Dimerization Pattern Research Articles

Numerical study of critical properties and hidden orders in dimerized spin ladders

Dimerized antiferromagnetic spin-1/2 ladders are known to exhibit a quantum critical phase transition in the ground state, the existence or absence of which is dependent on the dimerization pattern of the ladder. The gapped phases cannot be distinguished by the conventional Landau long-range order parameter. However, they possess a non-local (hidden) string order parameter, which is non-zero in one phase and vanishes in the other. We use an exact diagonalization technique to calculate ground state energies, energy gaps and string order parameters of dimerized two- and three-leg Heisenberg ladders, as well as a critical scaling analysis to yield estimates of the critical exponents nu and beta.

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

Oligomerization of isobutene with a beta-zeolite membrane: Effect of the acid properties of the catalytic membrane

Isobutene oligomerization was performed using a ceramic membrane with a film of zeolite beta, where three different zeolite molar ratios SiO 2/Al 2O 3 were evaluated. The reaction was studied in a membrane reactor within the 373–423 K temperature range. Analyses of the reaction products suggest a complex pattern of isobutene dimerization and isomerization and the main reaction product was 2,2,4-trimethypentane (2,2,4 TMP) for all catalytic tests conducted.

Modulated Nonlinear Optical Responses and Charge Transfer Transition in Endohedral Fullerene Dimers Na@C60C60@F with n-Fold Covalent Bond (n = 1, 2, 5, and 6) and Long Range Ion Bond

Isomer structures of four endohedral fullerene dimers Na@C60C60@F with an n-fold bond (n = 1, 2, 5 and 6) are obtained for the first time by using density functional theory. The n-fold bond depends on the dimeric pattern between endohedral fullerenes Na@C60 and F@C60. The pattern includes point−point (n = 1), side−side (n = 2), and face−face (n = 5, 6) mode. The four structures [1 + 1], [2 + 2], [5 + 5] and [6 + 6] have larger n-fold bond energies, as compared to that of the neutral π-(C60)2 dimer. In addition, the electronic properties of the endohedral dimers are first investigated. The dimers exhibit a strong nonlinear optical (NLO) response: large static first hyperpolarizabilities. Moreover, the first hyperpolarizability depends on the dimeric pattern. The large first hyperpolarizabilitiy is up to 25 169 au for [5 + 5], which is almost 110 times larger than that of the NaF molecule (228 au). The great enhancement of the first hyperpolarizability relates to the geometric effect of expanding the Na···F distance from 1.980 for NaF to 6.355 Å for [5 + 5], which provides a novel strategy for enhancing the first hyperpolarizability by altering the molecular structure. It is also found that the crucial charge transfer transition depends on the dimeric pattern, and controlling the transition may be performed by modulating the dimeric pattern. This work may promote the study of new nanomaterials, including high-performance NLO materials, and enrich knowledge of chemical bonds (for example, multifold bond between cages) and long-range interaction between two trapped atoms in different cages.

Contrasting Crystallographic Signatures of 9-Carboxypropyl Adeninium Cation: Adenine Dimerization vs Carboxylic Group Interaction

A change in dimerization pattern of the adeninium cation, having a carboxylic group at the N9 position, was observed due to competition between homodimerization versus cross-dimerization, which could be attributed to the conformation adopted by the protonated ligand.

Watching the Conformational Changes of Maleonitriledithiolate Chromophores Inside the Inclusion Complexes with Cyclodextrins: Probed by ICD Spectra and DFT Calculations

