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Ultraviolet C (UVC) light has long been used as a sterilizing agent, primarily through devices that emit at 254 nm. Depending on the dose and duration of exposure, UV 254 nm can cause erythema and photokeratitis and potentially cause skin cancer since it directly modifies nitrogenated nucleic acid bases. Filtered KrCl excimer lamps (emitting mainly at 222 nm) have emerged as safer germicidal tools and have even been proposed as devices to sterilize surgical wounds. All the studies that showed the safety of 222 nm analyzed cell number and viability, erythema generation, epidermal thickening, the formation of genetic lesions such as cyclobutane pyrimidine dimers (CPDs) and pyrimidine-(6-4)-pyrimidone photoproducts (6-4PPs) and cancer-inducing potential. Although nucleic acids can absorb and be modified by both UV 254 nm and UV 222 nm equally, compared to UV 254 nm, UV 222 nm is more intensely absorbed by proteins (especially aromatic side chains), causing photooxidation and cross-linking. Here, in addition to analyzing DNA lesion formation, for the first time, we evaluated changes in the proteome and cellular pathways, reactive oxygen species formation, and metalloproteinase (MMP) levels and activity in full-thicknessin vitroreconstructed human skin (RHS) exposed to UV 222 nm. We also performed the longest (40 days)in vivostudy of UV 222 nm exposure in the HRS/J mouse model at the occupational threshold limit value (TLV) for indirect exposure (25 mJ/cm2) and evaluated overall skin morphology, cellular pathological alterations, CPD and 6-4PP formation and MMP-9 activity. Our study showed that processes related to reactive oxygen species and inflammatory responses were more altered by UV 254 nm than by UV 222 nm. Our chronicin vivoexposure assay using the TLV confirmed that UV 222 nm causes minor damage to the skin. However, alterations in pathways related to skin regeneration raise concerns about direct exposure to UV 222 nm.

Ultraviolet (UV) light can inactivate SARS-CoV-2. However, the practicality of UV light is limited by the carcinogenic potential of mercury vapor-based UV lamps. Recent advances in the development of krypton chlorine (KrCl) excimer lamps hold promise, as these emit a shorter peak wavelength (222 nm), which is highly absorbed by the skin's stratum corneum and can filter out higher wavelengths. In this sense, UV 222 nm irradiation for the inactivation of virus particles in the air and surfaces is a potentially safer option as a germicidal technology. However, these same physical properties make it harder to reach microbes present in complex solutions, such as saliva, a critical source of SARS-CoV-2 transmission. We provide the first evaluation for using a commercial filtered KrCl excimer light source to inactivate SARS-CoV-2 in saliva spread on a surface. A conventional germicidal lamp (UV 254 nm) was also evaluated under the same condition. Using plaque-forming units (PFU) and Median Tissue Culture Infectious Dose (TCID

Many types of cancers have a well-established dependence on glutamine metabolism to support survival and growth, a process linked to glutaminase 1 (GLS) isoforms. Conversely, GLS2 variants often have tumor-suppressing activity. Triple-negative (TN) breast cancer (testing negative for estrogen, progesterone, and Her2 receptors) has elevated GLS protein levels and reportedly depends on exogenous glutamine and GLS activity for survival. Despite having high GLS levels, we verified that several breast cancer cells (including TN cells) express endogenous GLS2, defying its role as a bona fide tumor suppressor. Moreover, ectopic GLS2 expression rescued cell proliferation, TCA anaplerosis, redox balance, and mitochondrial function after GLS inhibition by the small molecule currently in clinical trials CB-839 or GLS knockdown of GLS-dependent cell lines. In several cell lines, GLS2 knockdown decreased cell proliferation and glutamine-linked metabolic phenotypes. Strikingly, long-term treatment of TN cells with another GLS-exclusive inhibitor bis-2'-(5-phenylacetamide-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES) selected for a drug-resistant population with increased endogenous GLS2 and restored proliferative capacity. GLS2 was linked to enhanced in vitro cell migration and invasion, mesenchymal markers (through the ERK-ZEB1-vimentin axis under certain conditions) and in vivo lung metastasis. Of concern, GLS2 amplification or overexpression is linked to an overall, disease-free and distant metastasis-free worse survival prognosis in breast cancer. Altogether, these data establish an unforeseen role of GLS2 in sustaining tumor proliferation and underlying metastasis in breast cancer and provide an initial framework for exploring GLS2 as a novel therapeutic target.

Simple Summary The atomic structure of a biological macromolecule determines its function. Discovering how one or more amino acid chains fold and interact to form a protein complex is critical, from understanding the most fundamental cellular processes to developing new therapies. However, this is far from a straightforward task, especially when studying a membrane protein. The functional link between the oligomeric state and complex composition of the proteins involved in the active mitochondrial transport of cytosolic pyruvate is a decades-old question but remains urgent. We present a brief historical review beginning with the identification of the so-called mitochondrial pyruvate carrier (MPC) proteins, followed by a rigorous conceptual analysis of technical approaches in more recent biochemical studies that seek to isolate and reconstitute the functional MPC complex(es) in vitro. We correlate these studies with early kinetic observations and current experimental and computational knowledge to assess their main contributions, identify gaps, resolve ambiguities, and better define the research goal. Abstract The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an unexpected interplay between one, two, or even three protein subunits defining different functional MPC assemblies in a metabolic-specific context. These have clear implications in cell homeostasis and disease, and on the development of future therapies. Despite intensive efforts by different research groups using state-of-the-art computational tools and experimental techniques, MPCs’ structure-based mechanism remains elusive. Here, we review the current state of knowledge concerning MPCs’ molecular structures by examining both earlier and recent studies and presenting novel data to identify the regulatory, structural, and core transport activities to each of the known MPC subunits. We also discuss the potential application of cryogenic electron microscopy (cryo-EM) studies of MPC reconstituted into nanodiscs of synthetic copolymers for solving human MPC2.

