been notorious for the lack of pathological features recognizable by light microscopy and immunohistochemistry.     

Live Cell Imaging of Enzymatic Turnover of an Adenosine 5′-Tetraphosphate Analog

The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as a tool to follow enzymatic activity. While a number of fluorescence sensors are known, so far, there are no methods available for the real-time monitoring of ATP hydrolysis inside live cells. We present the synthesis and application of a novel fluorogenic adenosine 5′-tetraphosphate (Ap4) analog suited for this task. Upon enzymatic hydrolysis, the molecule displays an increase in fluorescence intensity, which provides a readout of its turnover. We demonstrate how this can be used for monitoring cellular processes involving Ap4 hydrolysis. To this end, we visualized the enzymatic activity in live cells using confocal fluorescence microscopy of the Ap4 analog. Our results demonstrate that the Ap4 analog is hydrolyzed in lysosomes. We show that this approach is suited to visualize the lysosome distribution profiles within the live cell and discuss how it can be employed to gather information regarding autophagic flux.     

Axiomatizing the Logical Core of XPath 2.0

The first aim of this paper is to present the logical core of XPath 2.0: a logically clean, decidable fragment, which includes most navigational features of XPath 2.0 (complex counting conditions and data joins are not supported, as they lead to undecidability). The second aim is to provide a list of equations completely axiomatizing query equivalence in this language (i.e., all other query equivalences can be derived from these). A preliminary version of this paper was published in the proceedings of ICDT 2007. We would like to thank Jan Hidders for pointing us to the interesting question of stronger forms of completeness (cf. Sect. 4.3). We would also like to thank the anonymous reviewers for their extensive comments, which have greatly improved the quality of the paper. The first author is supported by NWO grant 639.021.508.