Ring Dimer Research Articles

Symmetry and Asymmetry of the RING–RING Dimer of Rad18

The human ubiquitin-conjugating enzyme Rad6 (E2), with ubiquitin ligase enzyme Rad18 (RING E3), monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Here, we determine the structure of the homodimeric Rad18 RING domains by X-ray crystallography and classify it to RING–RING dimers that dimerize through helices adjacent to the RING domains and through the canonical RING domains. Using NMR spectroscopy and site-directed mutagenesis, we demonstrate that the Rad6b binding site, for the Rad18 RING domain, strongly resembles that of other E2/E3 RING/U-box complexes. We show that the homodimeric Rad18 RING domain can recruit two Rad6b E2 enzymes, whereas the full-length Rad18 homodimer binds only to a single Rad6b molecule. Such asymmetry is a common feature of RING–RING heterodimers and has been observed for the CHIP U-box homodimer. We propose that asymmetry may be a common feature of dimeric RING E3 ligases.

6-(Trifluoromethyl)pyrimidine-2,4(1H,3H)-dione monohydrate

The title compound, C5H3F3N2O2·H2O, was prepared by the reaction of ethyl 4,4,4-trifluoro-3-oxobutano­ate with urea. In the crystal, the 6-(trifluoro­meth­yl)pyrimidine-2,4(1H,3H)-dione and water mol­ecules are linked by N—H⋯O and O—H⋯O hydrogen bonds. A ring dimer structure is formed by additional inter­molecular N—H⋯O hydrogen bonds.

Negative effective permeability at optical frequencies produced by rings of plasmonic dimers

Negative effective permeability at optical frequencies produced by rings of plasmonic dimers

Assembly of cyclic multi-nuclear Cu(I) cluster induced by Keggin-type arsenotungstate

An unprecedented 3D organic–inorganic hybrid compound [Cu 7(bipy) 7Cl 2(AsW 12O 40)]·2H 2O ( 1) has been hydrothermally synthesized and characterized by elemental analyses, IR and single-crystal X-ray diffraction. Compound 1 crystallizes in the triclinic system, space group P- 1 with a = 12.292(3) Å, b = 13.115(3) Å, c = 15.346(3) Å, α = 99.11(3)°, β = 91.35(3)°, γ = 104.34(3)°, V = 2361.5(8) Å 3 . X-ray diffraction reveals that compound 1 is the first 3D organic–inorganic hybrid based on the arsenotungstate Keggin POMs, in which the big 12-membered rings and the small four-membered ring dimers construct a 2D multi-nuclear Cu(I) cluster. The result again shows that the formation of the cyclic structure in the present work is attributed to the role of the polyoxoanion. Additionally, changing Cu metal ion into Ag, compound 2 (bipy) 4[AsW 12O 40]·2H 2O has been obtained and exhibits a supramolecular structure.

Bis(μ-1,2-bis{[2-(2-pyridyl)-1H-imidazol-1-yl]methyl}benzene)bis[bis(thiocyanato-κN)cadmium(II)

The asymmetric unit of the binuclear title compound, [Cd2(NCS)4(C24H20N6)2], contains one half-mol­ecule, consisting of one Cd2+ cation, two half 1,2-bis­{[2-(2-pyrid­yl)-1H-imidazol-1-yl]meth­yl}benzene (L) ligands and two SCN− anions. The dimeric cyclic mol­ecule is completed by crystallographic inversion symmetry. The Cd2+ cation is coordinated by two N atoms from two SCN− anions and four N atoms from two symmetry-related L ligands, exhibiting a distorted octrahedral coordination. A two-dimensional supra­molecular network stacked parallel to [210] is finally formed by linking these dimers through weak π–π stacking inter­actions between the pyridine rings and benzene rings of adjacent dimers, with a plane-to-plane distance of 3.36 (6) Å and a centroid–centroid distance of 3.67 (2) Å. One of the thio­cyanate S atoms is equally disordered over two positions.