Altered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA., G.A.C. is The Alan M. Gewirtz Leukemia & Lymphoma Society Scholar. Work in G.A.C.’s laboratory is supported in part by the NIH/NCI grants 1UH2TR00943-01 and 1 R01 CA182905-01, the UT MD Anderson Cancer Center SPORE in Melanoma grant from NCI (P50 CA093459), Aim at Melanoma Foundation and the Miriam and Jim Mulva research funds, the Brain SPORE (2P50CA127001), the Center for Radiation Oncology Research Project, the Center for Cancer Epigenetics Pilot project, a 2014 Knowledge GAP MDACC grant, a CLL Moonshot pilot project, the UT MD Anderson Cancer Center Duncan Family Institute for Cancer Prevention and Risk Assessment, a SINF grant in colon cancer, the Laura and John Arnold Foundation, the RGK Foundation, and the Estate of C.G. Johnson, Jr. I.B.-N. was financed by a grant entitled Non-Invasive Intelligent Systems for Colorectal Cancer Diagnosis and Prognosis Based on circulating miRNAs Integrated in the Clinical Workflow – INTELCOR. S.M.G.D., A.L.B.A., and D.A. are supported by the São Paulo Research Foundation FAPESP under grants 2014/15968-3, 2014/20673-2, and 2014/17820-3, respectively. W.L. was partly supported by grants from The University of Texas MD Anderson Cancer Center Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research. J.A.B. was supported by the Cancer Center Support Grant (P30 CA016672), and the HP imaging program of the Small Animal Facility (SAIF) was supported by the Cancer Prevention and Research Institutes of Texas grant RP-101243P5. H.L. was supported by NIH/NCI grant R01CA175486, a grant (RP140462) from the Cancer Prevention and Research Institute of Texas, and the R. Lee Clark Fellow Award from The Jeanne F. Shelby Scholarship Fund. I.B.-N. was financed by a Fulbright fellowship and by a grant entitled Non-Invasive Intelligent Systems for Colorectal Cancer Diagnosis and Prognosis Based on circulating miRNAs Integrated in the Clinical Workflow – INTELCOR.

Phosphate-activated glutaminases catalyze the deamidation of glutamine to glutamate and play key roles in several physiological and pathological processes. In humans, GLS encodes two multidomain splicing isoforms: KGA and GAC. In both isoforms, the canonical glutaminase domain is flanked by an N-terminal region that is folded into an EF-hand-like four-helix bundle. However, the splicing event replaces a well-structured three-repeat ankyrin domain in KGA with a shorter, unordered C-terminal stretch in GAC. The multidomain architecture, which contains putative protein-protein binding motifs, has led to speculation that glutaminases are involved in cellular processes other than glutamine metabolism; in fact, some proteins have been identified as binding partners of KGA and the isoforms of its paralogue gene, GLS2. Here, a yeast two-hybrid assay identified nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) as a new binding partner of the glutaminase. We show that KGA and GAC directly bind PPARγ with a low-micromolar dissociation constant; the interaction involves the N-terminal and catalytic domains of glutaminases as well as the ligand-binding domain of the nuclear receptor. The interaction occurs within the nucleus, and by sequestering PPARγ from its responsive element DR1, the glutaminases decreased nuclear receptor activity as assessed by a luciferase reporter assay. Altogether, our findings reveal an unexpected glutaminase-binding partner and, for the first time, directly link mitochondrial glutaminases to an unanticipated role in gene regulation.

The active transport of glycolytic pyruvate across the inner mitochondrial membrane is thought to involve two mitochondrial pyruvate carrier subunits, MPC1 and MPC2, assembled as a 150 kDa heterotypic oligomer. Here, the recombinant production of human MPC through a co-expression strategy is first described; however, substantial complex formation was not observed, and predominantly individual subunits were purified. In contrast to MPC1, which co-purifies with a host chaperone, we demonstrated that MPC2 homo-oligomers promote efficient pyruvate transport into proteoliposomes. The derived functional requirements and kinetic features of MPC2 resemble those previously demonstrated for MPC in the literature. Distinctly, chemical inhibition of transport is observed only for a thiazolidinedione derivative. The autonomous transport role for MPC2 is validated in cells when the ectopic expression of human MPC2 in yeast lacking endogenous MPC stimulated growth and increased oxygen consumption. Multiple oligomeric species of MPC2 across mitochondrial isolates, purified protein and artificial lipid bilayers suggest functional high-order complexes. Significant changes in the secondary structure content of MPC2, as probed by synchrotron radiation circular dichroism, further supports the interaction between the protein and ligands. Our results provide the initial framework for the independent role of MPC2 in homeostasis and diseases related to dysregulated pyruvate metabolism.

On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. However, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform, glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. To obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C-termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.

