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Picornavirus family members cause disease in humans. Human rhinoviruses (RV), the main causative agents of the common cold, increase the severity of asthma and COPD; hence, effective agents against RVs are required. The 2A proteinase (2Apro), found in all enteroviruses, represents an attractive target; inactivating mutations in poliovirus 2Apro result in an extension of the VP1 protein preventing infectious virion assembly. Variations in sequence and substrate specificity on eIF4G isoforms between RV 2Apro of genetic groups A and B hinder 2Apro as drug targets. Here, we demonstrate that although RV-A2 and RV-B4 2Apro cleave the substrate GAB1 at different sites, the 2Apro from both groups cleave equally efficiently an artificial site containing P1 methionine. We determined the RV-A2 2Apro structure complexed with zVAM.fmk, containing P1 methionine. Analysis of this first 2Apro-inhibitor complex reveals a conserved hydrophobic P4 pocket among enteroviral 2Apro as a potential target for broad-spectrum anti-enteroviral inhibitors.

Through interaction studies, the crystal structure of human DHTKD1 allows insight into a mitochondrial megacomplex in lysine catabolism. This creates the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism., DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de­hydrogenases. In complex with E2 (di­hydro­lipo­amide succinyltransferase, DLST) and E3 (dihydrolipo­amide de­hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de­carboxyl­ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Å resolution crystal structure of human DHTKD1 is solved in complex with the thi­amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de­hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Å resolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino­adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.

The folate and methionine cycles, constituting one-carbon metabolism, are critical pathways for cell survival. Intersecting these two cycles, 5,10-methylenetetrahydrofolate reductase (MTHFR) directs one-carbon units from the folate to methionine cycle, to be exclusively used for methionine and S-adenosylmethionine (AdoMet) synthesis. MTHFR deficiency and upregulation result in diverse disease states, rendering it an attractive drug target. The activity of MTHFR is inhibited by the binding of AdoMet to an allosteric regulatory domain distal to the enzyme’s active site, which we have previously identified to constitute a novel fold with a druggable pocket. Here, we screened 162 AdoMet mimetics using differential scanning fluorimetry, and identified 4 compounds that stabilized this regulatory domain. Three compounds were sinefungin analogues, closely related to AdoMet and S-adenosylhomocysteine (AdoHcy). The strongest thermal stabilisation was provided by (S)-SKI-72, a potent inhibitor originally developed for protein arginine methyltransferase 4 (PRMT4). Using surface plasmon resonance, we confirmed that (S)-SKI-72 binds MTHFR via its allosteric domain with nanomolar affinity. Assay of MTHFR activity in the presence of (S)-SKI-72 demonstrates inhibition of purified enzyme with sub-micromolar potency and endogenous MTHFR from HEK293 cell lysate in the low micromolar range, both of which are lower than AdoMet. Nevertheless, unlike AdoMet, (S)-SKI-72 is unable to completely abolish MTHFR activity, even at very high concentrations. Combining binding assays, kinetic characterization and compound docking, this work indicates the regulatory domain of MTHFR can be targeted by small molecules and presents (S)-SKI-72 as an excellent candidate for development of MTHFR inhibitors.

5′-aminolevulinate synthase (ALAS) catalyzes the first step in heme biosynthesis, generating 5′-aminolevulinate from glycine and succinyl-CoA. Inherited frameshift indel mutations of human erythroid-specific isozyme ALAS2, within a C-terminal (Ct) extension of its catalytic core that is only present in higher eukaryotes, lead to gain-of-function X-linked protoporphyria (XLP). Here, we report the human ALAS2 crystal structure, revealing that its Ct-extension folds onto the catalytic core, sits atop the active site, and precludes binding of substrate succinyl-CoA. The Ct-extension is therefore an autoinhibitory element that must re-orient during catalysis, as supported by molecular dynamics simulations. Our data explain how Ct deletions in XLP alleviate autoinhibition and increase enzyme activity. Crystallography-based fragment screening reveals a binding hotspot around the Ct-extension, where fragments interfere with the Ct conformational dynamics and inhibit ALAS2 activity. These fragments represent a starting point to develop ALAS2 inhibitors as substrate reduction therapy for porphyria disorders that accumulate toxic heme intermediates., Mutation of the C-terminal extension of 5′-aminolevulinate synthase 2 (ALAS2) is the molecular cause for X-linked protoporphyria, but the underlying mechanism is unclear. Based on crystal structures and MD simulations of ALAS2, the authors here show how the C-terminal extension regulates ALAS2 activity.

