A ubiquitous class of non-heme Fe(II) enzymes, the persulfide dioxygenases (PDOs), provide protection against hydrogen sulfide (H2S) poisoning. The PDO in humans is a single-domain enzyme, while bacterial PDOs, such as CstB of Staphylococcus aureus, are often fused to a sulfurtransferase (rhodanese) module. Canonical PDOs cleave the S-S bond of glutathione persulfide (GSSH) to produce GSH and sulfite (SO3 2-). In contrast, CstB, via an unknown mechanism, converts two RSSH to thiosulfate (S2O3 2-) without the release of sulfite. Six crystallographic structures of S. aureus CstB reveal that a Cys-Gly sequence (C201-G202) in a CstB-unique dynamic loop functions as a glutathione mimic, occupying one face of the hemifacial octahedral Fe(II) coordination site. We establish that CstB self-S-sulfonates C201 in a thiol persulfide, Fe(II) and O2-dependent manner, which is then shuttled to a persulfidated C408 in the rhodanese domain ≈27 Å away via electrostatic steering to generate thiosulfate as the sole oxidation product. Both C201A and C408A CstBs are inactive in O2-consumption. Self-S-sulfonation ensures rapid clearance of diverse reactive sulfur species under conditions where these species accumulate, permitting S. aureus to harness their cytoprotective effects while avoiding cellular toxicity.

The emergence of drug-resistant strains exacerbates the global challenge of tuberculosis caused by Mycobacterium tuberculosis (Mtb). Central to the pathogenicity of Mtb is its complex cell envelope, which serves as a barrier against both immune system and pharmacological attacks. Two key components of this envelope, arabinogalactan (AG) and lipoarabinomannan (LAM) are complex polysaccharides that contain integral arabinan domains important for cell wall structural and functional integrity. The arabinofuranosyltransferase AftB terminates the synthesis of these arabinan domains by catalyzing the addition of the addition of β-(1→2)-linked terminal arabinofuranose residues. Here, we present the cryo-EM structures of Mycobacterium chubuense AftB in its apo and donor substrate analog-bound form, determined to 2.9 Å and 3.4 Å resolution, respectively. Our structures reveal that AftB has a GT-C fold transmembrane (TM) domain comprised of eleven TM helices and a periplasmic cap domain. AftB has an irregular tube-shaped cavity that bridges the two proposed substrate binding sites. By integrating structural analysis, biochemical assays, and molecular dynamics simulations, we elucidate the molecular basis of the reaction mechanism of AftB and propose a model for catalysis.

Proteins are inherently unstable, which limits their use as therapeutic agents. However, the use of biocompatible cosolvents or surfactants can help to circumvent this problem through the stabilization of intramolecular and solvent-mediated interactions. Ionic liquids (ILs) have been known to act as cosolvents or surface-active compounds. In the presence of proteins, ILs can have a beneficial effect on their refolding, shelf life, stability, and enzymatic activities. In the work described herein, we used small-angle X-ray scattering (SAXS) to monitor the aggregation of different concentrations of ILs with protein models, lysozyme (Lys) and bovine serum albumin (BSA), and fluorescence microscopy to assess micelle formation of fluorinated ILs (FILs) with Lys. Furthermore, coarse-grained molecular dynamics (CG-MD) simulations provided a better understanding of Lys–FIL interactions. The results showed that the proteins maintain their globular structures in the presence of FILs, with signs of partial unfolding for Lys and compaction for BSA with increased flexibility at higher FIL concentrations. Lys was encapsulated by FIL, thus reinforcing the potential of ILs to be used in the formulation of protein-based pharmaceuticals.

The development of therapeutics against Zika virus (ZIKV) requires the design of molecules capable of neutralising the virus and preventing cell infection.

Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.

The marine cyanobacterium Prochlorococcus is one of the main primary producers on Earth, which can take up glucose by using the high affinity, multiphasic transporter GlcH. We report here the overexpression of glcH from Prochlorococcus marinus strain SS120 in Escherichia coli. Modeling studies of GlcH using the homologous MelB melibiose transporter from Salmonella enterica serovar Typhimurium showed high conservation at the overall fold. We observed that an important structural interaction, mediated by a strong hydrogen bond between D8 and R141, is conserved in Prochlorococcus, although the corresponding amino acids in MelB from Salmonella are different. Biased docking studies suggested that when glucose reaches the pocket of the transporter and interacts with D8 and R141, the hydrogen bond network in which these residues are involved could be disrupted, favoring a conformational change with the subsequent translocation of the glucose molecule towards the cytoplasmic region of the pmGlcH structure. Based on these theoretical predictions and on the conservation of N117 and W348 in other MelB structures, D8, N117, R141 and W348 were mutated to glycine residues. Their key role in glucose transport was evaluated by glucose uptake assays. N117G and W348G mutations led to 17 % decrease in glucose uptake, while D8G and R141G decreased the glucose transport by 66 % and 92 % respectively. Overall, our studies provide insights into the Prochlorococcus 3D-structure of GlcH, paving the way for further analysis to understand the features which are involved in the high affinity and multiphasic kinetics of this transporter.