Focal adhesion kinase (FAK) has emerged as a mediator of mechanotransduction in cardiomyocytes, regulating gene expression during hypertrophic remodeling. However, how FAK signaling is relayed onward to the nucleus is unclear. Here, we show that FAK interacts with and regulates myocyte enhancer factor 2 (MEF2), a master cardiac transcriptional regulator. In cardiomyocytes exposed to biomechanical stimulation, FAK accumulates in the nucleus, binds to and upregulates the transcriptional activity of MEF2 through an interaction with the FAK focal adhesion targeting (FAT) domain. In the crystal structure (2.9 A resolution), FAT binds to a stably folded groove in the MEF2 dimer, known to interact with regulatory cofactors. FAK cooperates with MEF2 to enhance the expression of Jun in cardiomyocytes, an important component of hypertrophic response to mechanical stress. These findings underscore a connection between the mechanotransduction involving FAK and transcriptional regulation by MEF2, with potential relevance to the pathogenesis of cardiac disease.

Glutamine is an essential nutrient for cancer cell proliferation, especially in the context of citric acid cycle anaplerosis. In this manuscript we present results that collectively demonstrate that, of the three major mammalian glutaminases identified to date, the lesser studied splice variant of the gene gls , known as Glutaminase C (GAC), is important for tumor metabolism. We show that, although levels of both the kidney-type isoforms are elevated in tumor vs. normal tissues, GAC is distinctly mitochondrial. GAC is also most responsive to the activator inorganic phosphate, the content of which is supposedly higher in mitochondria subject to hypoxia. Analysis of X-ray crystal structures of GAC in different bound states suggests a mechanism that introduces the tetramerization-induced lifting of a “gating loop” as essential for the phosphate-dependent activation process. Surprisingly, phosphate binds inside the catalytic pocket rather than at the oligomerization interface. Phosphate also mediates substrate entry by competing with glutamate. A greater tendency to oligomerize differentiates GAC from its alternatively spliced isoform and the cycling of phosphate in and out of the active site distinguishes it from the liver-type isozyme, which is known to be less dependent on this ion.

SummaryRho GTPases impact a number of activities important for oncogenesis. We describe a small molecule inhibitor that blocks oncogenic transformation induced by various Rho GTPases in fibroblasts, and the growth of human breast cancer and B lymphoma cells, without affecting normal cells. We identify the target of this inhibitor to be the metabolic enzyme glutaminase, which catalyzes the hydrolysis of glutamine to glutamate. We show that transformed fibroblasts and breast cancer cells exhibit elevated glutaminase activity that is dependent on Rho GTPases and NF-κB activity, and is blocked by the small molecule inhibitor. These findings highlight a previously unappreciated connection between Rho GTPase activation and cellular metabolism and demonstrate that targeting glutaminase activity can inhibit oncogenic transformation.

The binding of capped RNAs to the cap-binding complex (CBC) in the nucleus, and their dissociation from the CBC in the cytosol, represent essential steps in RNA processing. Here we show how the nucleocytoplasmic transport proteins importin-alpha and importin-beta have key roles in regulating these events. As a first step toward understanding the molecular basis for this regulation, we determined a 2.2-A resolution X-ray structure for a CBC-importin-alpha complex that provides a detailed picture for how importin-alpha binds to the CBP80 subunit of the CBC. Through a combination of biochemical studies, X-ray crystallographic information and small-angle scattering experiments, we then determined how importin-beta binds to the CBC through its CBP20 subunit. Together, these studies enable us to propose a model describing how importin-beta stimulates the dissociation of capped RNA from the CBC in the cytosol following its nuclear export.

Ajulemic acid (AJA) is a synthetic analog of THC-11-oic acid, a metabolite of tetrahydrocannabinol (THC), the major active ingredient of the recreational drug marijuana derived from the plant Cannabis sativa. AJA has potent analgesic and anti-inflammatory activity in vivo, but without the psychotropic action of THC. However, its precise mechanism of action remains unknown. Biochemical studies indicate that AJA binds directly and selectively to the isotype gamma of the peroxisome proliferator-activated receptor (PPARgamma) suggesting that this may be a pharmacologically relevant receptor for this compound and a potential target for drug development in the treatment of pain and inflammation. Here, we report the crystal structure of the ligand binding domain of the gamma isotype of human PPAR in complex with ajulemic acid, determined at 2.8-A resolution. Our results show a binding mode that is compatible with other known partial agonists of PPAR, explaining their moderate activation of the receptor, as well as the structural basis for isotype selectivity, as observed previously in vitro. The structure also provides clues to the understanding of partial agonism itself, suggesting a rational approach to the design of molecules capable of activating the receptor at levels that avoid undesirable side effects.

Hypoxia-inducible transcription factors (HIF) form heterodimeric complexes that mediate cell responses to hypoxia. The oxygen-dependent stability and activity of the HIF-α subunits is traditionally associated to post-translational modifications such as hydroxylation, acetylation, ubiquitination and phosphorylation. Here we report novel evidence showing that unsaturated fatty acids are naturally occurring, non-covalent structural ligands of HIF-3α, thus providing the initial framework for exploring its exceptional role as a lipid sensor under hypoxia.

