Intermolecular Dimerization Research Articles

Mechanistic insights in light-induced cAMP production by photoactivated adenylyl cyclase alpha (PACα)

The flagellate Euglena gracilis contains as photoreceptor complex a heterotetrameric light-sensitive adenylyl cyclase (AC), consisting of the flavoproteins PACalpha and PACbeta. Previously, we demonstrated the functional expression of PACalpha and PACbeta in oocytes from Xenopus laevis and of PACalpha in different animal cell types. Both yielded a blue light-induced increase of cellular [cAMP]. Here, we report that the action spectrum of PACalpha is flavoprotein-typical, with maxima at approximately 380 and approximately 470 nm. Mutational analysis of PACalpha yields a model for its structure and function. PACalpha shows a basal AC activity in the dark which is unaffected by mutating the conserved tyrosines in the two flavin-binding domains (F1, F2), Y60 in F1 and Y472 in F2. Y60 in F1 is, however, essential for photoactivation as light-stimulation of cyclase activity is completely lost in the F1 mutant Y60F. This effect does not occur in the respective mutation in F2 (Y472F). Mutating the two cyclase domains (C1, C2) indicated that C1 and C2 form a heterodimeric catalytic center as in mammalian class III cyclases. Interaction of C1 with C2 in the same molecule could be excluded as coexpression of non-functional C1 and C2 mutants restored light-induced cyclase activity. Our results strongly suggest an intermolecular dimerization of C1 and C2 domains on PACalpha for a functional enzyme.

Gold(III) Chloride Catalyzed Intermolecular Dimerization of 2-Ethynylanilines: Synthesis of Substituted Quinolines

An unprecedented gold(III)-catalyzed intermolecular dimerization of 2-ethynylanilines possessing terminal triple bond offers a general synthetic pathway to a wide range of highly substituted quinolines.

Bone Morphogenetic Protein 15 (BMP15) Acts as a BMP and Wnt Inhibitor during Early Embryogenesis

Bone morphogenetic protein 15 (BMP15) belongs to an unusual subgroup of the transforming growth factor beta (TGFbeta) superfamily of signaling ligands as it lacks a key cysteine residue in the mature region required for proper intermolecular dimerization. Naturally occurring BMP15 mutation leads to early ovarian failure in humans, and BMP15 has been shown to activate the Smad1/5/8 pathway in that context. Despite its important role in germ cell specification, the embryological function of BMP15 remains unknown. Surprisingly, we find that during early Xenopus embryogenesis BMP15 acts solely as an inhibitor of the Smad1/5/8 pathway and the Wnt pathway. BMP15 gain-of-function leads to embryos with secondary ectopic heads and to direct neural induction in intact explants. BMP15 inhibits BMP4-mediated epidermal induction in dissociated explants. BMP15 strongly inhibits BRE response induced by BMP4 and blocks phosphorylation and activation of Smad1/5/8 MH2-domain. Mechanistically, BMP15 protein specifically interacts with BMP4 protein, suggesting inhibition upstream of receptor binding. Loss-of-function experiments using morpholinos or a naturally occurring human BMP15 dominant-negative mutant (BMP15-Y235C) leads to embryos lacking head. BMP15-Y235C also eliminates the inhibitory activity of BMP15 on BRE (BMP-responsive element). Finally, we show that BMP15 inhibits the canonical branch of the Wnt pathway, upstream of beta-catenin. We, thus, demonstrate that BMP15 is necessary and sufficient for the specification of dorso-anterior structures and highlight novel mechanisms of BMP15 function that strongly suggest a reinterpretation of its function in ovaries specially for ovarian failure.

Ataxia telangiectasia mutated activation by transcription‐ and topoisomerase I‐induced DNA double‐strand breaks

Ataxia telangiectasia mutated (ATM), the deficiency of which causes a severe neurodegenerative disease, is a crucial mediator for the DNA damage response (DDR). As neurons have high rates of transcription that require topoisomerase I (TOP1), we investigated whether TOP1 cleavage complexes (TOP1cc)-which are potent transcription-blocking lesions-also produce transcription-dependent DNA double-strand breaks (DSBs) with ATM activation. We show the induction of DSBs and DDR activation in post-mitotic primary neurons and lymphocytes treated with camptothecin, with the induction of nuclear DDR foci containing activated ATM, gamma-H2AX (phosphorylated histone H2AX), activated CHK2 (checkpoint kinase 2), MDC1 (mediator of DNA damage checkpoint 1) and 53BP1 (p53 binding protein 1). The DSB-ATM-DDR pathway was suppressed by inhibiting transcription and gamma-H2AX signals were reduced by RNase H1 transfection, which removes transcription-mediated R-loops. Thus, we propose that Top1cc produce transcription arrests with R-loop formation and generate DSBs that activate ATM in post-mitotic cells.

