Open Dimer Research Articles

Coherent and Incoherent Interactions between Cofacial Π-Conjugated Oligomer Dimers in Macrocycle Templates

The interactions between two π-conjugated oligomers templated in molecular scaffolds are revealed as a function of separation and orientation, providing models of intermolecular interactions in bulk organic semiconductor materials. For a variety of dimer geometries (acyclic and macrocyclic) of the same model oligomer, no change in fluorescence spectra, fluorescence dynamics, or low-temperature single-molecule emission characteristics is observed. A small red-shift and slowing of fluorescence in the most closely spaced macrocyclic dimer structure is thought to arise both due to an intramolecular solvatochromic shift as well as from weak intramolecular aggregate formation. No corresponding effect is observed in bulk films of the acyclic model oligomer, implying the absence of intermolecular aggregate or excimer formation due to random relative dipole orientations. The largest effect of intramolecular geometry of the model dimer structures is seen in transient fluorescence depolarization, where an open ring geometry leads to rapid depolarization, compared to the corresponding macrocycle, due to the presence of a range of molecular transition dipole moment orientations. Self-assembled monolayers of the molecules on HOPG investigated by scanning-tunneling microscopy further illustrate the conformational variability of the open dimers in contrast to the fixed conformation of the closed dimers.

A Photophysical Study of the α‐Carboline (1‐Azacarbazole) Aggregation Process

This paper reports a comprehensive photophysical study of the aggregation process of 1-azacarbazole, or α-carboline (9H-pyrido[2,3-b]indole), AC, in low polar aprotic solvents by using absorption, steady state and time-resolved fluorescence spectroscopic techniques. To ascertain the characteristics of the aggregation process we have studied the changes produced by the increase of the AC concentration and the decrease of the temperature on the absorption and fluorescence spectra of the AC monomer. Previously, to aid the interpretation of these results, the hydrogen bonding interactions of the AC monomer with pyridine, PY, and indole, IND, have been also analyzed. The results obtained from these studies reveal that, under our experimental conditions, AC does not form doubly hydrogen bonded cyclic dimers, (AC)(2), but singly hydrogen bonded open dimers, AC-AC, and open higher aggregates, (-AC-)(n). The formation of these species shifts to the red the absorption spectrum of the AC monomer and quenches its fluorescence.

Enhanced Selectivity for Sulfatide by Engineered Human Glycolipid Transfer Protein

Human glycolipid transfer protein (GLTP) fold represents a novel structural motif for lipid binding/transfer and reversible membrane translocation. GLTPs transfer glycosphingolipids (GSLs) that are key regulators of cell growth, division, surface adhesion, and neurodevelopment. Herein, we report structure-guided engineering of the lipid binding features of GLTP. New crystal structures of wild-type GLTP and two mutants (D48V and A47D‖D48V), each containing bound N-nervonoyl-sulfatide, reveal the molecular basis for selective anchoring of sulfatide (3-O-sulfo-galactosylceramide) by D48V-GLTP. Directed point mutations of "portal entrance" residues, A47 and D48, reversibly regulate sphingosine access to the hydrophobic pocket via a mechanism that could involve homodimerization. "Door-opening" conformational changes by phenylalanines within the hydrophobic pocket are revealed during lipid encapsulation by new crystal structures of bona fide apo-GLTP and GLTP complexed with N-oleoyl-glucosylceramide. The development of "engineered GLTPs" with enhanced specificity for select GSLs provides a potential new therapeutic approach for targeting GSL-mediated pathologies.