The thyroid hormone receptor (TR) D-domain links the ligand-binding domain (LBD, EF-domain) to the DNA-binding domain (DBD, C-domain), but its structure, and even its existence as a functional unit, are controversial. The D domain is poorly conserved throughout the nuclear receptor family and was originally proposed to comprise an unfolded hinge that facilitates rotation between the LBD and the DBD. Previous TR LBD structures, however, have indicated that the true unstructured region is three to six amino acid residues long and that the D-domain N terminus folds into a short amphipathic alpha-helix (H0) contiguous with the DBD and that the C terminus of the D-domain comprises H1 and H2 of the LBD. Here, we solve structures of TR-LBDs in different crystal forms and show that the N terminus of the TRalpha D-domain can adopt two structures; it can either fold into an amphipathic helix that resembles TRbeta H0 or form an unstructured loop. H0 formation requires contacts with the AF-2 coactivator-binding groove of the neighboring TR LBD, which binds H0 sequences that resemble coactivator LXXLL motifs. Structural analysis of a liganded TR LBD with small angle X-ray scattering (SAXS) suggests that AF-2/H0 interactions mediate dimerization of this protein in solution. We propose that the TR D-domain has the potential to form functionally important extensions of the DBD and LBD or unfold to permit TRs to adapt to different DNA response elements. We also show that mutations of the D domain LXXLL-like motif indeed selectively inhibit TR interactions with an inverted palindromic response element (F2) in vitro and TR activity at this response element in cell-based transfection experiments.

Integrase (IN) is an essential retroviral enzyme, and human transcriptional coactivator p75, which is also referred to as lens epithelium-derived growth factor (LEDGF), is the dominant cellular binding partner of HIV-1 IN. Here, we report the crystal structure of the dimeric catalytic core domain of HIV-1 IN complexed to the IN-binding domain of LEDGF. Previously identified LEDGF hotspot residues anchor the protein to both monomers at the IN dimer interface. The principal structural features of IN that are recognized by the host factor are the backbone conformation of residues 168–171 from one monomer and a hydrophobic patch that is primarily comprised of α-helices 1 and 3 of the second IN monomer. Inspection of diverse retroviral primary and secondary sequence elements helps to explain the apparent lentiviral tropism of the LEDGF-IN interaction. Because the lethal phenotypes of HIV-1 mutant viruses unable to interact with LEDGF indicate that IN function is highly sensitive to perturbations of the structure around the LEDGF-binding site, we propose that small molecule inhibitors of the protein–protein interaction might similarly disrupt HIV-1 replication.

Members of MEF2 (Myocyte Enhancer Factor 2) family of transcription factors are major regulators of cardiac development and homeostasis. Their functions are regulated at several levels, including the association with a variety of protein partners. We have previously shown that FAK (Focal Adhesion Kinase) regulates the stretch-induced activation of MEF2 in cardiomyocytes. But, the molecular mechanisms, involved in this process, are unclear. Here, we integrated biochemical, imaging and structural analyses to characterize a novel interaction between MEF2 and FAK. An association between MEF2 and FAK was detected by co-immunoprecipitation in the extracts of stretched cardiomyocytes (10%, 60Hz, 2 hours). MEF2 and FAK staining were co-localized in the nuclei of stretched cells. Pull down assays indicated that the Focal Adhesion Targeting (FAT) domain is sufficient to confer FAK interaction with MEF2. Gene reporter assays indicated that the interaction with FAK enhances the MEF2C transcriptional activity in cultured cardiomyocytes. Also, we present a 2.9-Å X-ray crystal structure for the FAK_FAT domain bound to MEF2C (1-95), comprised by the MADS box/MEF2 domain. The structural information, when used in combination with biochemical studies, small-angle X-ray scattering (SAXS) data and reporter gene assay, lead to a mechanistic model describing how FAK binds to MEF2C and stimulates its transcription function in cardiomyocytes. We further validated this model by showing that the binding of FAK to MEF2C is essential for the hypertrophy of cardiomyocyte in response to mechanical stress. Our results present FAK as a new positive regulator of MEF2, implicated in the fine control of the signal transduction between focal adhesions and the nucleus of cardiac myocytes during mechanical stress.

The phosphate-dependent transition between enzymatically inert dimers into catalytically capable tetramers has long been the accepted mechanism for the glutaminase activation. Here, we demonstrate that activated glutaminase C (GAC) self-assembles into a helical, fiber-like double-stranded oligomer and propose a molecular model consisting of seven tetramer copies per turn per strand interacting via the N-terminal domains. The loop 321LRFNKL326 is projected as the major regulating element for self-assembly and enzyme activation. Furthermore, the previously identified in vivo lysine acetylation (Lys311 in humans, Lys316 in mouse) is here proposed as an important down-regulator of superoligomer assembly and protein activation. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide, a known glutaminase inhibitor, completely disrupted the higher order oligomer, explaining its allosteric mechanism of inhibition via tetramer stabilization. A direct correlation between the tendency to self-assemble and the activity levels of the three mammalian glutaminase isozymes was established, with GAC being the most active enzyme while forming the longest structures. Lastly, the ectopic expression of a fiber-prone superactive GAC mutant in MDA-MB 231 cancer cells provided considerable proliferative advantages to transformed cells. These findings yield unique implications for the development of GAC-oriented therapeutics targeting tumor metabolism. Background: GAC supplies for increased metabolic needs of tumors because of exclusive localization and kinetic properties. Results: Higher than tetramer oligomers are the active form in in vitro and in cellular assays. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide disrupts oligomers. Conclusion: A novel molecular mechanism for GAC activation is proposed. Significance: The data affect the development of therapies targeting GAC in tumors, with emphasis on allosteric inhibitors.

