Structural basis of transposon end recognition explains central features of Tn7 transposition systems.

Tn7 is a bacterial transposon with relatives containing element-encoded CRISPR-Cas systems mediating RNA-guided transposon insertion. Here, we present the 2.7 Å cryoelectron microscopy structure of prototypic Tn7 transposase TnsB interacting with the transposon end DNA. When TnsB interacts across repeating binding sites, it adopts a beads-on-a-string architecture, where the DNA-binding and catalytic domains are arranged in a tiled and intertwined fashion. The DNA-binding domains form few base-specific contacts leading to a binding preference that requires multiple weakly conserved sites at the appropriate spacing to achieve DNA sequence specificity. TnsB binding imparts differences in the global structure of the protein-bound DNA ends dictated by the spacing or overlap of binding sites explaining functional differences in the left and right ends of the element. We propose a model of the strand-transfer complex in which the terminal TnsB molecule is rearranged so that its catalytic domain is in a position conducive to transposition.

Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes.

Smad transcription factors are the main downstream effectors of the Transforming growth factor ß superfamily (TGFß) signalling network. The DNA complexes determined here by X-ray crystallography for the Bone Morphogenetic Proteins (BMP) activated Smad5 and Smad8 proteins reveal that all MH1 domains bind [GGC(GC)|(CG)] motifs similarly, although TGFß-activated Smad2/3 and Smad4 MH1 domains bind as monomers whereas Smad1/5/8 form helix-swapped dimers. Dimers and monomers are also present in solution, as revealed by NMR. To decipher the characteristics that defined these dimers, we designed chimeric MH1 domains and characterized them using X-ray crystallography. We found that swapping the loop1 between TGFß- and BMP- activated MH1 domains switches the dimer/monomer propensities. When we scanned the distribution of Smad-bound motifs in ChIP-Seq peaks (Chromatin immunoprecipitation followed by high-throughput sequencing) in Smad-responsive genes, we observed specific site clustering and spacing depending on whether the peaks correspond to BMP- or TGFß-responsive genes. We also identified significant correlations between site distribution and monomer or dimer propensities. We propose that the MH1 monomer or dimer propensity of Smads contributes to the distinct motif selection genome-wide and together with the MH2 domain association, help define the composition of R-Smad/Smad4 trimeric complexes.

Structural Bases for the Allergenicity of Fra a 1.02 in Strawberry Fruits.

Although strawberries are highly appreciated fruits, their intake can induce allergic reactions in atopic patients. These reactions can be due to the patient's previous sensitization to the major birch pollen allergen Bet v 1, by which IgE generated in response to Bet v 1 cross-reacts with the structurally related strawberry Fra a 1 protein family. Fra a 1.02 is the most expressed paralog in ripe strawberries and is highly allergenic. To better understand the molecular mechanisms regulating this allergic response, we have determined the three-dimensional structure of Fra a 1.02 and four site-directed mutants that were designed based on their positions in potential epitopes. Fra a 1.02 and mutants conform to the START fold. We show that the cross-reactivity of all the mutant variants to IgE from patients allergic to Bet v 1 was significantly reduced without altering the conserved structural fold, so that they could potentially be used as hypoallergenic Fra a 1 variants for the generation of vaccines against strawberry allergy in atopic patients.

Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-ß signaling.

TGF-ß receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-ß signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-ß signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-ß signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.

Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase.

Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and ß,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.

Complete blood count-derived inflammatory markers in adolescents with primary arterial hypertension: a preliminary report.