Synthesis and properties of a triphenylene–butadiynylenemacrocycle

The synthesis and characterization of a shape-persistent triphenylene–butadiynylene macrocycle formed by intermolecular Glaser-coupling of two “half-rings” and also by intramolecular coupling of the appropriate open dimer, respectively, are described in detail. The investigation of the photophysics has revealed that—compared to its open dimer—the macrocycle is more conjugated in the ground state and less so in the excited state, a result of the diacetylene bending in the macrocycle due to its constrained topology. The macrocycle is decorated with flexible side groups that support its adsorption on highly oriented pyrolytic graphite (HOPG) where a concentration-dependence of the 2D-structure is observed by means of scanning tunnelling microscopy (STM). The flexible side groups also guarantee a high compound solubility even in nonpolar solvents (cyclohexane). However, solvophobic interactions lead to the formation of a tube-like superstructure, as revealed by dynamic light scattering, X-ray scattering and atomic force microscopy.

Ｇｅｔ複合体によるＴａｉｌ‐ａｎｃｈｏｒｅｄタンパク質の膜埋込みメカニズム

Tail anchored proteins, defined by a single transmembrane domain at C-terminus, are post-translationally inserted into the membrane by Get3 ATPase. Here we report the crystal structure of Get3 in ADP-bound and nucleotide free forms. Get3 forms an open dimer conformation, in which two subunits are linked by a Zn2+ ion. Together with the biochemical studies, we propose the ATP independent TA protein binding, and the membrane insertion by conformational change of Get3 coupled with ATP hydrolysis.

IR spectra of cyclic hydrogen-bonded complexes of bifunctional nitrogen compounds in solution

We measured the IR absorption spectra of self-associates and complexes with carboxylic acids of 3,5-dimethylpyrazole (DMP), diphenylformamidine (DPFA), diphenyltriazene (DPT), and diphenylguanidine (DPG) in solutions in a wide range of concentrations and temperatures and calculated spectroscopic, geometric, and energy characteristics of complexes in the quantum-mechanical harmonic and anharmonic 1D and 2D approximations. Spectroscopic data show that, in the case of DMP, cyclic trimers are predominantly formed; DPFA and DPG form cyclic dimers with two NH...N bonds in inert solvents, whereas, upon the complexation of DPT, cyclic structures do not occur, and only open dimers are formed. Upon the interaction of DMP, DPFA, and DPT with weak carboxylic acids (HCOOH, CH3COOH, CH2ClCOOH) in CCl4 or in CH2Cl2, molecular cyclic structures with NH...O=C and OH...N H-bonds are formed, whereas cyclic dimer complexes with stronger acids (CHCl2COOH, CCl3COOH, CF3COOH) predominantly have the structure of hydrogen-bonded ion pairs with proton transfer from the hydroxyl group to the proton-acceptor nitrogen atom. The calculations of the structure and vibrational frequencies using various basis sets of atomic functions confirm the formation of cyclic complexes in accordance with experimental results and, in the case of interaction with strong carboxylic acids, the proton transfer along the OH...N hydrogen bridge.

Regioisomeric Control Induced by DABCO Coordination to Rotatable Self‐Assembled Bis‐ and Tetraporphyrin α,γ‐Cyclic Octapeptide Dimers

The design and synthesis of two α,γ-cyclic octapeptides decorated with one and two Zn-porphyrin units in their periphery is described. In nonpolar organic solvents the α,γ-cyclic octapeptides quantitatively self-assemble into Zn-bis- or -tetraporphyrin architectures that could act as molecular tweezers. The self-assembly process, however, is not regioselective and affords a mixture of different regioisomers that are involved in chemical exchange processes. The regioisomers with the Zn-porphyrin units positioned in register with respect to each other are proposed to be the less abundant species in the solution mixture. It has been demonstrated that the coordination of 1,4-diazabicyclo[2.2.2]octane (DABCO) to the supramolecular bis- or tetraporphyrin tweezers is an effective way to achieve regioisomeric control of the self-assembled mixture of dimers. Thus, DABCO functions as an external molecular trigger and, when used under strict stoichiometric control with respect to the Zn-porphyrin units, provokes the exclusive formation of self-assembled dimers with a cofacial arrangement of Zn-porphyrin units through the formation of sandwich-type complexes. The use of excess DABCO fragments the sandwich complexes and affords open dimers of high stoichiometry with DABCO molecules axially monocoordinated to the Zn-porphyrin units, probably as a regioisomeric mixture. In the case of Zn-tetraporphyrin tweezers, the ditopic coordination of DABCO at the two binding sites shows a moderate positive cooperativity factor, αP=5. These assemblies have potential applications as light-induced energy and electron-transfer switches regulated by DABCO coordination; such applications would require the introduction of additional chromophores in the cyclic peptide scaffold.

