Protein solubility is a problem for many protein chemists, including structural biologists and developers of protein pharmaceuticals. Knowledge about how intrinsic factors influence solubility is limited due to the difficulty of obtaining quantitative solubility measurements. Solubility measurements in buffer alone are difficult to reproduce, because gels or supersaturated solutions often form, making it impossible to determine solubility values for many proteins. Protein precipitants can be used to obtain comparative solubility measurements and, in some cases, estimations of solubility in buffer alone. Protein precipitants fall into three broad classes: salts, long-chain polymers, and organic solvents. Here, we compare the use of representatives from two classes of precipitants, ammonium sulfate and polyethylene glycol 8000, by measuring the solubility of seven proteins. We find that increased negative surface charge correlates strongly with increased protein solubility and may be due to strong binding of water by the acidic amino acids. We also find that the solubility results obtained for the two different precipitants agree closely with each other, suggesting that the two precipitants probe similar properties that are relevant to solubility in buffer alone.

Hydrogen sulfide (H2S) has emerged as an important gaseous signaling molecule that is produced endogenously by enzymes in the sulfur metabolic network. H2S exerts its effects on multiple physiological processes important under both normal and pathological conditions. These functions include neuromodulation, regulation of blood pressure and cardiac function, inflammation, cellular energetics and apoptosis. Despite the recognition of its biological importance and its beneficial effects, the mechanism of H2S action and the regulation of its tissue levels remain unclear in part owing to its chemical and physical properties that render handling and analysis challenging. Furthermore, the multitude of potential H2S effects has made it difficult to dissect its signaling mechanism and to identify specific targets. In this review, we focus on H2S metabolism and provide an overview of the recent literature that sheds some light on its mechanism of action in cellular redox signaling in health and disease. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.

ǂ These authors contributed equally to this work Rhodanese domains are structural modules present in the sulfurtransferase superfamily. These domains can exist as single units, in tandem repeats or fused to domains with other activities. Despite their prevalence across species, the specific physiological roles of most sulfurtransferases are not known. Mammalian rhodanese and mercaptopyruvate sulfurtransferase are perhaps the best-studied members of this protein superfamily and are involved in hydrogen sulfide metabolism. The relatively unstudied human thiosulfate sulfurtransferase like domain-containing 1 (TSTD1) protein, a single-domain cytoplasmic sulfurtransferase, was also postulated to play a role in the sulfide oxidation pathway using thiosulfate to form glutathione persulfide, for subsequent processing in the mitochondrial matrix. Prior kinetic analysis of TSTD1 was performed at pH 9.2, raising questions about relevance and the proposed model for TSTD1 function. In this study, we report a 1.04 Å resolution crystal structure of human TSTD1, which displays an exposed active site that is distinct from that of rhodanese and mercaptopyruvate sulfurtransferase. Kinetic studies with a combination of sulfur donors and acceptors reveal that TSTD1 exhibits a low K M for thioredoxin as a sulfane sulfur acceptor and that it utilizes thiosulfate inefficiently as a sulfur donor. The active site exposure and its interaction with thioredoxin, suggest that TSTD1 might play a role in sulfide-based signaling. The apical localization of TSTD1 in human colonic crypts, which interfaces with sulfide-releasing microbes, and the overexpression of TSTD1 in colon cancer, provides potentially intriguing clues as to its role in sulfide metabolism. Hydrogen sulfide (H 2 S)1 is an important signaling molecule with effects on multiple physiological processes including neuromodulation, inflammation and cardiac function (1-7). Maintaining healthy levels of H 2 S in mammalian cells requires tight control of its biosynthesis and its catabolism (8,9). H 2 S is produced endogenously by two enzymes in the transsulfuration pathway, cystathionine β-synthase and γ-cystathionase as well as by mercaptopyruvate sulfurtransferase (MST) (10-13). H 2 S is oxidized via the sulfide oxidation pathway to generate the end-products thiosulfate Protein persulfidation, a posttranslational modification of cysteine residues, is postulated to be a major mechanism by which H 2 S signals (17). However, the mechanism by which target proteins acquire this modification and the sulfur source(s) used in persulfidation reactions are unclear (18). Sulfurtransferases like rhodanese or the single rhodanese domain containing TSTD1 could potentially play a role in protein persulfidation because of their capacity to form an active site cysteine persulfide during their reaction cycle (18).The rhodanese superfamily members are distinguished by a structural module with an α/β topology in which α-helices surround a central five-stranded β-sheet core (19). At least three variations...

Hydrogen sulfide (HS) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts HS to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.