(E)-2-[(2-Ethylphenyl)iminiomethyl]-6-hydroxyphenolate

The mol­ecule of the title compound, C15H15NO2, crystallizes in a zwitterionic form, and displays an E configuration about the C=N bond. The dihedral angle between the two aromatic rings is 5.59 (6)°. An intra­molecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal structure, pairs of mol­ecules are linked into centrosymmetric R 2 2(10) dimers by pairs of O—H⋯O hydrogen bonds. Aromatic π–π inter­actions are observed between the benzene rings of adjacent dimers [centroid–centroid distance = 3.4808 (7) Å].

Structural and Functional Characterization of the Monomeric U-Box Domain from E4B

Substantial evidence has accumulated indicating a significant role for oligomerization in the function of E3 ubiquitin ligases. Among the many characterized E3 ligases, the yeast U-box protein Ufd2 and its mammalian homologue E4B appear to be unique in functioning as monomers. An E4B U-box domain construct (E4BU) has been subcloned, overexpressed in Escherichia coli, and purified, which enabled determination of a high-resolution NMR solution structure and detailed biophysical analysis. E4BU is a stable monomeric protein that folds into the same structure observed for other structurally characterized U-box domain homodimers. Multiple sequence alignment combined with comparative structural analysis reveals substitutions in the sequence that inhibit dimerization. The interaction between E4BU and the E2 conjugating enzyme UbcH5c has been mapped using NMR, and these data have been used to generate a structural model for the complex. The E2 binding site is found to be similar to that observed for dimeric U-box and RING domain E3 ligases. Despite the inability to dimerize, E4BU was found to be active in a standard autoubiquitination assay. The structure of E4BU and its ability to function as a monomer are discussed in light of the ubiquitous observation of U-box and RING domain oligomerization.

Yeast cohesin complex embraces 2 micron plasmid sisters in a tri-linked catenane complex

Sister chromatid cohesion, crucial for faithful segregation of replicated chromosomes in eukaryotes, is mediated by the multi-subunit protein complex cohesin. The Saccharomyces cerevisiae plasmid 2 micron circle mimics chromosomes in assembling cohesin at its partitioning locus. The plasmid is a multi-copy selfish DNA element that resides in the nucleus and propagates itself stably, presumably with assistance from cohesin. In metaphase cell lysates, or fractions enriched for their cohesed state by sedimentation, plasmid molecules are trapped topologically by the protein ring formed by cohesin. They can be released from cohesin’s embrace either by linearizing the DNA or by cleaving a cohesin subunit. Assays using two distinctly tagged cohesin molecules argue against the hand-cuff (an associated pair of monomeric cohesin rings) or the bracelet (a dimeric cohesin ring) model as responsible for establishing plasmid cohesion. Our cumulative results most easily fit a model in which a single monomeric cohesin ring, rather than a series of such rings, conjoins a pair of sister plasmids. These features of plasmid cohesion account for its sister-to-sister mode of segregation by cohesin disassembly during anaphase. The mechanistic similarities of cohesion between mini-chromosome sisters and 2 micron plasmid sisters suggest a potential kinship between the plasmid partitioning locus and centromeres.

N-METHYL-1H- INDOLE-2-CARBOXAMIDE FROM THE MARINE FUNGUS CLADOSPORIUM CLADOSPORIOIDES

The crystal structure of N-methyl-1H- indole-2-carboxamide C10H10N2O was determined by single crystal X-ray diffraction. The structure can be described as consisting of an indole group and as substituent, linked at C2, the N-methylcarboxamide group. The molecular structure is essentially planar. The crystal packing results in N-H ------ O hydrogen bonds which join the molecules into centrosymmetric dimeric rings. The knowledge of the crystal structure allows a complete assignment of the 1H and 13C-NMR spectra. The N-methyl-lH- indole-2-carboxamide is the first indole derivative isolated from marine fungus.