Kinetic mechanism and product characterization of the enzymatic peroxidation of pterostilbene as model of the detoxification process of stilbene-type phytoalexins

The enzymatic peroxidation of pterostilbene, a strong antifungal belonging to the stilbene family, by peroxidase (POX), is reported for the first time as a model of phytoalexin detoxification carried out by the enzymatic pool of pathogens. Kinetic characterization of the pterostilbene oxidation reaction pointed to an optimum pH of 7.0, at which value the thermal stability of POX was studied. Moreover, the data showed that pterostilbene inhibits POX activity at high concentrations of substrate. Several kinetic parameters, including V max, K m and K I, were calculated and values of 0.16 ΔAbs min −1, 14.61 μM, and 31.41 μM were reported. To understand the possible physiological role of this reaction in the phytoalexin detoxification process, the products of pterostilbene oxidation were identified using HPLC-MS and a radical–radical coupling reaction mechanism was proposed. Three main products with a high molecular weight and pronounced hydrophobicity were identified: pterostilbene cis dehydromer, pterostilbene trans dehydromer and pterostilbene open dimer. The dimeric structures of these molecules indicate that the pterostilbene oxidation reaction took place at the 4′-OH position of the hydroxystilbenic moieties and the three above mentioned dimeric products were found, due to the ability of electron-delocalized radicals to couple at various sites. Finally, the capacity of cyclodextrins (CDs) as starch model molecules in plants to complex both the substrate and the products of the oxidation reaction was evaluated. The inhibition process of POX activity was modified at high pterostilbene concentrations due to sequestering of the substrate reaction and to the different affinity of the reaction products for CDs.

Loop-Sheet Mechanism of Serpin Polymerization Tested by Reactive Center Loop Mutations

The serpin mechanism of protease inhibition involves the rapid and stable incorporation of the reactive center loop (RCL) into central β-sheet A. Serpins therefore require a folding mechanism that bypasses the most stable "loop-inserted" conformation to trap the RCL in an exposed and metastable state. This unusual feature of serpins renders them highly susceptible to point mutations that lead to the accumulation of hyperstable misfolded polymers in the endoplasmic reticulum of secretory cells. The ordered and stable protomer-protomer association in serpin polymers has led to the acceptance of the "loop-sheet" hypothesis of polymerization, where a portion of the RCL of one protomer incorporates in register into sheet A of another. Although this mechanism was proposed 20 years ago, no study has ever been conducted to test its validity. Here, we describe the properties of a variant of α(1)-antitrypsin with a critical hydrophobic section of the RCL substituted with aspartic acid (P8-P6). In contrast to the control, the variant was unable to polymerize when incubated with small peptides or when cleaved in the middle of the RCL (accepted models of loop-sheet polymerization). However, when induced by guanidine HCl or heat, the variant polymerized in a manner indistinguishable from the control. Importantly, the Asp mutations did not affect the ability of the Z or Siiyama α(1)-antitrypsin variants to polymerize in COS-7 cells. These results argue strongly against the loop-sheet hypothesis and suggest that, in serpin polymers, the P8-P6 region is only a small part of an extensive domain swap.

