Characterization of the Regions Involved in the Calcium-Induced Folding of the Intrinsically Disordered RTX Motifs from the Bordetella pertussis Adenylate Cyclase Toxin

Repeat in toxin (RTX) motifs are nonapeptide sequences found among numerous virulence factors of Gram-negative bacteria. In the presence of calcium, these RTX motifs are able to fold into an idiosyncratic structure called the parallel β-roll. The adenylate cyclase toxin (CyaA) produced by Bordetella pertussis, the causative agent of whooping cough, is one of the best-characterized RTX cytolysins. CyaA contains a C-terminal receptor domain (RD) that mediates toxin binding to the eukaryotic cell receptor. The receptor-binding domain is composed of about forty RTX motifs organized in five successive blocks (I to V). The RTX blocks are separated by non-RTX flanking regions of variable lengths. It has been shown that block V with its N- and C-terminal flanking regions constitutes an autonomous subdomain required for the toxicity of CyaA. Here, we investigated the calcium-induced biophysical changes of this subdomain to identify the respective contributions of the flanking regions to the folding process of the RTX motifs. We showed that the RTX polypeptides, in the absence of calcium, exhibited the hallmarks of intrinsically disordered proteins and that the C-terminal flanking region was critical for the calcium-dependent folding of the RTX polypeptides, while the N-terminal flanking region was not involved. Furthermore, the secondary and tertiary structures were acquired concomitantly upon cooperative binding of several calcium ions. This suggests that the RTX polypeptide folding is a two-state reaction, from a calcium-free unfolded state to a folded and compact conformation, in which the calcium-bound RTX motifs adopt a β-roll structure. The relevance of these results to the toxin physiology, in particular to its secretion, is discussed.     

Crystal Structure of the Electron Carrier Domain of the Reaction Center Cytochrome cz Subunit from Green Photosynthetic Bacterium Chlorobium tepidum

In green sulfur photosynthetic bacteria, the cytochrome c_z (cyt c_z) subunit in the reaction center complex mediates electron transfer mainly from menaquinol/cytochrome c oxidoreductase to the special pair (P840) of the reaction center. The cyt c_z subunit consists of an N-terminal transmembrane domain and a C-terminal soluble domain that binds a single heme group. The periplasmic soluble domain has been proposed to be highly mobile and to fluctuate between oxidoreductase and P840 during photosynthetic electron transfer. We have determined the crystal structure of the oxidized form of the C-terminal functional domain of the cyt c_z subunit (C-cyt c_z) from thermophilic green sulfur bacterium Chlorobium tepidum at 1.3-Å resolution. The overall fold of C-cyt c_z consists of four α-helices and is similar to that of class I cytochrome c proteins despite the low similarity in their amino acid sequences. The N-terminal structure of C-cyt c_z supports the swinging mechanism previously proposed in relation with electron transfer, and the surface properties provide useful information on possible interaction sites with its electron transfer partners. Several characteristic features are observed for the heme environment: These include orientation of the axial ligands with respect to the heme plane, surface-exposed area of the heme, positions of water molecules, and hydrogen-bond network involving heme propionate groups. These structural features are essential for elucidating the mechanism for regulating the redox state of cyt c_z.     

The Structure of Sedoheptulose-7-Phosphate Isomerase from Burkholderia pseudomallei Reveals a Zinc Binding Site at the Heart of the Active Site

Heptoses are found in the surface polysaccharides of most bacteria, contributing to structures that are essential for virulence and antibiotic resistance. Consequently, the biosynthetic enzymes for these sugars are attractive targets for novel antibiotics. The best characterized biosynthetic enzyme is GmhA, which catalyzes the conversion of sedoheptulose-7-phosphate into d-glycero-d-manno-heptopyranose-7-phosphate, the first step in the biosynthesis of heptose. Here, the structure of GmhA from Burkholderia pseudomallei is reported. This enzyme contains a zinc ion at the heart of its active site: this ion stabilizes the active, closed form of the enzyme and presents coordinating side chains as a potential acid and base to drive catalysis. A complex with the product demonstrates that the enzyme retains activity in the crystal and thus suggests that the closed conformation is catalytically relevant and is an excellent target for the development of therapeutics. A revised mechanism for the action of GmhA is postulated on the basis of this structure and the activity of B. pseudomallei GmhA mutants.     

Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

Protein kinase R (PKR) is an essential component of the innate immune response. In the presence of double-stranded RNA (dsRNA), PKR is autophosphorylated, which enables it to phosphorylate its substrate, eukaryotic initiation factor 2α, leading to translation cessation. Typical activators of PKR are long dsRNAs produced during viral infection, although certain other RNAs can also activate. A recent study indicated that full-length internal ribosome entry site (IRES), present in the 5′-untranslated region of hepatitis C virus (HCV) RNA, inhibits PKR, while another showed that it activates. We show here that both activation and inhibition by full-length IRES are possible. The HCV IRES has a complex secondary structure comprising four domains. While it has been demonstrated that domains III-IV activate PKR, we report here that domain II of the IRES also potently activates. Structure mapping and mutational analysis of domain II indicate that while the double-stranded regions of the RNA are important for activation, loop regions contribute as well. Structural comparison reveals that domain II has multiple, non-Watson-Crick features that mimic A-form dsRNA. The canonical and noncanonical features of domain II cumulate to a total of ∼ 33 unbranched base pairs, the minimum length of dsRNA required for PKR activation. These results provide further insight into the structural basis of PKR activation by a diverse array of RNA structural motifs that deviate from the long helical stretches found in traditional PKR activators. Activation of PKR by domain II of the HCV IRES has implications for the innate immune response when the other domains of the IRES may be inaccessible. We also study the ability of the HCV nonstructural protein 5A (NS5A) to bind various domains of the IRES and alter activation. A model is presented for how domain II of the IRES and NS5A operate to control host and viral translation during HCV infection.     

Light Activation of Rhodopsin: Insights from Molecular Dynamics Simulations Guided by Solid-State NMR Distance Restraints

Structural restraints provided by solid-state NMR measurements of the metarhodopsin II intermediate are combined with molecular dynamics simulations to help visualize structural changes in the light activation of rhodopsin. Since the timescale for the formation of the metarhodopsin II intermediate (> 1 ms) is beyond that readily accessible by molecular dynamics, we use NMR distance restraints derived from ¹³C dipolar recoupling measurements to guide the simulations. The simulations yield a working model for how photoisomerization of the 11-cis retinylidene chromophore bound within the interior of rhodopsin is coupled to transmembrane helix motion and receptor activation. The mechanism of activation that emerges is that multiple switches on the extracellular (or intradiscal) side of rhodopsin trigger structural changes that converge to disrupt the ionic lock between helices H3 and H6 on the intracellular side of the receptor.     

Architecture of the Tn7 Posttransposition Complex: An Elaborate Nucleoprotein Structure

Four transposition proteins encoded by the bacterial transposon Tn7, TnsA, TnsB, TnsC, and TnsD, mediate its site- and orientation-specific insertion into the chromosomal site attTn7. To establish which Tns proteins are actually present in the transpososome that executes DNA breakage and joining, we have determined the proteins present in the nucleoprotein product of transposition, the posttransposition complex (PTC), using fluorescently labeled Tns proteins. All four required Tns proteins are present in the PTC in which we also find that the Tn7 ends are paired by protein-protein contacts between Tns proteins bound to the ends. Quantification of the relative amounts of the fluorescent Tns proteins in the PTC indicates that oligomers of TnsA, TnsB, and TnsC mediate Tn7 transposition. High-resolution DNA footprinting of the DNA product of transposition attTn7∷Tn7 revealed that about 350 bp of DNA on the transposon ends and on attTn7 contact the Tns proteins. All seven binding sites for TnsB, the component of the transposase that specifically binds the ends and mediates 3′ end breakage and joining, are occupied in the PTC. However, the protection pattern of the sites closest to the Tn7 ends in the PTC are different from that observed with TnsB alone, likely reflecting the pairing of the ends and their interaction with the target nucleoprotein complex necessary for activation of the breakage and joining steps. We also observe extensive protection of the attTn7 sequences in the PTC and that alternative DNA structures in substrate attTn7 that are imposed by TnsD are maintained in the PTC.     

The synthesis of triethylphosphine gold(I) 4-nitrobenzenethiolate and solvent dependent visible absorption spectra of 4-nitrobenzenethiolate

The synthesis of triethylphosphine gold(I) 4-nitrobenzenethiolate, Et₃PAu(SC₆H₄NO₂-4), is reported. Et₃PAu(SC₆H₄NO₂-4) displays a low energy visible electronic absorption band which is solvent dependent: EtOH (λ_max = 385 nm), acetonitrile (λ_max = 391 nm), THF (λ_max = 395 nm), and DMSO (λ_max = 402 nm). The corresponding low energy visible electronic absorption band of 4-nitrobenzenethiolate, 4-NO₂C₆H₄S⁻ also shows solvent dependency: acetonitrile, (λ_max = 484 nm), DMSO (λ_max = 502 nm), dimethylformamide (λ_max = 505 nm). The positive solvatochromic shifts for Et₃PAu(SC₆H₄NO₂-4) and 4-NO₂C₆H₄S⁻ are consistent with an intraligand (IL) charge transfer transition, i.e. π(S) → ∗π (C₆H₄NO₂-4) or n(S) → ∗π (C₆H₄NO₂-4). Assignment of 4-NO₂C₆H₄S⁻ was aided by a DFT calculation.     