An unexpected dimerisation in ambient daylight

Base catalysed condensation of indan-1,3-dione with 2-naphthaldehyde gave a mixture of the expected products 2-naphthalen-2-ylmethylene-indan-1,3-dione and a four membered ring dimer resulting from a daylight catalysed photochemical dimerisation.

N,N′-Dicyclohexyl-N-[4-(1H-indol-3-yl)butanoyl]urea

The title compound, C(25)H(35)N(3)O(2), is a novel urea derivative. Pairs of intermolecular N-H...O hydrogen bonds join the molecules into centrosymmetric R(2)(2)(12) and R(2)(2)(18) dimeric rings, which are alternately linked into one-dimensional polymeric chains along the [010] direction. The parallel chains are connected via C-H...O hydrogen bonds to generate a two-dimensional framework structure parallel to the (001) plane. The title compound was also modelled by solid-state density functional theory (DFT) calculations. A comparison of the molecular conformation and hydrogen-bond geometry obtained from the X-ray structure analysis and the theoretical study clearly indicates that the DFT calculation agrees closely with the X-ray structure.

Probing Peptide Nanotube Self-Assembly at a Liquid−Liquid Interface with Coarse-Grained Molecular Dynamics

Self-assembly at a liquid-liquid interface is a powerful experimental route to novel nanomaterials. We report herein a computational study of peptide nanotube formation at an oil-water interface. We probe interfacial self-assembly and nanotube formation of the cyclic octapeptide, cyclo [(-L-Trp-D-Leu-)4] as an illustrative example. Individual peptide rings are rapidly adsorbed at the liquid-liquid interface where they self-assemble. Monomeric and dimeric peptide rings lie with their molecular planes mostly parallel to the interface. Longer oligomeric nanotubes are increasingly tilted at the interface and grow by an Oswald ripening mechanism to eventually align their tube axis parallel to the interface. The present results on nanotube assembly suggest that computation will be a useful complement to experiment in understanding the nature of self-assembly of nanomaterials at liquid-liquid interfaces.

Crystal structure of human DAAM1 formin homology 2 domain

Reorganization of the actin filament is an essential process for cell motility, cell–cell attachment and intracellular transport. Formin proteins promote nucleation and elongation of the actin filament, and thus are key regulators for this process. The formin homology 2 (FH2) domain forms a head-to-tail ring-shaped dimer, and processively moves towards the barbed end. Dishevelled-associated activator of morphogenesis (DAAM) is a Rho-regulated formin implicated in neuronal development. Here, we present the crystal structure of human DAAM1 FH2 dimer at 2.8 A resolution. This is the first dimeric structure of the mammalian formin. The core structure of human DAAM1 is similar to those of mouse mDia1 and yeast Bni1p, whereas the orientations of the FH2 dimeric rings are different between human DAAM1 and yeast Bni1p, despite their similar dimer interactions. This difference supports the previous prediction that the dimer architecture of the formin is highly flexible in the actin-free state. The results of the actin assembly assays using the DAAM1 mutants demonstrated that the length of the linker connecting the N-terminal domain and the core region is crucial for the activity.

Molecular Self-Assembly Inhibition Leads to Basket-Shaped Cyclophane Formation with Chiral Dynamics

Planar perylene derivatives form macrocyclic dimers and concatenated dimer-dimer rings under the action of molecular self-assembly. If this underpinning principle is true, highly twisted perylene derivatives should be more frustrated toward formation of multimeric cyclic compounds such as macrocyclic dimers and concatenated dimer-dimers because of perturbation resulting from intermolecular pi-pi stacking. Indeed, 1,6,7,12- tetraphenoxy-substituted perylene is highly twisted and undergoes unimolecular cyclization rather than bimolecular or multimolecular cyclization. The resulting monocyclic monomer exhibits interesting conformation switching from one chiral structure (left-handedness) to another chiral structure (right-handedness) at room temperature. NMR studies of conformational dynamics reveal that such configuration change between the two enantiomers can be frozen at low temperature (-45 degrees C). An activation enthalpy barrier of 13.4 +/- 0.5 kcal.mol-1 for twisting the perylene plane in order to convert from one enantiomer to the other has been found.