A series of inclusion complexes between cyclodextrins (alpha-, beta-, gamma-cyclodextrin and HP-beta-cyclodextrin, HP-beta-cyclodextrin = 2-hydroxypropyl-beta-cyclodextrin) and sodium maleonitriledithiolate (Na(2)mnt) were investigated by electronic spectra, induced circular dichroism (ICD) spectra, and quantum chemical studies. The inclusion complexes Na(2)mnt@alpha-cyclodextrin and Na(2)mnt@gamma-cyclodextrin did not show any ICD signals, whereas Na(2)mnt@HP-beta-cyclodextrin displayed two signs of splitting Cotton effects (CEs), with one positive CE couplet at 376 nm in the 365-410 nm region and the other negative at 277 nm in the 265-306 nm region. In addition, a dimeric host inclusion pattern of Na(2)mnt@HP-beta-cyclodextrin in solution was determined by the method of continuous variation. Density functional theory (DFT) was used to assist assignment of the ICD signals in inclusion complexes Na(2)mnt@beta-cyclodextrin and Na(2)mnt@HP-beta-cyclodextrin in combination with the well-known Harata's rule. The orientation of p --> pi* transition in Na(2)mnt chromophore was predicted by TD-DFT (time-dependent DFT) calculations to be along the C=C double bond instead of being perpendicular. Upon titrations with Zn(2+) solutions, reversals of the p --> pi* transition-relevant ICD peak and splitting CE were experimentally observed in the cases of Na(2)mnt@beta-cyclodextrin and Na(2)mnt@HP-beta-cyclodextrin, respectively, which strongly supported our hypotheses on their coconformations and the subsequent conformational changes of mnt chromophores occurring during the titration procedures. Therefore, on the basis of both the experimental data and TD-DFT calculations, the HP-beta-cyclodextrin dimer host in inclusion complex Na(2)mnt@HP-beta-cyclodextrin was disclosed, which in turn generated the exciton coupling between the two individually included guests and produced the splitting CEs as well as the reversals of CEs.

ErbB2 expression through heterodimerization with erbB1 is necessary for ionizing radiation- but not EGF-induced activation of Akt survival pathway

Purpose ErbB1-dependent Akt phosphorylation improves post-irradiation cellular survival. In the present study, we investigated the contribution of erbB2 as a heterodimerization partner of erbB1 in activation of Akt survival signaling after irradiation or EGF treatment. Materials and methods Pattern of receptor dimerization and protein phosphorylation were investigated by Western and immunoblotting as well as immunoprecipitation techniques. Residual DNA double-strand breaks (DNA-DSB) and clonogenic activity were analyzed by γH2AX and standard clonogenic assay. To knocked erbB2 expression siRNA was used. Results In lung carcinoma cell lines A549 and H661, the erbB1-tyrosine kinase (TK) inhibitor erlotinib blocked EGF as well as ionizing radiation (IR)-induced Akt and DNA-PKcs phosphorylation. Targeting Akt and erbB1 induced cellular radiation sensitivity while, the erbB2-TK inhibitor AG825 neither affected phosphorylation of Akt and DNA-PKcs nor induced radiosensitization. ErbB2-siRNA and the anti-erbB2 antibody trastuzumab blocked IR-induced, but not EGF-stimulated Akt phosphorylation and impaired the repair of DNA-DSB. Likewise, IR but not EGF enhanced erbB1/erbB2 heterodimerization and resulted in the release of phosphorylated erbB2 cleavage products p135 and p95. Trastuzumab prevented radiation-induced formation of an active erbB1/erbB2 heterodimer and increased cellular radiation sensitivity. ErbB1- but not erbB2-TK inhibition stabilized erbB2 (p185) through preventing its cleavage. Conclusions The data indicates that ErbB2 through heterodimerization with erbB1 is necessary for the activation of Akt signaling following irradiation but not following EGF treatment.

Deconfined fractional electric charges in graphene at high magnetic fields

The resistance at the charge neutral (Dirac) point was shown by Checkelsky et al in Phys. Rev. B 79, 115434 (2009) to diverge upon the application of a strong magnetic field normal to graphene. We argue that this divergence is the signature for a Kekule instability of graphene, which is induced by the magnetic field. We show that the strong magnetic field does not remove the zero modes that bind a fraction of the electron around vortices in the Kekule dimerization pattern, and that quenched disorder present in the system makes it energetically possible to separate the fractional charges. These findings, altogether, indicate that graphene can sustain deconfined fractionalized electrons.

Rapid Intramolecular Hole Hopping inmeso−mesoandmeta-Phenylene Linked Linear and Cyclic Multiporphyrin Arrays

A series of zinc porphyrin arrays comprised of a meso-meso linked porphyrin dimer, a meta-phenylene linked dimer, gable-like tetramers consisting of the meso-meso linked dimers bridged via a meta-phenylene linker, and a dodecameric ring composed of this alternating dimeric pattern were singly oxidized, and intramolecular hole hopping between the porphyrin moieties was probed using electron paramagnetic resonance (EPR) spectroscopy. Electron nuclear double resonance (ENDOR) spectroscopy was also used to probe hole hopping within the dimers. Rapid hole hopping occurs between both porphyrins within both dimers and among three porphyrins of the tetramers with rates >10(7) s(-1) at 290 K. Additionally, the hole hops among 8-12 porphyrins in the dodecameric ring with a rate that is >10(7) s(-1) at 290 K, but hopping is slow at 180 K. These results show that hole hopping is rapid even though the meta-phenyl bridges and direct meso-meso linkages do not provide optimal electronic coupling between the porphyrins within these multiporphyrin arrays. This greatly expands the scope of possible structures that can be employed to tailor the design of long distance charge transport systems.