A Fused α-β “Mini-spectrin” Mimics the Intact Erythrocyte Spectrin Head-to-head Tetramer

Head-to-head assembly of two spectrin heterodimers to form an actin-cross-linking tetramer is a physiologically dynamic interaction that contributes to red cell membrane integrity. Recombinant beta-spectrin C-terminal and alpha-spectrin N-terminal peptides can form tetramer-like univalent complexes, but they cannot evaluate effects of the open-closed dimer interactions or lateral associations of the two-spectrin strands on tetramer formation. In this study we produced and characterized a fused "mini-spectrin dimer" containing the beta-spectrin C-terminal region linked to the alpha-spectrin N-terminal region. This fused mini-spectrin mimics structural and functional properties of intact, full-length dimers and tetramers, including lateral association of the alpha and beta subunits in the dimer and formation of a closed dimer. High performance liquid chromatography gel filtration analyses of this mini-spectrin provide the first direct non-imaging experimental evidence for open and closed spectrin dimers and show that dimer-tetramer-oligomer interconversion is slow at low temperatures and accelerated at 30 degrees C, analogous to full-length spectrin. This protein exhibits wild type dimer-tetramer dissociation constants of approximately 1 mum at 30 degrees C, independent of initial oligomeric state. Conformational states of the mini-spectrin dimer were probed further using chemical cross-linking, which identified distinct groups of cross-links for "open" and "closed" dimers and confirmed the N-terminal region of alpha-spectrin remains highly flexible in the complex, exhibiting closely analogous structures to those observed for the isolated alpha-spectrin N-terminal using NMR (Park, S., Caffrey, M. S., Johnson, M. E., and Fung, L. W. (2003) J. Biol. Chem. 278, 21837-21844). This fusion protein should serve as a useful template for structural and functional studies of the divalent tetramer site.

Structure of propanoic acid dimers as studied by means of MIR and FIR spectroscopy

Infrared spectra of propanoic acid isolated in the neon and argon matrixes were obtained and studied with the aid of the DFT calculations. The geometric structures of the cyclic and open dimers of PA were elucidated. The calculations predict that among various types of the open dimers only one type with additional hydrogen bond between oxygen of hydroxyl group of a monomer and hydrogen of hydroxyl group of other monomer (OH dimer) is energetically favorable. Structure of this dimer differs from that of formic and acetic acids, where open dimers with the hydrogen bond between oxygen of hydroxyl group and hydrogen of terminal methylene group (CH dimer) are formed. This finding explains fact why formic and acetic acids in crystalline state form polymer chains while higher member of homological row of the monocarboxylic acids (starting from propanoic) acid crystallizes as cyclic dimers. Due to the low barrier between the open and cyclic dimers of propanoic acid the open dimer is experimentally observed only in the neon matrix formed by rapid freezing of the gaseous matrix mixture from 300 K down to 2.8 K. Similar structures were not observed in the conventional 15 K argon matrix.

The Origin of Nucleotide Dependence of Conformational Changes in ABC Transporters

ATP-binding cassette (ABC) transporters are one of the most ubiquitous membrane transporters. They are all powered by ATP binding and hydrolysis in the two highly conserved cytoplasmic nucleotide binding domains (NBDs). It has been structurally established that the NBDs adopt a closed dimeric conformation only in the ATP-bound state, while appearing as open dimers or separate monomers in their nucleotide-free and ADP-bound states. The origin of such conformational changes, however, is yet to be characterized. To study the mechanism of nucleotide-dependent conformational changes, an extensive set of molecular dynamics simulations was performed on several intact ABC transporter structures and in various nucleotide binding states. Through these simulations we identify significantly large electrostatic potential regions centered at each subdomain of the NBDs in all ABC transporters simulated. Interestingly, the magnitude and location of the charge centers are independent of the nucleotide binding state of the NBDs. We propose that the repulsion between these charge centers is the main drive for the large separation between the NBDs in the absence of ATP. In particular, a conserved charged residue in the helical subdomain of the NBD is found to significantly contribute to the electrostatic repulsion between the NBD monomers. Removing the charge of this conserved residue during the MD simulations results in drastic changes of the NBD conformations, such that the NBDs are unable to complete their opening or closing motion in response to the bound nucleotide, hence a semi-open conformation is maintained in the mutant NBDs both in nucleotide-free and ATP-bound states.