Mechanism underlying apolipoprotein E (ApoE) isoform-dependent lipid efflux from neural cells in culture.

We determined the molecular mechanisms underlying apolipoprotein E (ApoE)-isoform-dependent lipid efflux from neurons and ApoE-deficient astrocytes in culture. The ability of ApoE3 to induce lipid efflux was 2.5- to 3.9-fold greater than ApoE4. To explore the contributions of the amino- and carboxyl-terminal tertiary structure domains of ApoE to cellular lipid efflux, each domain was studied separately. The amino-terminal fragment of ApoE3 (22-kDa-ApoE3) induced lipid efflux greater than 22-kDa-ApoE4, whereas the common carboxyl-terminal fragment of ApoE induced very low levels of lipid efflux. Addition of segments of the carboxyl-terminal domain to 22-kDa-ApoE3 additively induced lipid efflux in a length-dependent manner; in contrast, this effect did not occur with ApoE4. This observation, coupled with the fact that introduction of the E255A mutation (which disrupts domain-domain interaction) into ApoE4 increases lipid efflux, indicates that interaction between the amino- and carboxyl-terminal domains in ApoE4 reduces the ability of this isoform to mediate lipid efflux from neural cells. Dimeric 22-kDa or intact ApoE3 induced higher lipid efflux than monomeric 22-kDa or intact ApoE3, respectively, indicating that dimerization of ApoE3 enhances the ability to release lipids. The adenosine triphosphate-binding cassette protein A1 (ABCA1) is involved in ApoE-induced lipid efflux. In conclusion, there are two major factors, intramolecular domain interaction and intermolecular dimerization, that cause ApoE-isoform-dependent lipid efflux from neural cells in culture.

MIII(dmit)2]−-Coordinated MnIII Salen-Type Dimers (MIII = NiIII, AuIII; dmit2− = 1,3-Dithiol-2-thione-4,5-dithiolate): Design of Single-Component Conducting Single-Molecule Magnet-Based Materials

Four linear-type tetranuclear complexes, [Mn(5-Rsaltmen){M(dmit)(2)}](2) (R = MeO, M = Ni, 1a; M = Au, 1b; R = Me, M = Ni, 2a; M = Au, 2b), were synthesized and structurally characterized (5-Rsaltmen(2-) = N,N '-(1,1,2,2-tetramethylethylene)-bis(5-Rsalicylideneiminate), dmit(2-) = 1,3-dithiol-2-thione-4,5-dithiolate). These compounds crystallize in the same triclinic P1 space group (Z = 1) and have a similar molecular structure with a bridging array of [M-(dmit)-Mn-(O(Ph))(2)-Mn-(dmit)-M] and a packing feature where the respective sets of 1a/1b and 2a/2b are isomorphous. Intermolecular pi-pi/S...S contacts are observed between the coordinating [M(dmit)(2)](-) moieties to form zigzag stair-like columns along the a axis direction. Huckel calculations revealed a strong intermolecular dimerization within the [Ni(dmit)(2)](-) column that makes them magnetically silent even at room temperature. Nevertheless, 1a and 2a with M = Ni behave as semiconductors with sigma(r.t.) = 7 x 10(-4) S x cm(-1) and E(a) = 182 meV for 1a and sigma(r.t.) = 1 x 10(-4) S x cm(-1) and E(a) = 292 meV for 2a, while 1b and 2b with M = Au are insulators. As a result of the strong dimerization of the [Ni(dmit)(2)](-) anions, the magnetic properties of 1a are essentially identical to those of 1b and 2b, which can be described as isolated Mn(III) dimers, acting as single-molecule magnets (SMM). Meanwhile, the magnetic properties of 2a are dominated by the intermolecular Mn...Mn antiferromagnetic interactions via the singlet [Ni(dmit)(2)](2)(2-) dimer (J(Mn...Mn)/k(B) = -2.85 K), inducing a long-range antiferromagnetic order at T(N) = 6.4 K. The present systems are unique materials made of neutral single-component complexes that exhibit two major solid-state properties, that is, electrical conductivity and magnetism, varied as semiconductor/SMM for 1a, insulator/SMM for 1b and 2b, and semiconductor/antiferromagnet for 2a by tuning metal center and partial structural modification.