Thioacidolytic analysis of residual lignins isolated from the chemical pulps of spruce (Picea abies) and beech (Fagus sylvatica) wood

Eight different residual lignins isolated from unbleached chemical pulps [sulfite, kraft, alkaline sulfite-anthraquinone-methanol (ASAM), soda/AQ/MeOH] of spruce and beech were characterized using gel permeation chromatography (GPC), thioacidolysis, and desulfurization to determine average molecular weight, amounts of uncondensed β-O-4 linkages, and dimeric linkage patterns, respectively. The total amounts of G-CHSEt-CHSEt-CH2SEt and S-CHSEt-CHSEt-CH2SEt were markedly reduced in residual lignins to 40% to 80% of the values for the corresponding milled wood lignins (MWLs). The number of dimeric units determined by thioacidolysis and desulfurization of the residual lignins was decreased by onehalf to one-fifth compared to the MWLs. Among the diverse types of dimeric units, reduction of β-1 and β-5 units was significant in most of the residual lignins, with the exception of beech ASAM residual lignin. Compared to beech MWL, 40% more C6–C3 main monomers were detected, whereas the relative composition of the dimeric units in the beech residual lignin was very similar to that in the beech MWL. The average molecular weights of residual lignins were less than those of the MWLs. However, the average molecular weights of the spruce kraft and soda residual lignins were determined to be higher than those of the corresponding MWLs.

Regulation of prostate cancer cell proliferation by somatostatin receptor activation

Although some evidence supports the antitumoral effects of somatostatin (SRIF) and related agonists, the available data in prostate cancer (PCa) model systems and clinical studies are few, conflicting and not conclusive. This study investigated the effects of lanreotide and new mono- and bi-specific SRIF agonists on proliferation, ligand-driven SRIF receptor (sst) dimerization and secretory pattern of the IGF system in LNCaP cells, a model of androgen-dependent PCa. LNCaP expressed all sst(s), but sst(4). Among them, sst(1) and sst(3) were inversely regulated by serum concentration. sst(1)/sst(2) and sst(2)/sst(5) dimers were constitutively present and further stabilized by treatment with BIM-23704 (sst(1)/sst(2)) and BIM-23244 (sst(2)/sst(5)), respectively. Dose-response studies showed that lanreotide and BIM-23244 were significantly more potent in inhibiting LNCaP cell proliferation than BIM-23120 (sst(2)) and BIM-23206 (sst(5)) alone or in combination. Treatment with BIM-23926 [corrected] (sst(1)) markedly reduced cell proliferation, whereas exposure to BIM-23704 resulted in a lower cell growth inhibition. The antiproliferative effects of BIM-23244, lanreotide and BIM-23704 were unchanged, reduced and abolished by the sst(2) antagonist BIM-23627, respectively. All SRIF analogs caused a significant induction in p27(KipI) and p21 and down-regulation of protein expression of cyclin E, as well as reduced IGF-I and IGF-II secretion. In particular, the administration of exogenous IGF-I, at variance to IGF-II, counteracted the inhibitory effect on cell proliferation of these compounds. Moreover, SRIF agonists reduced endogenous IGFBP-3 proteolysis. These results show that, in LNCaP cells, activation of sst(1) and sst(2)/sst(5) results in relevant antiproliferative/antisecretive actions.

Masses in graphenelike two-dimensional electronic systems: Topological defects in order parameters and their fractional exchange statistics

We classify all possible 36 gap-opening instabilities in graphene-like structures in two dimensions, i.e., masses of Dirac Hamiltonian when the spin, valley, and superconducting channels are included. These 36 order parameters break up into 56 possible quintuplets of masses that add in quadrature, and hence do not compete and thus can coexist. There is additionally a 6th competing mass, the one added by Haldane to obtain the quantum Hall effect in graphene without magnetic fields, that breaks time-reversal symmetry and competes with all other masses in any of the quintuplets. Topological defects in these 5-dimensional order parameters can generically bind excitations with fractionalized quantum numbers. The problem simplifies greatly if we consider spin-rotation invariant systems without superconductivity. In such simplified systems, the possible masses are only 4 and correspond to the Kekul\'e dimerization pattern, the staggered chemical potential, and the Haldane mass. Vortices in the Kekul\'e pattern are topological defects that have Abelian fractional statistics in the presence of the Haldane term. We calculate the statistical angle by integrating out the massive fermions and constructing the effective field theory for the system. Finally, we discuss how one can have generically non-Landau-Ginzburg-type transitions, with direct transitions between phases characterized by distinct order parameters.