The necrosis- and ethylene-inducing peptide 1 (NEP1)-like proteins (NLPs) are proteins secreted from bacteria, fungi and oomycetes, triggering immune responses and cell death in dicotyledonous plants. Genomic-scale studies of Moniliophthora perniciosa, the fungus that causes the Witches' Broom disease in cacao, which is a serious economic concern for South and Central American crops, have identified five members of this family (termed MpNEP1-5). Here, we show by RNA-seq that MpNEP2 is virtually the only NLP expressed during the fungus infection. The quantitative real-time polymerase chain reaction results revealed that MpNEP2 has an expression pattern that positively correlates with the necrotic symptoms, with MpNEP2 reaching its highest level of expression at the advanced necrotic stage. To improve our understanding of MpNEP2's molecular mechanism of action, we determined the crystallographic structure of MpNEP2 at 1.8 Å resolution, unveiling some key structural features. The implications of a cation coordination found in the crystal structure were explored, and we show that MpNEP2, in contrast to another previously described member of the NLP family, NLP(Pya) from Pythium aphanidermatum, does not depend on an ion to accomplish its necrosis- and electrolyte leakage-promoting activities. Results of site-directed mutagenesis experiments confirmed the importance of a negatively charged cavity and an unforeseen hydrophobic β-hairpin loop for MpNEP2 activity, thus offering a platform for compound design with implications for disease control. Electron paramagnetic resonance and fluorescence assays with MpNEP2 performed in the presence of lipid vesicles of different compositions showed no sign of interaction between the protein and the lipids, implying that MpNEP2 likely requires other anchoring elements from the membrane to promote cytolysis or send death signals.

Bothropasin is a 48 kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys 189 is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from PII SVMPs. The ECD motif is stabilized by the Cys 277 –Cys 310 disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu 276 of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other PIII SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other PIII members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain.

Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokinase member of the ribokinase-like superfamily, is a homodimer of 66 kDa subunits whose oligomerization state is necessary for catalysis and stability. The presence of MgATP favors the tetrameric form of the enzyme. In this work, we describe the structure of Pfk-2 in its inhibited tetrameric form, with each subunit bound to two ATP molecules and two Mg ions. The present structure indicates that substrate inhibition occurs due to the sequential binding of two MgATP molecules per subunit, the first at the usual site occupied by the nucleotide in homologous enzymes and the second at the allosteric site, making a number of direct and Mg-mediated interactions with the first. Two configurations are observed for the second MgATP, one of which involves interactions with Tyr23 from the adjacent subunit in the dimer and the other making an unusual non-Watson-Crick base pairing with the adenine in the substrate ATP. The oligomeric state observed in the crystal is tetrameric, and some of the structural elements involved in the binding of the substrate and allosteric ATPs are also participating in the dimer–dimer interface. This structure also provides the grounds to compare analogous features of the nonhomologous phosphofructokinases from E. coli.

Escherichia coli contains two phosphofructokinases, Pfk-1 and Pfk-2, which belong to unrelated protein families. In addition to catalytic function, the enzymes have converged in showing substrate inhibition by the nucleotide MgATP. However, although both Pfk-1 and Pfk-2 have been extensively characterized biochemically, only the structure of the former has been solved by X-ray diffraction. In order to fully understand how the same function has evolved on different structural folds, Pfk-2 has been crystallized by the hanging-drop vapour-diffusion method using PEG 6000 as precipitant. Single crystals were grown in the presence of MgATP and diffracted to 1.98 A. The crystals belong to the orthorhombic system, space group P222(1), with unit-cell parameters a = 42.8, b = 86.8, c = 171.3 A. The calculated Matthews coefficient of 2.45 A(3) Da(-1) indicates the presence of two monomers in the asymmetric unit, corresponding to a solvent content of 49%. Structure determination is ongoing.

The structures of a 14 kDa phospholipase, an 18 kDa proteinase inhibitor and a novel glycoside hydrolase with molecular weight 60 kDa were solved using the SAD technique and the effects of the amount of anomalous signal, completeness and redundancy of data on heavy-atom substructure determination, phasing and model building were analyzed. All diffraction data sets were collected on a Cu-anode X-ray home source. The structure of the phospholipase was obtained using the anomalous scattering contribution from its 16 S atoms. Three-dimensional models for the other two macromolecules were obtained using the anomalous contribution of I atoms rapidly incorporated into the crystal through the quick cryo-soaking method of derivatization. These results were used to discuss the application of sulfur- and iodine-SAD approaches in combination with X-ray home sources for high-throughput protein crystal structure solution. The estimates of the anomalous signal from S atoms in the gene products of four genomes are given and the prospects for increasing the anomalous contribution using longer wavelengths (e.g. from a chromium home source) and quick cryo-soaking derivatization are discussed. The possibility of rapidly preparing tangible home-source isomorphous derivatives suggests that this approach might become a valuable tool in the future of post-genomic projects.

Agkistrodon contortrix laticinctus myotoxin is a Lys(49)-phospholipase A(2) (EC 3.1.1.4) isolated from the venom of the serpent A. contortrix laticinctus (broad-banded copperhead). We present here three monomeric crystal structures of the myotoxin, obtained under different crystallization conditions. The three forms present notable structural differences and reveal that the presence of a ligand in the active site (naturally presumed to be a fatty acid) induces the exposure of a hydrophobic surface (the hydrophobic knuckle) toward the C terminus. The knuckle in A. contortrix laticinctus myotoxin involves the side chains of Phe(121) and Phe(124) and is a consequence of the formation of a canonical structure for the main chain within the region of residues 118-125. Comparison with other Lys(49)-phospholipase A(2) myotoxins shows that although the knuckle is a generic structural motif common to all members of the family, it is not readily recognizable by simple sequence analyses. An activation mechanism is proposed that relates fatty acid retention at the active site to conformational changes within the C-terminal region, a part of the molecule that has long been associated with Ca(2+)-independent membrane damaging activity and myotoxicity. This provides, for the first time, a direct structural connection between the phospholipase "active site" and the C-terminal "myotoxic site," justifying the otherwise enigmatic conservation of the residues of the former in supposedly catalytically inactive molecules.