Hydrogen-Bonded Cyclic Dimer Formation in Temperature-Induced Reversal of Tautomerism of Salicylideneanilines

Tautomeric equilibrium of salicylideneanilines is in favor of the enol form in most organic solvents at room temperature. We have previously reported that the equilibrium in saturated hydrocarbon solvents is reversed at low temperature, being totally in favor of the cis-keto form, which is unfavorable at room temperature. Although this stabilization of the cis-keto form has been explained in terms of aggregation of molecules at low temperature, the structure of the aggregate has remained uncharacterized. In this study, we measured UV-vis absorption spectra of salicylideneanilines including those which have tert-butyl groups at various positions of the benzene rings. The cis-keto form did not appear at low temperature, when salicylideneanilines have a tert-butyl group at a specific position or is restrained to a planar conformation. From these results we propose here that the temperature-induced reversal of the tautomeric equilibrium proceeds through the formation of intermolecular hydrogen-bonded cyclic dimers and the subsequent formation of the higher-order aggregates.

Bis(BF2)-2,2′-bidipyrrins, a class of BODIPY dyes with new spectroscopic and photophysical properties

The photophysical and spectroscopic characterization of four new dimeric bis(BF2)-2,2′-bidipyrrins (BisBODIPYs) recently synthesized and characterized (Chem. Eur. J., 2008, 14, 2976–2983) has been undertaken along with that of the component BODIPY monomers. The monomers display the typical photophysical properties of this family; (i) narrow and intense single absorption band in the visible range at 530 nm; (ii) intense, solvent independent emission (Φflca. 1); (iii) narrow emission band with a 200–400 cm−1 Stokes shifted emission, independent of solvent polarity; (iv) no absorption features for the singlet excited state; (v) very little triplet yield and no ability to sensitize singlet oxygen. The absorption spectra of the corresponding new dimers exhibit split band maxima in the visible range at about 490 and 560 nm, corresponding to an exciton splitting of ca. 2600 cm−1. The luminescence in toluene is strong (Φflca. 0.7, τ =3.4 ns), broad and Stokes shifted by ca. 2200 cm−1, but both luminescence yield and Stokes shift are solvent polarity dependent; Φfl < 0.1, τ < 1 ns and the Stokes shift is close to 2700 cm−1 in acetonitrile. Solvent viscosity does not appear to play an important role and freezing of the solvents to 77 K in a solid matrix cancels the differences in luminescence parameters. Singlet and triplet excited state absorbance was measured in toluene and acetonitrile and the ability of these new dyes to sensitize singlet oxygen was examined. The nature and dynamics of the excited state is discussed in comparison with the monomers properties and with some intra- or inter-molecular BODIPY dimers reported in the literature. Potential applications of these new dyes with respect to BODIPYs are pointed out on the basis of their spectroscopic and photophysical properties.

Redox-induced partner radical formation and its dynamic balance with radical dimer in cucurbit[8]uril

N-(4-Hydroxy-phenoxyethyl)-N'-ethyl-4,4'-bipyridium (1) can form a stable 1 : 1 inclusion complex with CB[8] in aqueous solution, in which the hydroxyphenol (HP) moiety is back-folded and inserted together with the viologen moiety into the cavity of CB[8]. When the ethyl viologen dication (EV(2+)) in 1 is reduced, chemically or electrochemically, an intramolecular partner radical (EV(+)*-HP)/CB[8] can be detected, meanwhile, a dynamic balance between the partner radical and the intermolecular radical dimer (EV(+)*-HP)(2)/CB[8] can be observed.

Competition between Reversible Aggregation and Loop Formation in Denatured Iso-1-cytochrome c