An ab initio study of the mechanisms of the di- and tri-merization of thiocarbonyl compounds resulting in cyclic oligomers

The dimerization and trimerization of thioformaldehyde as well as the dimerization of thioketene has been studied using G3(MP2) calculations. The investigations have elucidated the reaction mechanisms. The activation Gibbs energy of the trimerization of thioformaldehyde has been determined as 118.1 kJ/mol and that of the dimerization of thioketene as 139.2 kJ/mol. The trimerization of thioformaldehyde is shown to proceed through an open chain dimer with the activation Gibbs energy 74.0 kJ/mol. The results explain that the direct dimerization of thioformaldehyde to 1,3-dithietane is not experimentally observed.

Structural insight into the membrane insertion of tail‐anchored proteins by Get3

Tail anchored (TA) proteins, which are important for numerous cellular processes, are defined by a single transmembrane domain (TMD) near the C-terminus. The membrane insertion of TA proteins is mediated by the highly conserved ATPase Get3. Here we report the crystal structures of Get3 in ADP-bound and nucleotide-free forms at 3.0 A and 2.8 A resolutions, respectively. Get3 consists of a nucleotide binding domain and a helical domain. Both structures exhibit a Zn(2+)-mediated homodimer in a head-to-head orientation, representing an open dimer conformation. Our cross-link experiments indicated the closed dimer-stimulating ATP hydrolysis, which might be coupled with TA-protein release. Further, our coexpression-based binding assays using a model TA protein Sec22p revealed the direct interaction between the helical domain of Get3 and the Sec22p TMD. This interaction is independent of ATP and dimer formation. Finally, we propose a structural mechanism that links ATP hydrolysis with the TA-protein insertion mediated by the conserved DTAPTGH motif.

β-Keto ester aminolysis of pheophorbide a methyl ester: a facile route for asymmetric chlorin ring substitution

A chemoselective aminolysis of the β-keto ester of pheophorbide a methyl ester is demonstrated opening a facile access to an asymmetric amide functionalization of a chlorin ring using a range of aromatic and aliphatic, primary and secondary amine nucleophiles. Aminolysis of pheophorbide a methyl ester with trans-1,2-diaminocyclohexane is shown to give a symmetric open face chlorin dimer.

Hydration mechanism on a poly(methacrylic acid) film studied by in situ attenuated total reflection infrared spectroscopy

A drastic structure change during a hydration process of a poly(methacrylic acid) (PMAA) film was observed by time-resolved in situ attenuated total reflection infrared (ATR-IR) spectroscopy. Inter- or intra-hydrogen-bonds via side-chain carboxyl groups are formed as cyclic dimers, side-on dimers and linear open chain oligomers including open dimers in a dried PMAA film. By contacting water, the side-chain hydrogen-bonds in PMAA are dissociated instantly, and then the subsequent carboxyl groups which have no hydrogen-bond newly hydrate with water molecules in a side-on form. Quantum chemical calculations (QCCs) using a model monomer of propionic acid (PA) also support the hydrogen-bonded and hydrated structures explored by the ATR-IR spectroscopy. It has been concluded from the present study that the dissociation of hydrogen-bonded and newly created hydrated structures via the carboxyl groups play an important role for the swelling of PMAA in water.