Mycobacterium tuberculosis remains the leading cause of mortality from a single infectious organism, infecting nearly one-third of the global population. The current emergence of multidrug-resistant strains represents a serious health problem nowadays. Moreover, regulation of gene expression through RNA metabolism is a key mechanism for bacterial growth, division and rapid accommodation to environmental conditions. Ribonucleases are enzymes present in all living organisms that play an important role in RNA processing and degradation. Particularly, ribonucleases belonging to the RNB-family are often essential for viability of prokaryotes and are implicated in the establishment of virulence of several pathogens. In the present study we aim to structurally and functionally characterize two putative exoribonucleases from the RNB-family of enzymes inM. tuberculosis. Overexpression and purification of the proteins was performed and further in vitro activity, binding and helicase assays using synthetic RNA substrates were accomplished. In parallel, a biophysical characterization proceeded with several crystallization trials and protein stability tests. We have demonstrated that both RNases are 3’-5’ exoribonucleases with different degradation properties and unravelled the importance of highly conserved residues for catalysis. Moreover, we were able to identify improved buffer formulations that increase protein stability, possibly enhancing their propensity to crystallize. The information regarding RNA metabolism in M. tuberculosis is limited and RNB-family enzymes have not been previously characterized in this important human pathogen. Thus, a complete knowledge of these ribonucleases is an approach to recognize their influence in M. tuberculosis metabolism and to better understand the post-transcriptional control in this pathogen.

Phenylketonuria (PKU) is an autosomal recessive disease caused by deficient activity of human phenylalanine hydroxylase (hPAH), which can lead to neurologic impairments in untreated patients. Although some therapies are already available for PKU, these are not without drawbacks. Enzyme-replacement therapy through the delivery of functional hPAH could be a promising strategy. In this work, biophysical methods were used to evaluate the potential of [N-1112(OH)][C4F9SO3], a biocompatible fluorinated ionic liquid (FIL), as a delivery system of hPAH. The results herein presented show that [N-1112(OH)][C4F9SO3] spontaneously forms micelles in a solution that can encapsulate hPAH. This FIL has no significant effect on the secondary structure of hPAH and is able to increase its enzymatic activity, despite the negative impact on protein thermostability. The influence of [N-1112(OH)][C4F9SO3] on the complex oligomerization equilibrium of hPAH was also assessed.

Studies on membrane proteins can help to develop new drug targets and treatments for a variety of diseases. However, membrane proteins continue to be among the most challenging targets in structural biology. This uphill endeavor can be even harder for membrane proteins from Mycobacterium species, which are notoriously difficult to express in heterologous systems. Arabinofuranosyltransferases are involved in mycobacterial cell wall synthesis and thus potential targets for antituberculosis drugs. A set of 96 mycobacterial genes coding for Arabinofuranosyltransferases was selected, of which 17 were successfully expressed in E. coli and purified by metal-affinity chromatography. We herein present an efficient high-throughput strategy to screen in microplates a large number of targets from Mycobacteria and select the best conditions for large-scale protein production to pursue functional and structural studies. This methodology can be applied to other targets, is cost and time effective and can be implemented in common laboratories.

An investigation of the pathologic events occurring during experimental Strongyloides ratti infection in rats was done. The chronologic sequence of the cellular responses to the infecting larvae as they migrated through the skin and lungs was determined. Larvae penetrate the skin very quickly, eliciting considerable mast cell degranulation within the first few minutes, a modest neutrophil response within the first few hours, and an occasional mononuclear response within the first 2 days. The larval passage in the lungs appears to cause little damage except for microhemorrhages and an occasional microabscess. In the intestine S ratti adult worms lie in the cryptae without penetrating mucosa, and except for an increase in the number of mast cells at the time of expulsion (Days 20--25), there is no detectable cellular response. Differences from the human disease are discussed.

The unique physicochemical properties of Ionic liquids (ILs) make them very desirable for biomedical applications, namely as surface active ionic liquids (SAILs). SAILs surface activity, intrinsically higher than conventional surfactants, allows them to enhance drug permeability across biomembranes and, thus, become better drug carriers than current solutions. To harvest the full potential of these materials, in-depth studies of ILs interactions with model proteins are necessary to understand the mechanisms controlling these biological processes. Albumin, a key protein of blood serum, is of particular relevance, namely in drug carrier applications. Thus, here we characterize the interaction of bovine serum albumin (BSA) with fluorinated ionic liquids which are SAILs that possess fluorous tags equal to or longer than four carbon atoms. Their impact on BSA stability and structure was evaluated using different biophysical techniques. Differential scanning fluorimetry (DSF) and calorimetry (DSC), as well as circular dichroism (CD), yielded insights on the stabilization and secondary structure of BSA upon incubation with the ILs. Binding dynamics of the interaction were studied by conductimetry and isothermal titration calorimetry (ITC), which give the values of critical aggregation concentration (CAC) of the BSA-IL complex formation, as well as thermodynamic parameters. The results presented herein support the hypothesis that BSA is stabilized and encapsulated in the presence of FILs. Thus, the FILs studied in this work have potential for uses in biomedical applications.

Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides—arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.

3-Oxo-β-sultams are four-membered ring ambident electrophiles that can react with nucleophiles either at the carbonyl carbon or at the sulfonyl sulfur atoms, and that have been reported to inhibit serine hydrolases via acylation of the active-site serine residue. We have developed a panel of 3-oxo-β-sultam inhibitors and show, through crystallographic data, that they are regioselective sulfonylating electrophiles, covalently binding to the catalytic serine of human and porcine elastases through the sulfur atom. Application of 3-oxo-β-sultam-derived activity-based probes in a human proteome revealed their potential to label disease-related serine hydrolases and proteasome subunits. Activity-based protein profiling applications of 3-oxo-β-sultams should open up new opportunities to investigate these classes of enzymes in complex proteomes and expand the toolbox of available sulfur-based covalent protein modifiers in chemical biology.

X-ray crystallography is one of the most commonly used techniques to characterize the three-dimensional (3D) structure of biological macromolecules. A critical step in the process of 3D structure determination of macromolecules by X-ray crystallography is the production of well-ordered, diffraction quality crystals. Other techniques do not present this limitation but rather study the biomolecules in solution, such as single-particle cryo-electron microscopy and small-angle X-ray scattering. We aim to provide graduate students or researchers working with metalloproteins with an overview on some of the methodologies available for the determination of the 3D structure of proteins, and what information can be extracted from these models.

Streptococcus pneumoniae is a frequent bacterial pathogen of the human respiratory tract causing pneumonia, meningitis and sepsis, a serious healthcare burden in all age groups. S. pneumoniae lacks complete respiratory chain and relies on carbohydrate fermentation for energy generation. One of the essential components for this includes the mannose phosphotransferase system (Man-PTS), which plays a central role in glucose transport and exhibits a broad specificity for a range of hexoses. Importantly, Man-PTS is involved in the global regulation of gene expression for virulence determinants. We herein report the three-dimensional structure of the EIIA domain of S. pneumoniae mannose phosphotransferase system (SpEIIA-Man). Our structure shows a dimeric arrangement of EIIA and reveals a detailed molecular description of the active site. Since PTS transporters are exclusively present in microbes and sugar transporters have already been suggested as valid targets for antistreptococcal antibiotics, our work sets foundation for the future development of antimicrobial strategies against Streptococcus pneumoniae.

Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding.

The AceTr transporter family is a group of Acetate Transporters with six predicted transmembrane segments. It has homologues in fungi, bacteria, archaea and protozoa. As acetate transporters, these proteins play a crucial role on cell metabolism being involved in the capacity of cells to adapt to nutrient availability. As these membrane transporters also transport other substrates, they may be an important asset for biotechnological purposes. To better understand the mechanism of acetate transport, we have investigated functional and structural features of the AceTr family. We have performed site-directed mutagenesis in residues highly conserved, or possibly involved in substrate binding, from the Saccharomyces cerevisiae Ady2. Functional assays determined the influence of these residues on the transport capacity and protein localization. Another goal of this work is to determine the structure of the AceTr family. Accordingly, several of its members were cloned in different expression vectors and their expression was evaluated in different E. coli expression strains. SatP from E. coli and its AceP from Methanosarcina acetivorans presented satisfactory levels of protein production and are currently being tested in production, purification and crystallization trials.

Tuberculosis has been, and still is, a huge health problem for the world, being the 9th most deadly disease in the world, responsible for 1.3 million deaths in 2015. With the rise of fully drug resistant variants of Mycobacterium tuberculosis, the causative agent for tuberculosis, there is a real need to seek out new drug targets against M. tuberculosis. The M. tuberculosis cell wall is a common target for many existing antibiotics, and it is unique in structure because of the presence of additional lipid-sugar moieties, arabinogalactans and lipoarabinomannoses, which are essential for mycobacterium survival and virulence. Membrane-bound glycosyltransferases build these essential lipid-sugar moieties. Here, we present the full-length membrane-bound structure of a mycobacterial glycosyltransferase solved to 3.3 Å resolution using single-particle cryo-electron microscopy. The structure provides insights into the catalytic activity and sugar binding capability of these proteins, and serves as a tool for future structure-based drug design efforts.