The competition between intramolecular histidine-heme loop formation and ligand-mediated oligomer formation in the denatured state is investigated for two yeast iso-1-cytochrome c variants, AcH26I52 and AcA25H26I52. Besides the native His 18 heme ligand, both variants contain a single His at position 26. The AcA25H26I52 variant has Pro 25 mutated to Ala. The concentration dependence of the apparent pK(a) for His 26-heme binding in 3 M guanidine hydrochloride indicates that the P25A mutation disfavors oligomerization mediated by intermolecular heme ligation by 10-fold. Single- and double-pH-jump stopped-flow experiments with the AcH26I52 variant show that fast phases for His-heme bond formation and breakage are due to intramolecular loop formation and slow phases for His-heme bond formation and breakage are due to intermolecular aggregation. The presence of two closely spaced slow phases in the kinetics of loop formation for both variants suggests that intermolecular His 26-heme ligation results in both dimers and higher-order aggregates. The P25A mutation slows formation and speeds breakdown of an initial dimer, demonstrating a strong effect of local sequence on aggregation. Analysis of the kinetic data yields equilibrium constants for intramolecular loop formation and intermolecular dimerization at pH 7.1 and indicates that the rate constant for intermolecular aggregation is very fast at this pH (10(7)-10(8) M(-1) s(-1)). In light of the very fast rates of aggregation in the denatured state, comparison of models involving reversible or irreversible oligomerization steps suggests that equilibrium control of the partitioning between folding and aggregation is advantageous for productive protein folding in vivo.

A simple approach towards shape-persistent nanoscale pyridine macrocycles

Abstract Two new shape-persistent macrocycles with intraannular pyridine groups are described. The cyclization is performed by an intermolecular oxidative acetylene dimerization of two “half-rings” which is prepared by Pd-catalyzed aryl acetylene coupling reactions. In both cases the ring building blocks are synthesized from pyrylium salts, either by treating with sodium pyridyl acetate or with ammonia. One macrocycle could be crystallized from pyridine as a solvate. It adopts a cyclohexane-like chair conformation in which the empty space inside the rings hosts the solvent molecules.

Water-soluble xanthobilirubinic acids?

Xanthobilirubinic acid, a model dipyrrinone for one-half of the bilirubin molecule in photochemical and metabolism studies, is more polar than bilirubin and insoluble in water and in chloroform. Replacing the b-alkyl substituents on the lactam ring of xanthobilirubinic acid with methyl-capped ethylene glycol, diethylene glycol, and triethylene glycol (PEG) groups steadily increased the water solubility of the pigment so that the last is com- pletely soluble in both water and chloroform. Synthesized by base-catalyzed condensation of the corresponding methyl-capped 3,4-diPEG-pyrrolin-2-one with 3,5-dime- thyl-4(2-ethoxycarbonylethyl)-2-formyl-1H-pyrrole, these new PEGylated analogs of xanthobilirubinic acid are yel- low-colored dipyrrinones that form intermolecular hydrogen-bonded dimers in chloroform solution but are monomeric in methanol and water, as revealed by 1 HN MR spectroscopy and vapor pressure osmometry. Methyl xanthobilirubinate has served as a synthetic precursor to bilirubinoids; its amphiphilic PEGylated analogs suggest a route to water-soluble bilirubinoids and biliverdinoids.

ChemInform Abstract: InBr3‐Promoted Divergent Approach to Polysubstituted Indoles and Quinolines from 2‐Ethynylanilines: Switch from an Intramolecular Cyclization to an Intermolecular Dimerization by a Type of Terminal Substituent Group.

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Allochromatium vinosum DsrC: Solution-State NMR Structure, Redox Properties, and Interaction with DsrEFH, a Protein Essential for Purple Sulfur Bacterial Sulfur Oxidation

Sequenced genomes of dissimilatory sulfur-oxidizing and sulfate-reducing bacteria containing genes coding for DsrAB, the enzyme dissimilatory sulfite reductase, inevitably also contain the gene coding for the 12-kDa DsrC protein. DsrC is thought to have a yet unidentified role associated with the activity of DsrAB. Here we report the solution structure of DsrC from the sulfur-oxidizing purple sulfur bacterium Allochromatium vinosum determined with NMR spectroscopy in reducing conditions, and we describe the redox behavior of two conserved cysteine residues upon transfer to an oxidizing environment. In reducing conditions, the DsrC structure is disordered in the highly conserved carboxy-terminus. We present multiple lines of evidence that, in oxidizing conditions, a strictly conserved cysteine (Cys111) at the penultimate position in the sequence forms an intramolecular disulfide bond with Cys100, which is conserved in DsrC in all organisms with DsrAB. While an intermolecular Cys111-Cys111 disulfide-bonded dimer is rapidly formed under oxidizing conditions, the intramolecularly disulfide-bonded species (Cys100-Cys111) is the thermodynamically stable form of the protein under these conditions. Treatment of the disulfidic forms with reducing agent regenerates the monomeric species that was structurally characterized. Using a band-shift technique under nondenaturing conditions, we obtained evidence for the interaction of DsrC with heterohexameric DsrEFH, a protein encoded in the same operon. Mutation of Cys100 to serine prevented formation of the DsrC species assigned as an intramolecular disulfide in oxidizing conditions, while still allowing formation of the intermolecular Cys111-Cys111 dimer. In the reduced form, this mutant protein still interacted with DsrEFH. This was not the case for the Cys111Ser and Cys100Ser/Cys111Ser mutants, both of which also did not form protein dimers. Our observations highlight the central importance of the carboxy-terminal DsrC cysteine residues and are consistent with a role as a sulfur–substrate binding/transferring protein, as well as with an electron-transfer function via thiol–disulfide interchanges.