Septinas são proteínas envolvidas em diversos processos celulares (citocinese, espermatogênese, apoptose etc.), razão pela qual estão relacionadas com o desenvolvimento de várias doenças. Pertencentes à família das GTPases, apresentam três domínios: N e C terminal altamente variável e um domínio G (ligação a GTP/GDP) conservado. Para realizar suas funções, uma septina de cada grupo (4 grupos diferentes em humanos) se associa para formar heterofilamentos usando dois tipos de interfaces: a interface G e a interface NC. Embora seja conhecido o tipo de interface de contato e a ordem específica das septinas na montagem do filamento, os mecanismos moleculares que controlam a polimerização correta do filamento ainda são desconhecidos. Aqui, descrevemos os estudos realizados nas interfaces G e NC das septinas, a fim de encontrar os mecanismos moleculares de interação específica e verificar a substituição das septinas por outras do mesmo grupo. Oito combinações de heterocomplexos “G” de septinas foram co-expressas e purificadas para serem caracterizadas por técnicas biofísicas, apresentando heterodímeros homogêneos em solução (SEC e SEC-MALS) com presença de GTP e GDP em proporções aproximadamente equimolares. Além disso, cada dímero exibe uma estabilidade térmica diferente, o que pode indicar uma preferência de interação para a formação de complexos. Os estudos cristalográficos dos heterodímeros G permitiu identificar interações específicas que determinam a especificidade do complexo formado por septinas do grupo II e grupo III (validando a substituição de septinas do mesmo grupo), ajudando também a explicar a presença de um grupo catalíticamente inativo em estas proteínas. Por outro lado, as estruturas cristalográficas dos coiled-coils das septinas 1, 4 e 5 (Interface NC) permitiu observar um novo motivo proteico que sugere estar relacionado com a interação entre dois heterofilamentos, formando estruturas de alta complexidade em septinas (redes etc.). Septins are involved in several cellular processes (cytokinesis, spermatogenesis, apoptosis, etc.), which is why they are related to the development of several diseases. Belonging to the GTPase family, they present three domains: highly variable N and C terminal and a conserved G domain (binding to GTP/GDP). To perform their functions, one septin from each group (4 different groups in humans) associate to form heterofilaments using two types of interface: the G interface and the NC interface. Although the type of contact interface and the specific order of septins in the filament are known, the molecular mechanisms that control the correct polymerization of the filament are still unknown. Here, we describe studies carried out on the G and NC interfaces of septins, in order to shed light on the molecular mechanisms of specific interaction and to verify the replacement of septins by others from the same group. Eight combinations of septin “G” heterocomplexes were co-expressed and purified and characterized by biophysical techniques. They were present as homogeneous heterodimers in solution (SEC and SEC-MALS) with the presence of GTP and GDP in approximately equimolar proportions. In addition, each dimer exhibited a different thermal stability, which may indicate an interaction preference for complex formation. Crystallographic studies of the G heterodimers allowed for the identification of specific interactions that determine the specificity of the complex formed by septins from group II and group III (validating the replacement of septins from the same group) and helping to explain the presence of a catalytically inactive group in these proteins. On the other hand, the crystal structures of the coiled-coils of septins 1, 4 and 5 (NC interface) allowed us to observe a new protein motif that suggests that it is related to the interaction between two heterofilaments, forming highly complex structures of septins (networks etc.).