Breeding by releasing eggs into stable biofoams (>foam nests>) is a peculiar reproduction mode within anurans, fish, and tunicates; not much is known regarding the biochemistry or molecular mechanisms involved. Lv-ranaspumin (Lv-RSN-1) is the predominant protein from the foam nest of the frog Leptodactylus vastus. This protein shows natural surfactant activity, which is assumed to be crucial for stabilizing foam nests. We elucidated the amino acid sequence of Lv-RSN-1 by de novo sequencing with mass-spectrometry and determined the high-resolution X-ray structure of the protein. It has a unique fold mainly composed of a bundle of 11 α-helices and two small antiparallel β-strands. Lv-RSN-1 has a surface rich in hydrophilic residues and a lipophilic cavity in the region of the antiparallel β-sheet. It possesses intrinsic surface-active properties, reducing the surface tension of water from 73 to 61 mN m-1 (15 μg mL-1). Lv-RSN-1 belongs to a new class of surfactants proteins for which little has been reported regarding structure or function. Making the perfect egg: Frog eggs and sperm are matured in >foam nests> that are stabilized by the naturally occurring surfactant protein ranaspumin. We report the amino acid sequence, crystal structure (which corresponds to a novel fold), and biochemical properties of Lv-RSN-1, the uncommon ranaspumin from the frog Leptodactylus vastus. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim., D.C.H. was recipient of a scholarship provided by Consehlo Nacional de Desenvolvimento Científico e Tecnológico (CNPq; Process No. 201633/2012-8). This work was financially supported by Coordenaçao de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), by CNPq and by the Austrian Science Funds (FWF) through project W901 (DK >Molecular Enzymology>, to K.G.)

Lectins from Diocleinae subtribe belong to the family of legume lectins and are characterized by high identity between their amino acids sequences. It has been shown that punctual differences in amino acid sequences, such as one single amino acid or an alternative conformation, represent changes in biological activities caused by these lectins. Therefore, a more detailed understanding of three-dimensional structures of these proteins is essential for accurate analyzing the relationship between structure and function. In this study lectins purified from the seeds of Dioclea violacea (DVL) and Dioclea rostrata (DRL) were compared with regard to crystal structure and vasorelaxant properties. Differences in structure of lectins were found to be reflected in differences in vasorelaxant effects based on their high specificity and selectivity for cell glycans. Binding activity was related to the position of specific residues in the carbohydrate recognition domain (CRD). DVL complexed structure was solved by X-ray crystallography and was compared to native DVL and DRL. Therefore, DVL was co-crystallized with X-Man, and a molecular modeling with X-Man complexed with DVL was done to compare the complexed and native forms adjusted fit. The relatively narrow and deep CRD in DVL promotes little interaction with carbohydrates; in contrast, the wider and shallower CRD in DRL favors interaction. This seems to explain differences in the level of relaxation induced by DVL (43%) and DRL (96%) in rat aortic rings.

The crystal structure and pro-inflammatory property of a lectin from the seeds of Dioclea wilsonii (DwL) were analyzed to gain a better understanding of structure/function relationships of Diocleinae lectins. Following crystallization and structural determination by standard molecular replacement techniques, DwL was found to be a tetramer based on PISA analysis, and composed by two metal-binding sites per monomer and loops which are involved in molecular oligomerization. DwL presents 96% and 99% identity with two other previously described lectins of Dioclea rostrata (DRL) and Dioclea grandiflora (DGL). DwL differs structurally from DVL and DRL with regard to the conformation of the carbohydrate recognition domain and related biological activities. The structural analysis of DwL in comparison to other Diocleinae lectins can be related to the differences in the dose-dependent pro-inflammatory effect elicited in Wistar rats, probably via specific interactions with mast cells complex carbohydrate, resulting in significant paw edema. DwL appears to be involved in positive modulation of mast cell degranulation via recognition of surface carbohydrates. Since this recognition is dependent on site volume and CRD configuration, edematogenesis mediated by resident cells varies in potency and efficacy among different Diocleinae lectins.

Diocleinae lectins are highly homologous in their primary structure which features metal binding sites and a carbohydrate recognition domain (CRD). Differences in the biological activity of legume lectins have been widely investigated using hemagglutination inhibition assays, isothermal titration microcalorimetry and co-crystallization with mono- and oligosaccharides. Here we report a new lectin crystal structure (ConBr) extracted from seeds of Canavalia brasiliensis, predict dimannoside binding by docking, identify the α-aminobutyric acid (Abu) binding pocket and compare the CRD of ConBr to that of homologous lectins. Based on the hypothesis that the carbohydrate affinity of lectins depends on CRD configuration, the relationship between tridimensional structure and endothelial NO synthase activation was used to clarify differences in biological activity. Our study established a correlation between the position of CRD amino acid side chains and the stimulation of NO release from endothelium.