Immobilization of Grubbs Catalyst as Supported Ionic Liquid Catalyst (Ru-SILC)

Grubbs olefin metathesis catalyst was immobilized as a ruthenium-supported ionic liquid catalyst (Ru-SILC) in pores of amorphous alumina with the aid of ionic liquid [hmim]PF6. This Ru-SILC was effective for various olefin metathesis reactions such as intra- or intermolecular macrocyclization and dimerization, and used up to six times after simple decantation.

Unsaturated Strained Cyclophanes Based on Dibenz[a,j]anthracene by an Intramolecular McMurry Olefination

A new type of rigid conjugated unsaturated strained cyclophane derivative containing dibenz[a,j]anthracene units was facilely synthesized through an intramolecular McMurry reaction without intermolecular dimerization products in good yields. The photophysical properties of these cyclophane derivatives in dilute solution were investigated, and molecular modeling was employed to study their electronic properties.

InBr3-Promoted Divergent Approach to Polysubstituted Indoles and Quinolines from 2-Ethynylanilines: Switch from an Intramolecular Cyclization to an Intermolecular Dimerization by a Type of Terminal Substituent Group

Use of a 2-ethynylaniline having an alkyl or aryl group on the terminal alkyne selectively produced a variety of polyfunctionalized indole derivatives in moderate to excellent yields via indium-catalyzed intramolecular cyclization of the corresponding alkynylaniline. In contrast, employment of a substrate with a trimethylsilyl group or with no substituent group on the terminal triple bond, exclusively afforded polysubstituted quinoline derivatives in good yields via indium-promoted intermolecular dimerization of the ethynylaniline. This indium catalytic system successfully accommodated the intramolecular cyclization of other arylalkyne skeletons involving a carboxylic acid and an amide group.

Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites

Protein kinase autophosphorylation of activation segment residues is a common regulatory mechanism in phosphorylation-dependent signalling cascades. However, the molecular mechanisms that guarantee specific and efficient phosphorylation of these sites have not been elucidated. Here, we report on three novel and diverse protein kinase structures that reveal an exchanged activation segment conformation. This dimeric arrangement results in an active kinase conformation in trans, with activation segment phosphorylation sites in close proximity to the active site of the interacting protomer. Analytical ultracentrifugation and chemical cross-linking confirmed the presence of dimers in solution. Consensus substrate sequences for each kinase showed that the identified activation segment autophosphorylation sites are non-consensus substrate sites. Based on the presented structural and functional data, a model for specific activation segment phosphorylation at non-consensus substrate sites is proposed that is likely to be common to other kinases from diverse subfamilies.

Solvent‐Free Photosynthesis of Cyclobutanes: Photodimerization of Crystalline Olefins

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Role of the C-terminal domains of rice (Oryza sativa L.) bZIP proteins RF2a and RF2b in regulating transcription

Rice (Oryza sativa L.) transcription factors RF2a and RF2b are bZIP (basic leucine zipper) proteins that interact with, and activate transcription from the RTBV (rice tungro bacilliform virus) promoter. Here we characterize the C-terminal domains of RF2a and RF2b: these domains are rich in glutamine and proline/glutamine, respectively. Affinity pull-down assays demonstrated that the C-terminal domains of RF2a and RF2b can associate to form either homodimers or heterodimers; however, they do not interact with other domains of RF2a or RF2b. Results of in vitro transcription assays using a rice whole-cell extract demonstrate that the C-terminal domains of both RF2a and RF2b activate transcription from the RTBV promoter. In addition, dimerization of the RF2a C-terminal domain is involved in regulating the transcription activation function of RF2a. The predicted helical region within the RF2a C-terminal glutamine-rich domain was determined to be involved in inter-molecular dimerization, and contributed to the regulatory functions of RF2a in these assays.