Homologous gene recombination is crucial for the repair of DNA. A superfamily of recombinases facilitate a central strand exchange reaction in the repair process. This reaction is initiated by coating single-stranded DNA (ssDNA) with recombinases in the presence of ATP and Mg 2؉ co-factors to form helical nucleoprotein filaments with elevated ATPase and strand invasion activities (1). At the amino acid sequence level, archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA (2). Unlike the extensively studied Escherichia coli RecA (EcRecA), increasing evidences on yeast and human recombinases imply that their optimal activities are dependent on the presence of a monovalent cation, particularly potassium (3-5). Here we present the finding that archaeal RadA from Methanococcus voltae (MvRadA) is a stringent potassiumdependent ATPase, and the crystal structure of this protein in complex with the non-hydrolyzable ATP analog adenosine 5-(␤,␥-iminotriphosphate), Mg 2؉ , and K ؉ at 2.4 Å resolution. Potassium triggered an in situ conformational change in the ssDNA-binding L2 region concerted with incorporation of two potassium ions at the ATPase site in the RadA crystals preformed in K ؉ -free medium. Both potassium ions were observed in contact with the ␥-phosphate of the ATP analog, implying a direct role by the monovalent cations in stimulating the ATPase activity. Cross-talk between the ATPase site and the ssDNA-binding L2 region visualized in the MvRadA structure provides an explanation to the co-factor-induced allosteric effect on RecA-like recombinases.

Homologous recombination of DNA plays crucial roles in repairing severe DNA damage and in generating genetic diversity. The process is facilitated by a superfamily of recombinases: bacterial RecA, archaeal RadA and Rad51, and eukaryal Rad51 and DMC1. These recombinases share a common ATP-dependent filamentous quaternary structure for binding DNA and facilitating strand exchange. We have determined the crystal structure of Methanococcus voltae RadA in complex with the ATP analog AMP-PNP at 2.0 A resolution. The RadA filament is a 106.7 A pitch helix with six subunits per turn. The DNA binding loops L1 and L2 are located in close proximity to the filament axis. The ATP analog is buried between two RadA subunits, a feature similar to that of the active filament of Escherichia coli RecA revealed by electron microscopy. The disposition of the N-terminal domain suggests a role of the Helix-hairpin-Helix motif in binding double-stranded DNA.

Cathepsin B (CTB) is a cysteine protease believed to be an important therapeutic target or biomarker for several diseases including aggressive cancer, arthritis, and parasitic infections. The development of probes capable of assessing CTB activity in cell lysates, living cells, and animal models of disease are needed to understand its role in disease progression. However, discovering probes selective to cathepsin B over other cysteine cathepsins is a significant challenge due to overlap of preferred substrates and binding site homology in this family of proteases. Herein we report the synthesis and detailed evaluation of two prodrug-inspired fluorogenic peptides designed to be efficient and selective substrate-based probes for CTB. Through cell lysate and cell assays, a promising lead candidate was identified that is efficiently processed and has high specificity for CTB over other cysteine cathepsins. This work represents a key step toward the design of rapid release prodrugs or substrate-based molecular imaging probes specific to CTB.

TFM (L-trifluoromethionine), a potential prodrug, was reported to be toxic towards human pathogens that express MGL (L-methionine γ-lyase; EC 4.4.1.11), a pyridoxal phosphate-containing enzyme that converts L-methionine into α-oxobutyrate, ammonia and methyl mercaptan. It has been hypothesized that the extremely reactive thiocarbonyl difluoride is produced when the enzyme acts upon TFM, resulting in cellular toxicity. The potential application of the fluorinated thiomethyl group in other areas of biochemistry and medicinal chemistry requires additional studies. Therefore a detailed investigation of the theoretical and experimental chemistry and biochemistry of these fluorinated groups (CF₃S⁻ and CF₂HS⁻) has been undertaken to trap and identify chemical intermediates produced by enzyme processing of molecules containing these fluorinated moieties. TvMGL (MGL from Trichomonas vaginalis) and a chemical model system of the reaction were utilized in order to investigate the cofactor-dependent activation of TFM and previously uninvestigated DFM (L-difluoromethionine). The differences in toxicity between TFM and DFM were evaluated against Escherichia coli expressing TvMGL1, as well as the intact human pathogen T. vaginalis. The relationship between the chemical structure of the reactive intermediates produced from the enzymatic processing of these analogues and their cellular toxicity are discussed.

Trichomonas vaginalis and Entamoeba histolytica are clinically important protozoa that affect humans. T. vaginalis produces sexually transmitted infections and E. histolytica is the causative agent of amebic dysentery. Metronidazole, a compound first used to treat T. vaginalis in 1959, is still the main drug used worldwide to treat these pathogens. It is essential to find new biochemical differences in these organisms that could be exploited to develop new antiprotozoal chemotherapeutics. Recent findings associated with T. vaginalis and E. histolytica biochemistry and host-pathogen interactions are surveyed. Knowledge concerning the biochemistry of these parasites is serving to form the foundation for the development of new approaches to control these important human pathogens.