C-type lectins are animal proteins that contain at least one carbohydrate recognition domain (CRD) capable of mediating sugar and calcium binding. Carbohydrate recognition is directly required for some biological functions, including the innate immune response. We cloned two novel C-type lectin (CTL) precursors from the commercial marine shrimp Litopenaeus vannamei. The cloned cDNAs encompass ORFs of 1044 nucleotides and encode highly similar two-domain polypeptides of 347 residues. The predicted proteins, LvCTL-br1 and -br2, contain the consensus triad that recognizes galactose (-GlnProAsp-) in CRD1 but also contain a mutated mannose-binding site (-GluProAsn-) in the second domain (CRD2). Phylogenetic analysis of LvCTL-br1 and -br2 and hundreds of CTL-like domain-containing proteins have allowed grouping of penaeid shrimp CTLs into three functional clusters. Reverse transcription coupled to PCR indicated that LvCTL-br1 expression is induced in shrimp gills upon IHHNV infection. Computational molecular modeling of LvCTL-br1 and -br2 revealed that three amino acid substitutions in CRD1 occur near the sugar binding site. Also, the 3-D models show a long loop of LvCTL-br1 CRD2 that might accommodate complex sugars. The structural data, evolutionary history and functional analysis support the hypothesis that gene duplication and accelerated evolution have caused functional diversification of penaeid shrimp C-type lectins.

Biofilms are assemblages of microorganisms and their associated extracellular products at an interface and typically with an abiotic or biotic surface. The study of the morphology of biofilms is important because they are associated with processes of biofouling, corrosion, catalysis, pollutant transformation, dental caries, drug resistance, and so forth. In the literature, biofilms have been examined by atomic force microscopy (AFM), which has proven to be a potent tool to study different aspects of the biofilm development on solid surfaces. In this work, we used AFM to investigate topographical changes during the development process ofEnterococcus faecalisbiofilms, which were generated on sterile cellulose nitrate membrane (CNM) filters in brain heart infusion (BHI) broth agar blood plates after 24, 36, 72, 192, and 360 h. AFM height images showed topographical changes due to biofilm development, which were used to characterize several aspects of the bacterial surface, such as the presence of extracellular polymeric substance, and the biofilm development stage. Changes in the development stage of the biofilm were shown to correlate with changes in the surface roughness as quantified through the mean roughness.

Lotus tetragonolobus lectin (LTA) is a fucose-specific legume lectin. Although several studies report a diverse combination of biological activities for LTA, little is known about the mechanisms involved in l -fucosyl oligosaccharide recognition. The crystal structure of LTA at 2.0 A resolution reveals a different legume lectin tetramer. Its structure consists of a homotetramer composed of two back-to-back GS4-like dimers arranged in a new mode, resulting in a novel tetramer. The LTA N -linked carbohydrate at Asn4 and the unusual LTA dimer–dimer interaction are related to its particular mode of tetramerization. In addition, we used small angle X-ray scattering to investigate the quaternary structure of LTA in solution and to compare it to the crystalline structure. Although the crystal structure of LTA has revealed a conserved metal-binding site, its l -fucose-binding site presents some punctual differences. Our investigation of the new tetramer of LTA and its fucose-binding site is essential for further studies related to cross-linking between LTA and complex divalent l -fucosyl carbohydrates.

A novel method for using residues from the cashew culture is presented. This work aimed to produce and characterize the incineration ashes of the primary residue derived from the cashew’s juice extraction, the peduncle bagasse. Measurements showed that these ashes represent only 3% of the incinerated material. EDX analysis indicated the presence of the following elements: C, O, P, K, Mg, S, Na, Al and Si. X-ray diffraction and thermal analyses pointed KHCO 3 (54.17%), K 2 SO 4 (34.08%) and MgKPO 4 · 6H 2 O (10.06%) as the most significant crystalline phases. These results indicate a possible use of this material as an imperishable source of potassium, sulfur, phosphor and magnesium in fertilizers and animal ration. Moreover, it may have many applications since its most abundant component is potassium bicarbonate, compound with several uses.