Copper N 2S 2 Schiff base macrocycles: The effect of structure on redox potential

A series of bis-salicylidene based N 2S 2 copper macrocycles were prepared, structurally characterised and subjected to electrochemical analysis. The aim was to investigate the effects of length of polymethylene chains between either the imine donors or the sulfur donors on redox state and potential of the metal. The complexes structurally characterised had either distorted square planar or tetrahedral geometries depending on their oxidation state (Cu 2+ or Cu +, respectively), and the N–(CH 2) n –N bridge was found to be most critical moiety in determining the redox potential and oxidation state of the copper macrocycles, with relatively little change in these properties caused by lengthening the S–(CH 2) n –S bridge from two to three carbons. In fact, a weakness was observed in the complexes at the sulfur donor, as further lengthening of the S–(CH 2) n –S methylene bridge to four carbons caused fission of the carbon–sulfur bond to give dimeric rings and supramolecular assemblies. Cu + complexes could be oxidised to Cu 2+ by tert-butylhydroperoxide, with a corresponding change in the spectrophotometric properties, and likewise Cu 2+ complexes could be reduced to Cu + by treatment with β-mercaptoethylamine. However, repeated redox cycles appeared to compromise the stability of the macrocycles, most probably by a competing oxidation of the ligand. Thus the copper N 2S 2 macrocycles show potential as redox sensors, but further development is required to improve their performance in a biochemical environment.

Structure of the MID1 Tandem B-Boxes Reveals an Interaction Reminiscent of Intermolecular Ring Heterodimers,

The tripartite motif (TRIM) protein family, defined by N-terminal RING, B-box, and coiled-coil (RBCC) domains, consists of either a single type 2 B-box domain or tandem B-box domains of type 1 and type 2 (B1B2). Here, we report the first structure of the B-box domains in their native tandem orientation. The B-boxes are from Midline-1, a putative ubiquitin E3 ligase that is required for the proteosomal degradation of the catalytic subunit of protein phosphatase 2A (PP2Ac). This function of MID1 is facilitated by the direct binding of Alpha4, a regulatory subunit of PP2Ac, to B-box1, while B-box2 appears to influence this interaction. Both B-box1 and B-box2 bind two zinc atoms in a cross-brace motif and adopt a similar betabetaalpha structure reminiscent of the RING, PHD, ZZ, and U-box domains, although they differ from each other and with RING domains in the spacing of their zinc-binding residues. The two B-box domains pack against each other with the interface formed by residues located on the structured loop consisting of the two antiparallel beta-strands. The surface area of the interface is 188 A2 (17% of the total surface). Consistent with the globular structure, the Tm of the tandem B-box domain (59 degrees C) is higher than the individual domains, supporting a stable interaction between the B-box 1 and 2 domains. Notably, the interaction is reminiscent of the interaction of recently determined RING dimers, suggesting the possibility of an evolutionarily conserved role for B-box2 domains in regulating functional RING-type folds.