Structural, photolysis and biological studies of the bis(μ2-chloro)-tris(triphenylphosphine)-di-copper(I) and chloro-tris(triphenylphosphine)-copper(I) complexes. Study of copper(I)-copper(I) interactions

Direct reaction of copper(I) chloride with triphenylphosphine (tpp) in molar ratio 2:3 and 1:3, results in the formation of the [(tpp)Cu(μ₂-Cl)₂Cu(tpp)₂] (1) and {[CuCl(tpp)₃]·(CH₃CN)} (2) complexes. The complexes have been characterized by melting point, FT-IR, UV-Vis spectroscopic data and X-ray crystallography. Complex 1 is di-nuclear. Two μ₂-Cl atoms bridge two copper(I) ions with tetrahedral and trigonal geometry respectively. The short copper-copper bond distance of 2.9039(6) ? in case of 1 indicates d¹⁰-d¹⁰ interaction between metal centers. Thus, our studies were extended here in the determination of the quasi-aromaticity, which results in strong Cu-Cu interactions, using the computational method of nucleus-independent chemical shifts (NICS). The NICS calculated at the inner region of the Cu₂Cl₂P₃ core in complex 1 is shielded up to −6.05 ppm. Complex 2 is mono-nuclear where three phosphorus and one chloride atoms form a tetrahedron around the copper(I) ion. Photolysis of both complexes 1 and 2, results in the formation of triphenylphosphine oxide.The complexes 1 and 2, were tested for their in vitro cytotoxic activity against leiomyosarcoma cells (LMS) and human breast adenocarcinoma cells (MCF-7). The type of LMS cell death caused by the complexes was also evaluated by use of a flow cytometry assay. The results show that at concentration of 5 μΜ of complexes 1 and 2, 34.1% (1) and 19.6 (2)% of LMS cells undergo programmed cell death (apoptosis), while at 10 μΜ, 80.4% (1) and 65.2% (2) of LMS cells undergo apoptosis. The light sensitivity of the complex is discussed in relation with the biological activity.     

Versatile nuclearity in copper complexes with ortho functionalized 1,3-bis(aryl)triazenido ligands

The synthesis, characterization and crystal structures of three new copper complexes derived from 1,3-bis(aryl)triazenido ligands bearing either a methoxycarbonyl, methylthio or a hydroxymethyl group in the ortho position of one of the aromatic rings are reported. In addition to the coordination of the triazenido fragment, the Lewis basic groups coordinate to the copper centers to form complexes with different nuclearity: {1-[2-(methoxycarbonyl)phenyl]-3-[4-methylphenyl]}triazene and {1-[2-(methylthio)phenyl]-3-[4-methylphenyl]}triazene form stable dinuclear and tetranuclear Cu(I) complexes, respectively. Reaction of {1-[2-(hydroxymethyl)phenyl]-3-[4-methylphenyl]}triazene with either Cu(I) or Cu(II) results in a novel Cu(II) hexanuclear macrocyclic complex.     

Synthesis, structure and electronic spectra of new three-coordinated copper(I) complexes with tricyclohexylphosphine and diimine ligands

Three new copper(I) complexes with tricyclohexylphosphine (PCy₃) and different diimine ligands, [Cu(phen)(PCy₃)]BF₄ (1) (phen = 1,10′-phennanthroline), [Cu(bpy)(PCy₃)₂]BF₄ (2) (bpy = 2,2′-bipyridine) and [Cu(MeO-CNN)(PCy₃)]BF₄ (3) (MeO-CNN = 6-(4-methoxyl)phenyl-2,2′-bipyridine), have been synthesized and characterized. X-ray structure reveals that complexes 1 and 3 are three-coordinated with trigonal geometry, while complex 2 adopts distorted tetrahedron geometry. Complexes 1 and 3 exhibit ligand redistribution reactions in chloromethane solution by addition of excess amount of PCy₃, in which three-coordinated 1 changes into four-coordinated [Cu(phen)(PCy₃)₂]⁺, and 3 leads to form [Cu(PCy₃)₂]BF₄ and CNN-OMe. All the three complexes display yellow ³MLCT emissions in solid state at room temperature with λ_max at 558, 564 and 582 nm for 1, 2 and 3, respectively, and red-shift to 605, 628 and 643 nm at 77 K in dichloromethane solution.