Schistomiasis is a neglected tropical disease caused by trematodes worms from the genus Schistosoma. Schistosomiasis is the second most devastating parasitic disease after malaria. The disease has a high economic burden and affects mainly poor population without access to proper sanitation. Praziquantel is the only drug approved for the treatment of schistosomiasis and resistance is already reported. Fumarate hydratases or fumarases are enzymes that catalyze the reversible hydration of fumarate to L-malate. This enzyme participates in DNA repair and important metabolic processes such as the urea and the tricarboxylic acid cycles. Fumarases are divided in two classes, and Schistosoma mansoni possess both, being class I localized in mitochondria, while class II is cytosolic. The fundamental role of fumarases in the metabolism make them potential target for drug design against schistosomiasis. This work describes, for the first time, the cloning, expression and purification protocol for the class II fumarate hydratase from Schistosoma mansoni (SmFHII). In order to estimate the contribution of the reverse reaction, the enzyme was kinetically characterized using both substrates concomitantly. SmFHII was shown to follow a MichaelisMenten mechanism of catalysis with of 19 mM-1s-1 and of 49 mM-1s-1, and of 0.56 mM and of 0.15 mM. Differential scanning fluorimetry (DSF) performed under different chemical environments shows that the highest thermal stability is reached at pH 7.5 and at higher ionic strength. The significant thermoshift observed for SmFHII in presence of well known ligands makes DSF the adequate technique for ligand screening. SmFHII structure in complex with L-malate was determined by single crystal X-ray diffraction, at 1.85 Å resolution. A new construct [SmFHII(Δ263-277)] lacking the additional portion only found in trematode worms was also evaluated by kinetic and DSF experiments. Although not essential for activity, the results suggest that the removal of this region impacts on protein stability and may has influence on L-malate catalysis. The differences between SmFHII and human fumarase are distributed all over the structure, and could be explored to design new selective inhibitors. A esquistossomose é uma doença tropical negligenciada causada por parasitas trematódeos do gênero Schistosoma. A esquistossomose é a segunda doença parasitária mais devastadora do mundo, atrás apenas da malária. A doença tem um alto impacto econômico, afetando principalmente a população pobre sem acesso a saneamento adequado. Praziquantel é o único medicamento aprovado para o tratamento da esquistossomose e já existem relatos de parasitas resistentes a esse fármaco. Fumarato hidratases ou fumarases são enzimas que catalisam a hidratação reversível de fumarato em L-malato. Essa enzima participa do reparo ao dano do DNA e de processos metabólicos importantes, como os ciclos da uréia e do ácido tricarboxílico. As fumarases são divididas em duas classes e o S. mansoni possui ambas, sendo a classe I mitocondrial, enquanto a classe II é citosólica. O papel fundamental da fumarase no metabolismo faz dela um alvo potencial para o planejamento de fármacos contra a esquistossomose. Este trabalho descreve, pela primeira vez, o protocolo de clonagem, expressão e purificação da fumarato hidratase classe II de Schistosoma mansoni (SmFHII). De forma a estimar a contribuição da reação reversa, a enzima foi caracterizada cineticamente utilizando os dois substratos concomitantemente. A SmFHII demonstrou seguir o mecanismo de catálise de Michaelis-Menten, tendo um de 19 mM-1s-1 e de 49 mM-1s-1, e de 0,56 mM e de 0,15 mM. Fluorimetria de varredura diferencial (DSF) realizada em diferentes ambientes químicos demonstrou que a maior estabilidade térmica da proteína é alcançada em pH 7,5 e também com o aumento alta força iônica, além de ser uma técnica útil para a triagem de ligantes. A estrutura da SmFHII foi determinada por difração de raios-X de monocristal, com uma resolução de 1,85 Å. Uma nova construção [SmFHII(Δ263-277)] sem a porção adicional, encontrada apenas em vermes de trematódeos, também foi avaliada por ensaios cinéticos e de DSF. Embora não seja essencial para a atividade enzimática, os resultados sugerem que a remoção dessa região afeta a estabilidade da proteína e pode ter influência na catálise do L-malato. As diferenças entre SmFHII e fumarase humana estão distribuídas por toda a estrutura e podem ser exploradas para delinear novos inibidores seletivos.

Este documento de Tese é o resultado de um trabalho de pesquisa voltado à análise cristalográfica de novas formas sólidas cristalinas derivadas de fármacos antirretrovirais, diante do contexto da engenharia de cristais para o desenho das novas formas sólidas, e principalmente diante da ótica da análise das densidades de carga, o que permitiu um entendimento mais acurado da estrutura eletrônica molecular desta classe de compostos. Compostos farmacêuticos antirretrovirais do tipo inibidores nucleosídeos da transcriptase reversa (INTRs), são de grande importância, uma vez que são amplamente usados na terapêutica antirretroviral, principalmente contra o vírus HIV. Nesse contexto, são conhecidos alguns problemas associados na manufatura destes fármacos, principalmente aos processos de extração e purificação dos fármacos Lamivudina (3TC) e Emtricitabina (FTC). Diante desta problemática, a engenharia de cristais fornece uma solução, mediante o planejamento racional de formas sólidas (sais, cocristais, solvatos, polimorfos, etc.) que apresentam maior estabilidade e facilitem principalmente o processo de purificação em grande escala. Daí surge a importância de estudar a estrutura molecular das diferentes formas sólidas derivadas destes fármacos, sendo uma das principais técnicas para este estudo a difração de raios X em monocristais (DRXM). Neste trabalho um total de nove novas formas sólidas foram avaliadas e reportadas, com uma discussão detalhada das conformações moleculares e supramoleculares. Entretanto, é realizada uma análise das densidades de carga mediante métodos experimentais, uma vez que foram conduzidos experimentos de DRXM em alta resolução, em virtude da boa qualidade dos cristais que algumas das formas sólidas apresentaram. Desta maneira foi possível propor modelos de densidade de carga experimentais construídos mediante o formalismo de Hansen & Coppens, utilizando refinamento por mínimos quadrados baseados nos dados de difração em alta resolução. Por último, com o intuito de ter um estudo mais completo e detalhado da estrutura eletrônica, foram realizados cálculos teóricos de primeiros princípios em condições gasosas e periódicas de contorno. Desta forma, é apresentada uma sinergia entre os resultados obtidos pelas análises das distribuições de densidade de cargas de algumas formas sólidas, com os resultados gerais da engenharia de cristais e, portanto, concluir e extrapolar alguns aspectos importantes, principalmente no que se refere às energias associadas com as interações intermoleculares. A sinergia dos estudos de engenharia de cristais e de densidade de carga, é um tipo de pesquisa pouco publicada dentro da área da cristalografia de pequenas moléculas. This Thesis is the result of the research proposal aimed to the crystallographic analysis of new crystalline solid forms derived from antiretroviral drugs, in the context of the crystal engineering for the design of the new solid forms, mainly since the viewpoint of the charge density analysis, which allowed an accurate comprehension of the molecular electronic structure of this kind of compounds. Antiretroviral drug compounds of nucleoside analog reverse-transcriptase inhibitors (NRTI) type, are of great importance once they are large used in the antiretroviral therapy, mainly against the HIV. In this context, some problems are known regard to the manufacture process of these drugs, mainly in the extraction and purification procedures of the lamivudine (3TC) and emtricitabine (FTC) drugs. On this issue, the crystal engineering provides an answer, through the rational planning of solid forms (salts, cocrystals, solvates, polymorphs, etc.) that exhibit an increased stability and facilitate mainly the large-scale purification process. Hence is important to study the molecular structure of the diverse solid forms derived from these drugs, mainly through the single-crystal X-ray diffraction (SCXD) experiments. In this research a total of nine new solid forms were assessed and reported, along with a detailed discussion of the molecular and supramolecular conformations. Meantime, it was carried out an analysis of the experimental charge density, once it was performed high-resolution SCXD experiments, since some of the solid forms showed good quality single crystals. In this way, it was possible to propose models of experimental charge density through the Hansen & Coppens formalism, using least-square refinement against high-resolution X-ray diffraction data. Finally, with the aim to have a more complete and detailed study of the electronic structure, it was also carried out first principles theoretical calculations in gas-phase and periodic boundary conditions. Thus, it is shown a synergy between the results obtained by the analysis of the charge density distributions of some solid forms and the crystal engineering results and, therefore, to conclude and to extrapolate some important aspects, mainly involved with the intermolecular interaction energies. The synergy of the crystal engineering and charge density studies is a kind of research little published, within the small molecule crystallography area.