Pollens appear like a fine to coarse powder that is liberated by the microsporangia of Gimnosperms and Angiosperms. The pollen grain wall, the sporoderm, envelopes the microgametophytes (male gametophytes), which produce the male gametes of seed plants. Pollen grains are interesting from the material science point of view since the native polymer, the sporopollenin, found in the sporoderm outer layer (exine), is one of the toughest known materials which is degraded by oxidation but is resistant to reduction. This property permits the sporopollenin persistence as an unaltered polymer in sediments of great age, e.g the Ordovician period, 400 million years ago. Sporopollenin is a mixture of fatty acids, phenyl-derivatives as p-coumaric acid, and carotenes [1]. Its nanostructure is not yet completed revealed. Therefore, more studies must be performed. A number of models have been proposed for the sporopollenin nanostructure of spores and pollen grains [2]. Rowley et al. [3-4] interpret exine structure as being formed by helical subunits, based on transmission and scanning electron microscope (TEM and SEM) studies. The atomic force microscopy (AFM) is the ideal method to study the sporopollenin nanostructure [5] since the arrangement of components is not visualized easily through other microscope techniques (e.g. TEM and SEM). In the present work, we used AFM to study the sporopollenin nanostructure of the Ilex paraguariensis A.St.Hil. exine, an Angiosperm (Aquifoliaceae).

Lv-ranaspumin is a natural surfactant protein with a molecular mass of 23.5 kDa which was isolated from the foam nest of the frog Leptodactylus vastus. Only a partial amino-acid sequence is available for this protein and it shows it to be distinct from any protein sequence reported to date. The protein was purified from the natural source by ion-exchange and size-exclusion chromatography and was crystallized by sitting-drop vapour diffusion using the PEG/Ion screen at 293 K. A complete data set was collected to 3.5 Å resolution. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 51.96, b = 89.99, c = 106.00 Å. Assuming the presence of two molecules in the asymmetric unit, the solvent content was estimated to be 54%.

Plant lectins have been studied as histological markers and promising antineoplastic molecules for a long time, and structural characterization of different lectins bound to specific cancer epitopes has been carried out successfully. The crystal structures of Vatairea macrocarpa (VML) seed lectin in complex with GalNAc-α-O-Ser (Tn antigen) and GalNAc have been determined at the resolution of 1.4A and 1.7A, respectively. Molecular docking analysis of this new structure and other Tn-binding legume lectins to O-mucin fragments differently decorated with this antigen provides a comparative binding profile among these proteins, stressing that subtle alterations that may not influence monosaccharide binding can, nonetheless, directly impact the ability of these lectins to recognize naturally occurring antigens. In addition to the specific biological effects of VML, the structural and binding similarities between it and other lectins commonly used as histological markers (e.g., VVLB4 and SBA) strongly suggest VML as a candidate tool for cancer research.

Plant lectins, especially those purified from species of the Leguminosae family, represent the best-studied group of carbohydrate-binding proteins. Lectins purified from seeds of the Diocleinae subtribe exhibit a high degree of sequence identity notwithstanding that they show very distinct biological activities. Two main factors have been related to this feature: variance in key residues influencing the carbohydrate-binding site geometry and differences in the pH-dependent oligomeric state profile. In this work, we have isolated a lectin from Canavalia boliviana (Cbol) and solved its x-ray crystal structure in the unbound form and in complex with the carbohydrates Man(α1-3)Man(α1-O)Me, Man(α1-4)Man(α1-O)Me and 5-bromo-4-chloro-3-indolyl-α-D-mannose. We evaluated its oligomerization profile at different pH values using Small Angle X-ray Scattering and compared it to that of Concanavalin A. Based on predicted pKa-shifts of amino acids in the subunit interfaces we devised a model for the dimer-tetramer equilibrium phenomena of these proteins. Additionally, we demonstrated Cbol anti-inflammatory properties and further characterized them using in vivo and in vitro models.

A chitin-binding protein named PPL-2 was purified from Parkia platycephala seeds and crystallized. Crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 55.19, b = 59.95, c = 76.60 A, and grew over several days at 293 K using the hanging-drop method. Using synchrotron radiation, a complete structural data set was collected to 1.73 A resolution. The preliminary crystal structure of PPL-2, determined by molecular replacement, presents a correlation coefficient of 0.558 and an R factor of 0.439. Crystallographic refinement is in progress.

Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.

