MISTRAL: a transmission soft X‐ray microscopy beamline for cryo nano‐tomography of biological samples and magnetic domains imaging

The performance of MISTRAL is reported, the soft X‐ray transmission microscopy beamline at the ALBA light source (Barcelona, Spain) which is primarily dedicated to cryo soft X‐ray tomography (cryo‐SXT) for three‐dimensional visualization of whole unstained cells at spatial resolutions down to 30 nm (half pitch). Short acquisition times allowing for high‐throughput and correlative microscopy studies have promoted cryo‐SXT as an emerging cellular imaging tool for structural cell biologists bridging the gap between optical and electron microscopy. In addition, the beamline offers the possibility of imaging magnetic domains in thin magnetic films that are illustrated here with an example.     

Predicting substrates by docking high-energy intermediates to enzyme structures

With the emergence of sequences and even structures for proteins of unknown function, structure-based prediction of enzyme activity has become a pragmatic as well as an interesting question. Here we investigate a method to predict substrates for enzymes of known structure by docking high-energy intermediate forms of the potential substrates. A database of such high-energy transition-state analogues was created from the KEGG metabolites. To reduce the number of possible reactions to consider, we restricted ourselves to enzymes of the amidohydrolase superfamily. We docked each metabolite into seven different amidohydrolases in both the ground-state and the high-energy intermediate forms. Docking the high-energy intermediates improved the discrimination between decoys and substrates significantly over the corresponding standard ground-state database, both by enrichment of the true substrates and by geometric fidelity. To test this method prospectively, we attempted to predict the enantioselectivity of a set of chiral substrates for phosphotriesterase, for both wild-type and mutant forms of this enzyme. The stereoselectivity ratios of the six enzymes considered for those four substrate enantiomer pairs differed over a range of 10- to 10,000-fold and underwent 20 switches in stereoselectivities for favored enantiomers, compared to the wild type. The docking of the high-energy intermediates correctly predicted the stereoselectivities for 18 of the 20 substrate/enzyme combinations when compared to subsequent experimental synthesis and testing. The possible applications of this approach to other enzymes are considered.     

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from 12 unique complexes whose ligands vary in size and flexibility. For all testcases, at least one docked position is generated within 2 Å of the crystallographic position. For 7 of 15 testcases, the top scoring position is also within 2 Å of the crystallographic position. The algorithm is fast enough to successfully dock a few testcases within seconds and most within 100 s. The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases. Incremental construction outperforms random search and is fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.     

Methylglyoxal synthetase,enol-pyruvaldehyde,glutathione and the glyoxalase system

enol-Pyruvaldehyde (ePY or 2-hydroxypropenal, O=C(H)-C(OH)=CH(2)) a transient intermediate in the alkaline decomposition of the triosephosphates to methylglyoxal is now observed by UV and (1)H NMR spectroscopy as the immediate product of the methylglyoxal synthetase (MGS) reaction: dihydroxyacetone-P --> P(i) + ePY --> methylglyoxal (MG). Analysis of ePY formed from 1-(13)C- and (1R, 3S) -[1,3-(2)H]-DHAP establishes the stereochemical course of its formation by MGS. Its rate of ketonization is much too slow to be in the sequence required for the assay of MGS by coupling of the MG produced to glyoxalase I (Glx I): MG + glutathione (GSH) --> (S)-lactylglutathione (D-LG). Instead, ketonization occurs by way of the hemithioacetal (HTA) formed between ePY and GSH, and could be either an enzymatic function of Glx I or occur nonenzymatically at an activated rate. Enzymatic ketonization was ruled out because the methyl group of D-LG formed from specifically labeled ePY is achiral. Chemical ketonization of ePY is activated by general bases, such as acetate, and by thiols such as GSH and 2-mercaptoethanol, which disrupt its stabilizing double bond conjugation as hemithioacetal (HTA) adducts. 2-Mercaptoacetate combines both functions, acting as the HTA adduct of ePY with the appended carboxylate group presumably positioned to promote abstraction of the enol proton and protonation of the enolate carbon at an accelerated rate. In the MGS-Glx I system (dihydroxyacetone-P --> ePY, ePY + GSH --> GS-ePY, GS-ePY --> GS-MG, GS-MG --> D-LG), the nonenzymatic 2nd and 3rd steps describe the catalytic role of GSH in the critical ketonization process and set the stage for its participation in the glyoxalase system.     

Production of O2- in photolyzed water demonstrated through the use of superoxide dismutase

Abstract— The photolysis of water has been studied using ferricytochrome c as the detector of reducing radicals and ferrocytochrome c as the detector of oxidizing radicals. Mannitol was used as a scavenger of hydroxyl radicals and superoxide dismutase was used to expose the specific involvement of superoxide radicals. Aerobic photolysis caused a reduction of ferricytochrome c, which was inhibited by superoxide dismutase and was enhanced by mannitol. Aerobic photolysis also caused the oxidation of ferrocytochrome c, which was inhibited by mannitol and augmented by superoxide dismutase. The presence of superoxide dismutase also eliminated the effects of mannitol on the aerobic oxidation of ferrocytochrome c. Photolysis in the absence of oxygen also caused the reduction of ferricytochrome c and the oxidation of ferrocytochrome c, but under these anaerobic conditions neither mannitol nor superoxide dismutase exerted significant effects. An explanation of these observations is offered in terms of the reactivities of H^., OH^. and O^-2 radicals.