Constructing Gold−Thiolate Oligomers and Polymers on Au(111) Based on the Linear S−Au−S Geometry

Although neat gold−thiolate oligomers and polymers made of linear S−Au−S bonds have been well-known, observation of RS−Au−SR linear complexes (RS− being an alkylthiolate group) on Au(111) has been reported only recently. On the basis of the unique geometry and bonding of the RS−Au−SR complex on Au(111), we construct simple geometric models of Au-SR oligomers and polymers on Au(111) by fusing linear S−Au−S units matched to the underlying Au(111) surface lattice. We then optimize these models by density functional theory. The hexagonal geometry of the Au(111) lattice determines three possible angles (60°, 120°, and 180°) for connecting two linear S−Au−S units, which lead to isomerism of the Au−SR oligomers and polymer on Au(111). Here we explore open dimers, trimers, and tetramers and cyclic trimers, tetramers, and hexamers of the Au−SR oligomers on Au(111). We also examine four isomers of the Au−SR polymer on Au(111). We find that the 120° Au−S−Au angle is preferred in constructing both oligomeric and polymeric isomers. The two polymeric isomers with 120° Au−S−Au angles are found to be energetically competitive with a previous model proposed for the Au−SR polymer on Au(111). We also discuss potential ways to create Au−SR oligomers on Au(111).

Topological investigations of the molecular species and molecular interactions that characterize pyrrolidin-2-one + lower alkanol mixtures

Molar excess volumes, V E, molar excess enthalpies, H E, and speeds of sound data, u, of pyrrolidin-2-one ( i) + ethanol or propan-1-ol or propan-2-ol or butan-1-ol ( j) binary mixtures have been determined over entire composition range at 308.15 K. The observed speeds of sound data have been utilized to predict excess isentropic compressibilities, κ S E of the investigated binary mixtures. The observed excess thermodynamic properties V E, H E and κ S E have been analyzed in terms of Graph theory. The analysis of V E data by the Graph theory suggests that pyrrolidin-2-one exists mainly as a mixture of cyclic and open dimer; ethanol as a mixture of dimer and trimer; butan-1-ol and propan-2-ol as mixture of monomer and dimer and propan-1-ol as a dimer in the pure state, and their mixtures contain 1:1 molecular complex. The IR studies lend additional credence to the nature and extent of interactions for the proposed molecular entities in the mixtures. Also, it has been observed that V E, H E and κ S E values predicted by the Graph theory compare well to with their corresponding experimental values.

A scissors mechanism for stimulation of SNARE-mediated lipid mixing by cholesterol

Neurotransmitter release at the synapse requires membrane fusion. The SNARE complex, composed of the plasma membrane t-SNAREs syntaxin 1A and SNAP-25 and the vesicle v-SNARE synaptobrevin, mediates the fusion of 2 membranes. Synaptic vesicles contain unusually high cholesterol, but the exact role of cholesterol in fusion is not known. In this study, cholesterol was found to stimulate SNARE-mediated lipid mixing of proteoliposomes by a factor of 5 at a physiological concentration. Surprisingly, however, the stimulatory effect was more pronounced when cholesterol was on the v-SNARE side than when it was on the t-SNARE side. Site-directed spin labeling and both continuous wave (CW) and pulsed EPR revealed that cholesterol induces a conformational change of the v-SNARE transmembrane domain (TMD) from an open scissors-like dimer to a parallel dimer. When the TMD was forced to form a parallel dimer by the disulfide bond, the rate was stimulated 2.3-fold even without cholesterol, supporting the relevance of the open-to-closed conformational change to the fusion activity. The open scissors-like conformation may be unfavorable for fusion and cholesterol may relieve this inhibitory factor.

Raman spectroscopy of formic acid and its dimers isolated in low temperature argon matrices

Raman spectroscopy combined with matrix isolation technique was employed to study formic acid monomer and its dimers. Nine fundamentals of the HCOOH monomer were identified. Additionally, the OH torsion overtone is observed and it is engaged in Fermi resonance with the δCOH mode. Several bands of the cyclic (C 2h) dimer were identified and assigned. The less stable open form (C s) of the dimer was also present in the experiment. Three intermolecular modes for the cyclic and one mode for the open dimer were found in the low frequency region. The experimental studies were supported by harmonic and anharmonic DFT calculations.