AIM OF THE STUDY: The aim of our study was to evaluate selected inflammatory markers in children with untreated primary hypertension and to establish the relation between inflammatory markers and 24-hour ambulatory blood pressure monitoring (ABPM) and clinical and biochemical parameters. MATERIAL AND METHODS: In 54 children (15.12 ±2.02 years) with untreated primary hypertension, with excluded overt inflammation, we evaluated: neutrophils (NEU; 1000/µl), lymphocytes (LYM; 1000/µl), platelets (PLT; 1000/µl), mean platelet volume (MPV; fl), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), ABPM (OSCAR 2 SUNTECH), and selected clinical and biochemical parameters. The control group consisted of 20 healthy children (15.55 ±2.27 years). RESULTS: Children with primary hypertension had (p < 0.01) higher 24-hour systolic, diastolic and mean blood pressure, systolic and diastolic blood pressure loads, and pulse pressure. Hypertensive children did not differ in inflammatory indicators (NEU, LYM, PLT, MPV, NLR, PLR) from the control group. In 54 hypertensive children we found the following correlations: between office systolic and diastolic blood pressure and MPV (r = 0.35, p = 0.011, r = 0.36, p = 0.008), between 24-hour ambulatory mean arterial pressure Z-score and NLR (r = 0.30, p = 0.030), 24-hour systolic blood pressure load and NLR (r = 0.38, p = 0.005), plasma renin activity and neutrophil count, NLR, PLR (r = 0.47, p = 0.016, r = 0.64, p < 0.001, r = 0.42, p = 0.033), urinary albumin loss and neutrophil count, NLR (r = 0.46, p = 0.001 and r = 0.42, p = 0.003). Multivariate analysis revealed that office SBP Z-score was related to MPV (ß = 0.35, p = 0.008) and albuminuria to neutrophil count (ß = 0.62, p = 0.018). CONCLUSIONS: In children with primary arterial hypertension there may be a relation between blood pressure, urinary albumin loss, and subclinical inflammation.

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

Smad transcription factors activated by TGF-ß or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-ß and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-ß and BMP pathways.

Structure of p300 in complex with acyl-CoA variants.

Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer. Lysine substrate binding is predicted to remodel the acyl-CoA ligands into a conformation compatible with acyl-chain transfer. This remodeling requires that the aliphatic portion of acyl-CoA be accommodated in a hydrophobic pocket in the enzymes active site. The size of the pocket and its aliphatic nature exclude long-chain and charged acyl-CoA variants, presumably explaining the cofactor preference for p300.

Food exchange estimation by children with type 1 diabetes at summer camp.

BACKGROUND: As exchange counting poses difficulty for children with type 1 diabetes (T1D) attending diabetes camps, they often guesstimate food amount without performing an exchange calculation. The aim of the study was to compare the accuracy of estimation with exchange counting using the mobile food exchange calculator (MFEC). METHODS: During a summer camp, 25 children with T1D on pumps estimated the number of carbohydrate (CE) and fat/protein exchanges (FPE) appropriate for main meals. Afterwards, the number of exchanges was counted with MFEC and electronic scales. RESULTS: There was a difference between CE (p<0.0001) and FPE (p<0.0001) estimations and counting using MFEC. The youth miscalculated the true values of ≥1 CE and ≥1 FPE by 31% and 23%, respectively. They more often underestimated than overestimated CE and FPE (p<0.0001). The estimation error increased with younger age. CONCLUSIONS: Carbohydrate counting caused significant error in the exchange number. The use of MFEC facilitates correct exchange calculation. Patients should weigh food and calculate exchanges themselves using mobile applications.

Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments.

Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors. A protein-binding nucleophile reacts reversibly with a bis-electrophilic warhead, thereby positioning the second electrophile in close proximity of the active site of a viral protease, resulting in the covalent de-activation of the enzyme. The concept is implemented for Coxsackie virus B3 3C protease, a pharmacological target against enteroviral infections. Using an aldehyde-epoxide as bis-electrophile, active fragment combinations are validated through measuring the protein inactivation rate and by detecting covalent protein modification in mass spectrometry. The structure of one enzyme-inhibitor complex is determined by X-ray crystallography. The presented warhead activation assay provides potent non-peptidic, broad-spectrum inhibitors of enteroviral proteases.

AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action.

Efficient repair by Escherichia coli AlkB dioxygenase of exocyclic DNA adducts 3,N(4)-ethenocytosine, 1,N(6)-ethenoadenine, 3,N(4)-α-hydroxyethanocytosine, and reported here for the first time 3,N(4)-α-hydroxypropanocytosine requires higher Fe(II) concentration than the reference 3-methylcytosine. The pH optimum for the repair follows the order of pK(a) values for protonation of the adduct, suggesting that positively charged substrates favorably interact with the negatively charged carboxylic group of Asp-135 side chain in the enzyme active center. This interaction is supported by molecular modeling, indicating that 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine are bound to AlkB more favorably in their protonated cationic forms. An analysis of the pattern of intermolecular interactions that stabilize the location of the ligand points to a role of Asp-135 in recognition of the adduct in its protonated form. Moreover, ab initio calculations also underline the role of substrate protonation in lowering the free energy barrier of the transition state of epoxidation of the etheno adducts studied. The observed time courses of repair of mixtures of stereoisomers of 3,N(4)-α-hydroxyethanocytosine or 3,N(4)-α-hydroxypropanocytosine are unequivocally two-exponential curves, indicating that the respective isomers are repaired by AlkB with different efficiencies. Molecular modeling of these adducts bound by AlkB allowed evaluation of the participation of their possible conformational states in the enzymatic reaction.

Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93.

Members of the Enterovirus genus of the Picornaviridae family are abundant, with common human pathogens that belong to the rhinovirus (HRV) and enterovirus (EV) species, including diverse echo-, coxsackie- and polioviruses. They cause a wide spectrum of clinical manifestations ranging from asymptomatic to severe diseases with neurological and/or cardiac manifestations. Pandemic outbreaks of EVs may be accompanied by meningitis and/or paralysis and can be fatal. However, no effective prophylaxis or antiviral treatment against most EVs is available. The EV RNA genome directs the synthesis of a single polyprotein that is autocatalytically processed into mature proteins at Gln↓Gly cleavage sites by the 3C protease (3C(pro)), which has narrow, conserved substrate specificity. These cleavages are essential for virus replication, making 3C(pro) an excellent target for antivirus drug development. In this study, we report the first determination of the crystal structure of 3C(pro) from an enterovirus B, EV-93, a recently identified pathogen, alone and in complex with the anti-HRV molecules compound 1 (AG7404) and rupintrivir (AG7088) at resolutions of 1.9, 1.3, and 1.5 Å, respectively. The EV-93 3C(pro) adopts a chymotrypsin-like fold with a canonically configured oxyanion hole and a substrate binding pocket similar to that of rhino-, coxsackie- and poliovirus 3C proteases. We show that compound 1 and rupintrivir are both active against EV-93 in infected cells and inhibit the proteolytic activity of EV-93 3C(pro) in vitro. These results provide a framework for further structure-guided optimization of the tested compounds to produce antiviral drugs against a broad range of EV species.

Practical highly enantioselective synthesis of (R)- and (S)-(E)-4-hydroxynon-2-enal.

Oxidative stress enhances lipid peroxidation (LPO) implicated in cancer promotion and progression. (E)-4-Hydroxynon-2-enal 1 (trans-4-hydroxy-2-nonenal, HNE) is one of the most abundant products of LPO. Reactions of HNE with DNA and proteins are responsible for its mutagenic and toxic effects. On the other hand, HNE is regarded as a key molecule in stress mediated cell cycle signaling. LPO generates racemic HNE (rac-1); however, it is expected that the individual enantiomers will behave differently in their interactions with cell components. The study of HNE stereochemistry in its chemical and biochemical interactions is hindered by the lack of expedient methods for preparation of pure enantiomers. This study presents one step synthesis of HNE in a cross-metathesis reaction between the commercially available oct-1-en-3-ol and acrolein in the presence of 2nd generation Grubbs catalyst. The use in the metathesis reaction of enantiomers of oct-1-en-3-ol obtained via Candida antarctica lipase resolution of the racemate allowed us to prepare of 4-(R)- and 4-(S)-enantiomers of HNE (R-1 and S-1, respectively) with excellent optical purity (97.5 and 98.4% ee, respectively) and good chemical yields (70%).

A highly active aqueous olefin metathesis catalyst bearing a quaternary ammonium group.

A polar olefin metathesis catalyst that bears a quaternary ammonium group was prepared from commercially available reagents. The electron-withdrawing quaternary ammonium group not only activates the Ru catalyst electronically but at the same time makes the catalyst more hydrophilic. The catalyst can therefore be efficiently used both in traditional media, such as dichloromethane and toluene, as well as in technical-grade alcohols, alcohol-water mixtures and in neat water. Various metathesis reactions, including ring-closing, cross- and enyne metathesis, were conducted in these solvents in the presence of air. In addition, the Ru catalyst can act as an inisurf (initiator and surfactant) molecule, promoting metathesis under heterogeneous aqueous conditions.