Light absorption of $\ensuremath{\alpha}$-glycine crystals grown by slow evaporation at room temperature was measured, indicating a $5.11\ifmmode\pm\else\textpm\fi{}0.02\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ energy band gap. Structural, electronic, and optical absorption properties of $\ensuremath{\alpha}$-glycine crystals were obtained by first-principles quantum mechanical calculations using density functional theory within the generalized gradient approximation in order to understand this result. To take into account the contribution of core electrons, ultrasoft and norm-conserving pseudopotentials, as well as an all electron approach were considered to compute the electronic density of states and band structure of $\ensuremath{\alpha}$-glycine crystals. They exhibit three indirect energy band gaps and one direct $\ensuremath{\Gamma}\text{\ensuremath{-}}\ensuremath{\Gamma}$ energy gap around $4.95\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. The optical absorption related to transitions between the top of the valence band and the bottom of the conduction band involves $\mathrm{O}\phantom{\rule{0.2em}{0ex}}2p$ valence states and $\mathrm{C},\mathrm{O}\phantom{\rule{0.2em}{0ex}}2p$ conduction states, with the carboxyl group contributing significantly to the origin of the energy band gap. The calculated optical absorption is highly dependent on the polarization of the incident radiation due to the spatial arrangement of the dipolar glycine molecules; in the case of a polycrystalline sample, the first-principles calculated optical absorption is in good agreement with the measurement when a rigid energy shift is applied.

The legume lectins from the subtribe Diocleinae, often referred to as concanavalin A-like lectins, are a typical example of highly similar proteins that show distinct biological activities. The pH-dependent oligomerization that some of these lectins undergo and the relative position of amino acids within the carbohydrate-binding site are factors that have been reported to contribute to these differences in the activities of Diocleinae lectins. In the present work, we determined the amino acid sequence and the crystal structure of the lectin of Dioclea rostrata seeds (DRL), with the aim of investigating the structural bases of the different behavior displayed by this lectin in comparison to other Diocleinae lectins and determining the reason for the distinct pH-dependent dimer-tetramer equilibrium. In addition, we discovered a novel multimeric arrangement for this lectin.

Plant lectins, especially those purified from species of the Leguminosae family, represent the best studied group of carbohydrate-binding proteins. The legume lectins from Diocleinae subtribe are highly similar proteins that present significant differences in the potency/efficacy of their biological activities. The structural studies of the interactions between lectins and sugars may clarify the origin of the distinct biological activities observed in this high similar class of proteins. In this way, this work presents a crystallographic study of the ConM and CGL (agglutinins from Canavalia maritima and Canavalia gladiata , respectively) in the following complexes: ConM/CGL:Man(α1-2)Man(α1- O )Me, ConM/CGL:Man(α1-3)Man(α1- O )Me and ConM/CGL:Man(α1-4)Man(α1- O )Me, which crystallized in different conditions and space group from the native proteins. The structures were solved by molecular replacement, presenting satisfactory values for R factor and R free . Comparisons between ConM, CGL and ConA ( Canavalia ensiformis lectin) binding mode with the dimannosides in subject, presented different interactions patterns, which may account for a structural explanation of the distincts biological properties observed in the lectins of Diocleinae subtribe.

Single crystals of monohydrated $L$-asparagine have been grown from aqueous solutions using $\mathrm{Mn}{\mathrm{Cl}}_{2}$ as doping material. Electron paramagnetic resonance (EPR) was used to determine the incorporation sites of ${\mathrm{Mn}}^{2+}$ ions in the crystal structure. Depending on small $p\mathrm{H}$ changes and crystal growth kinetics in the aqueous solutions, ${\mathrm{Mn}}^{2+}$ ions are incorporated in two chemically distinct sites in asparagine crystals. The first shows isotropic six-line hyperfine-split EPR spectra, whereas the second shows anisotropic multiple line splitting due to ${\mathrm{Mn}}^{2+}$ fine structure $(S=5∕2)$ and hyperfine interaction $(I=5∕2)$. Angular dependencies of the ${\mathrm{Mn}}^{2+}$ EPR spectra in three mutually perpendicular crystal planes were measured and analyzed. The results are discussed in terms of the metal incorporation site symmetry in the crystal structure of monohydrated $L$-asparagine.

We present the photoluminescence spectra of α‐glycine, L‐alanine, and L‐asparagine crystals. They are broad and structured, comprising green to ultraviolet emission in the 1.75–3.60 eV range. Absorption measurements show that the band gap energies of the crystals are of the order of 5.0 eV. Ab initio calculations of their electronic structures allow for the assignment of the observed peaks in the visible region to lattice‐related processes of exciton nature associated with polaron levels. The very thin photoluminescence peaks in the ultraviolet region are assigned to intramolecular transitions, being a signature of the weakly interacting amino acid molecules in the crystals.