Proteínas sinalizadoras membranares são amplamente usadas por bactérias para adequar seu metabolismo a estímulos ambientais. Elas possuem ainda um grande potencial de aplicação, como em técnicas para controle de infecções e o desenvolvimento de ferramentas biotecnológicas, como biossensores. Entretanto, pouco é conhecido sobre os mecanismos estruturais de transdução bacterianos. Em particular, pouco é descrito sobre proteínas sinalizadoras que possuem os domínios GGDEF e/ou EAL, responsáveis por desencadear a síntese, degradação ou captação da molécula c-di-GMP, um dos principais reguladores do metabolismo bacteriano. Por isso, esse estudo objetivou a caracterização de duas proteínas sinalizadoras transmembrana de Pseudomonas aeruginosa, codificadas nos genes PA0847 e PA3343 (HsbD), além de trazer análises por bioinformática de proteínas com domínios GGDEF e EAL consecutivos, comumente associados a membrana celular. É relatado que PA0847 e HsbD são ambas diguanilato ciclases (DGC), que impactam consideravelmente em fenótipos de P. aeruginosa, patógeno modelo de estudo e que infecta pacientes imunocomprometidos. Além disso, um estudo anterior mostrou a interação entre a porção citoplasmática de PA0847 e a região N-terminal de HsbD (HsbD-Nt), pela técnica de duplo híbrido. Nesse estudo, é mostrado que essa interação, associada à presença de um padrão conservado em HsbD-Nt, sugere a presença um sistema de controle específico de c-di-GMP. Ensaios in vitro de pulldown, termoforese e duplo híbrido, utilizando domínios isolados de PA0847, confirmaram a interação com HsbD-Nt e mostraram que a interação é dependente de todos os domínios de PA0847. Análises de massa molecular e de cinética enzimática mostraram que o HAMP eleva a atividade DGC e promove a formação de tetrâmeros. A presença de um transportador de sulfato compartilhando um operon com PA0847, associado a modelos computacionais da região periplasmática de PA0847, suportam o envolvimento de PA0847 na homeostase desse íon. Nesse estudo foram ainda identificados, por meio de análises de sequências, novos potenciais grupos de resíduos que estariam envolvidos na regulação de proteínas GGDEF-EAL. Análises adicionais de sequências e de estruturas indicaram também um mecanismo de dimerização alternativo para EALs, quando a região de dimerização está ausente. Estes resultados são inéditos e fornecem passos para uma melhor compreensão da sinalização bacteriana intermediada pelo c-di-GMP. Membrane signaling protein are widely used by bacteria to adequate their metabolism of environmental cues. They present a great potential of applicability, such as techniques to control bacterial infections and development of biotecnological devices, for example in biosensors. However, little is known regarding the mechanisms of signal transduction in bacteria. In particular, about receptors that posses GGDEF and/or EAL domains, performing synthesis, degradation or recognition of c-di-GMP, which is one of the major bacteria metabolism regulators. For this reason, the present study aimed characterize two important transmembrane signaling proteins from Pseudomonas aeruginosa, coded in genes PA0847 and PA3343 (HsbD) and performed bioinformatic analysis of proteins with GGDEF and EAL in tandem, usually associated with membrane. Previous studies indicated that PA0847 and HsbD are both diguanylate cyclases (DGCs) that significantly impair phenotypes of P. aeruginosa, which is a model organism and common cause of infection in immunocompromised patients. In the present study we have shown that this interaction associated with the presence of a wellconserved pattern from HsbD-Nt, suggests the presence a system used for specific downregulation of c-di-GMP. Furthermore, using isolated domains of PA0847 in thermophoresis, pull down and two-hybrid confirmed the interaction and showed that the full PA0847 cytoplasmic is necessary to interaction with HsbD. Additional amalysis of molecular mass and enzyme kinetic showed that HAMP increases DGC activity, alters the co-purification patern of c-di-GMP and promotes tetramers formation in PA0847 soluble constructs. The presence of sulfate transporter in a common operon with PA0847, associated with computation model of periplasmatic region of PA0847 supports the relation of this protein in sulfate homeostasis. We also identified using new residues groups copled that are potential play roles in GGDEF-EAL proteins. We found by stuctural analisys alternative mechanisms of dimerization in EAL domais that do not posses dimerization site conserved. These results have not been presented elsewhere and provide insights into the bacterial signaling of c-di-GMP pathways.