Energetics and Mechanism of the Decomposition of Trifluoromethanol

The thermal instability of alpha-fluoroalcohols is generally attributed to a unimolecular 1,2-elimination of HF, but the barrier to intramolecular HF elimination from CF3OH is predicted to be 45.1 +/- 2 kcal/mol. The thermochemical parameters of trifluoromethanol were calculated using coupled-cluster theory (CCSD(T)) extrapolated to the complete basis set limit. High barriers of 42.9, 43.1, and 45.0 kcal/mol were predicted for the unimolecular decompositions of CH2FOH, CHF2OH, and CF3OH, respectively. These barriers are lowered substantially if cyclic H-bonded dimers of CF3OH with complexation energies of approximately 5 kcal/mol are involved. A six-membered ring dimer has an energy barrier of 28.7 kcal/mol and an eight-membered dimer has an energy barrier of 32.9 kcal/mol. Complexes of CF3OH with HF lead to strong H-bonded dimers, trimers and tetramers with complexation energies of approximately 6, 11, and 16 kcal/mol, respectively. The dimer, CH3OH:HF, and the trimers, CF3OH:2HF and (CH3OH)2:HF, have decomposition energy barriers of 26.7, 20.3, and 22.8 kcal/mol, respectively. The tetramer (CH3OH:HF)2 gives rise to elimination of two HF molecules with a barrier of 32.5 kcal/mol. Either CF3OH or HF can act as catalysts for HF-elimination via an H-transfer relay. Because HF is one of the decomposition products, the decomposition reactions become autocatalytic. If the energies due to complexation for the CF3OH-HF adducts are not dissipated, the effective barriers to HF elimination are lowered from approximately 20 to approximately 9 kcal/mol, which reconciles the computational results with the experimentally observed stabilities.

Synthesis and Thermal Chemistry of Copper (I) Guanidinates

Copper (I) guanidinate dimers were generated by a salt metathesis route and structurally characterized. The guanidinates differed from the known amidinate dimers because of a large torsion of the dimer ring. This had a direct effect on their thermal chemistry. The thermal reactivity was investigated by several methods, including a novel temperature-resolved, gas-phase method that was monitored by mass spectrometry. The copper guanidinates underwent carbodiimide deinsertion to produce copper metal at temperatures between 225 -and 250 degrees C in the gas phase and at 125 degrees C in solution. The amidinate investigated also showed copper deposition at 190 degrees C in the gas phase, and 135 degrees C in solution, but without carbodiimide deinsertion. The guanidinate compounds deposited crystalline copper at 225 degrees C in a simple chemical vapor deposition experiment.

Thermodynamics and Kinetics of Glyoxal Dimer Formation: A Computational Study

Density functional theory (B3LYP//6-311+G) calculations including Poisson-Boltzmann implicit solvent were used to study the hydration of glyoxal and subsequent formation of dimeric species in solution. Our calculations show that the dioxolane ring dimer is the thermodynamic sink among all monomers and dimers with varying degrees of hydration. Although fully hydrated species are thermodynamically favored over their less hydrated counterparts, we find that a preliminary dehydration step precedes dimerization and ring closure. Ring closure of the open dimer monohydrate to the dioxolane ring dimer is kinetically favored over both hydration to the open dimer dihydrate and ring closure to form the dioxane ring dimer. The kinetic barriers for different geometric approaches for dimerization suggest an explanation why oligomerization stops after the formation of a dioxolane ring trimer as observed experimentally.

Crystal structure of human DAAM1 formin homology 2 domain

Reorganization of the actin filament is an essential process for cell motility, cell-cell attachment and intracellular transport. Formin proteins promote nucleation and elongation of the actin filament, and thus are key regulators for this process. The formin homology 2 (FH2) domain forms a head-to-tail ring-shaped dimer, and processively moves towards the barbed end. Dishevelled-associated activator of morphogenesis (DAAM) is a Rho-regulated formin implicated in neuronal development. Here, we present the crystal structure of human DAAM1 FH2 dimer at 2.8 A resolution. This is the first dimeric structure of the mammalian formin. The core structure of human DAAM1 is similar to those of mouse mDia1 and yeast Bni1p, whereas the orientations of the FH2 dimeric rings are different between human DAAM1 and yeast Bni1p, despite their similar dimer interactions. This difference supports the previous prediction that the dimer architecture of the formin is highly flexible in the actin-free state. The results of the actin assembly assays using the DAAM1 mutants demonstrated that the length of the linker connecting the N-terminal domain and the core region is crucial for the activity.