H2S is produced from sulfur-containing amino acids, cysteine and homocysteine, or a catabolite, 3-mercaptopyruvate, by three known enzymes: cystathionine β-synthase, γ-cystathionase, and 3-mercaptopyruvate sulfurtransferase. Of these, the first two enzymes reside in the cytoplasm and comprise the transsulfuration pathway, while the third enzyme is found both in the cytoplasm and in the mitochondrion. The following mitochondrial enzymes oxidize H2S: sulfide quinone oxidoreductase, sulfur dioxygenase, rhodanese, and sulfite oxidase. The products of the sulfide oxidation pathway are thiosulfate and sulfate. Assays for enzymes involved in the production and oxidative clearance of sulfide to thiosulfate are described in this chapter.

Superoxide generated by human NADPH oxidase 5 (NOX5) is of growing importance for various physiological and pathological processes. The activity of NOX5 appears to be regulated by a self-contained Ca2+ binding domain (CaBD). Recently Bánfi et al. suggest that the conformational change of CaBD upon Ca2+ binding is essential for domain-domain interaction and superoxide production. The authors studied its structural change using intrinsic Trp fluorescence and hydrophobic dye binding; however, their conformational study was not thorough and the kinetics of metal binding was not demonstrated. Here we generated the recombinant CaBD and an E99Q/E143Q mutant to characterize them using fluorescence spectroscopy. Ca2+ binding to CaBD induces a conformational change that exposes hydrophobic patches and increases the quenching accessibilities of its Trp residues and AEDANS at Cys107. The circular dichroism spectra indicated no significant changes in the secondary structures of CaBD upon metal binding. Stopped-flow spectrometry revealed a fast Ca2+ dissociation from the N-terminal half, followed by a slow Ca2+ dissociation from the C-terminal half. Combined with a chemical stability study, we concluded that the C-terminal half of CaBD has a higher Ca2+ binding affinity, a higher chemical stability, and a slow Ca2+ dissociation. The Mg2+-bound CaBD was also investigated and the results indicate that its structure is similar to the apo form. The rate of Mg2+ dissociation was close to that of Ca2+ dissociation. Our data suggest that the N- and C-terminal halves of CaBD are not completely structurally independent.

Hydrogen sulfide (H 2 S) is a signaling molecule with many beneficial effects. However, its cellular concentration is strictly regulated to avoid toxicity. Persulfide dioxygenase (PDO or ETHE1) is a mononuclear non-heme ironcontaining protein in the sulfide oxidation pathway catalyzing the conversion of glutathione persulfide (GSSH) to sulfite and glutathione. PDO mutations result in the autosomal recessive disorder, ethylmalonic encephalopathy (EE). Here, we developed γ-glutamyl-homocysteinyl-glycine (GHcySH) in which the cysteinyl moiety in glutathione is substituted with homocysteine, as a mechanismbased PDO inhibitor. Human PDO used GHcySH as an alternate substrate and converted it to GHcy-SO 2 H, mimicking GS-SO 2 H, the putative oxygenated intermediate formed with the natural substrate. Since GHcy-SO 2 H contains a C-S bond rather than an S-S bond in GS-SO 2 H, it failed to undergo the final hydrolysis step in the catalytic cycle, leading to PDO inhibition. We also characterized the biochemical penalties incurred by the L55P, T136A, C161Y and R163W mutations reported in EE patients. The variants displayed lower iron content (1.4-to 11-fold) and lower thermal stability (1.2-to 1.7-fold) than wild-type PDO. They also exhibited varying degrees of catalytic impairment; the k cat /K m values for R163W, L55P and C161Y PDOs were 18-, 42-and 65-fold lower, respectively and the T136A variant was most affected with a 200-fold lower k cat /K m . Like wild-type enzyme, these variants were inhibited by GHcySH. This study provides the first characterization of an intermediate in the PDO-catalyzed reaction and reports on deficits associated with EE-linked mutations that are distal from the active site.Ethylmalonic encephalopathy (EE) 1 is an autosomal recessive disorder that is associated with pathological effects in the brain, gastrointestinal tract and peripheral vessels (1-3). It results in acrocyanosis, petechiae, hemorrhagic diarrhea, developmental delay and progressive neurological failure leading to necrotic lesions in the deep gray matter of the brain. Patients with EE usually succumb to the disease within the first decade of life (4). The clinical profile of EE includes elevated ethylmalonic acid in urine, C4 and C5 acrylcarnitines in blood and a deficiency of cytochrome c oxidase in brain and muscle (5). EE is caused by mutations in the ethe1 gene that encodes persulfide dioxygenase (PDO or ETHE1). Over 20 mutations have been described in the ethe1 gene, of which a subset represents missense mutations (3,4,6).PDO is a mitochondrial matrix protein that participates in the mitochondrial sulfide oxidation pathway, which converts H 2 S to the end products, thiosulfate and sulfate (7,8). In addition to PDO, the other enzymes involved in the mitochondrial sulfur oxidation pathway are sulfide quinone oxidoreductase (9), rhodanese (10), and sulfite oxidase (11). PDO catalyzes the second step in the pathway, i.e. the oxidation of glutathione persulfide (GSSH) to sulfite (Eq. 1) (12). Sulfite is either oxidized b...

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