2-[(1-Methyl-1H-pyrrol-2-yl)carbonylmethyl]isoindoline-1,3-dione

The asymmetric unit of the title compound, C15H12N2O3, contains two almost identical mol­ecules forming an nearly C 2-symmetric dimeric pattern. The dihedral angles between the pyrrole ring and the phthalimide unit are 82.95 (8) and 86.57 (8)° for the two mol­ecules. Within such a dimer, the phthalimide units of the two mol­ecules form a dihedral angle of 1.5 (5)°.

Flow cytometric in situ proximity ligation analyses of protein interactions and post‐translational modification of the epidermal growth factor receptor family

Interactions between members of the epidermal growth factor receptor (EGFR) family mediates cellular responses to ligand stimulation. Measurement of these interactions could provide important information and may prove useful as prognostic markers in malignancy. Therefore, to develop methods to study these interactions in genetically unmodified cells, such as clinical samples, in a sensitive and selective way, with good statistical accuracy, is important. The in situ proximity ligation assay (in situ PLA) was used to quantify homo- and heteromeric interactions between EGFR and HER2 in cultured cells, using flow cytometry as the readout method. Cells were monitored for changes in dimerization patterns and phosphorylation status upon stimulation. The different cell lines displayed varying amounts of interactions between EGFR and HER2, but the amount of dimerization was not found to be affected significantly upon stimulation by EGF. Activation of EGFR could be visualized by in situ PLA, but not by immunofluorescence staining. In situ PLA was successfully used to study receptor dimerization and activation of the EGF-receptor family with high selectivity and sensitivity. The combination of in situ PLA and flow cytometry provided a statistically powerful way of analyzing protein-protein interactions and post-translational modifications on a single-cell basis.

Synthesis and X-ray Structure of Acetoxy-4-methyl Phenyl Methyl Acetate

The title compound belongs to acylal class of organic materials and it crystallizes in the monoclinic space group P21/c with unit cell parameters a = 7.643(2) A, b = 20.546(6) A, c = 7.783 A, β = 112.206(2)°, V = 1131.50(5) A3 and Z = 4. The structure has been solved by direct methods and the final R-factor is 0.0401 for 2579 unique reflections. The acetate groups are deviated significantly from the plane of phenyl ring atoms. There are two C–H···O intermolecular hydrogen bonds which gives rise to an antiparallel dimer pattern. The title compound belongs to acylal class of organic materials and it crystallizes in the monoclinic space group P21/c with unit cell parameters a = 7.643(2) A, b = 20.546(6) A, c = 7.783 A, β = 112.206(2)°, V = 1131.50(5) A3 and Z = 4. The structure has been solved by direct methods and the final R-factor is 0.0401 for 2579 unique reflections. The acetate groups are deviated significantly from the plane of phenyl ring atoms. There are two C–H···O intermolecular hydrogen bonds which gives rise to an antiparallel dimer pattern.

Interaction of Charge Carriers with Lattice Vibrations in Organic Molecular Semiconductors: Naphthalene as a Case Study

Recent theoretical studies suggest that the modulation of the electronic couplings (transfer integrals) between adjacent molecules by lattice vibrations, i.e., the so-called nonlocal electron−phonon coupling, plays a key role in the charge-transport properties of molecular organic semiconductors. However, a detailed understanding of this mechanism is still missing. Here, we combine density functional theory calculations and molecular mechanics simulations and use a chemistry-based insight to derive the nonlocal electron−phonon coupling constants due to the interaction of charge carriers with the optical lattice vibrations in the naphthalene crystal. The results point to a very strong coupling to both translational and librational intermolecular vibrational modes as well as to intramolecular modes. Along some crystal directions, the nonlocal interactions are found to be dominated by nontotally symmetric vibrational modes which lead to an alternation (Peierls-type dimerization) pattern. Importantly, we intr...

Atomic and electronic structures ofAg/Si(111)-c(12×2)surface: A first-principles study

Structural models for the $\text{Ag}/\text{Si}(111)\text{-c}(12\ifmmode\times\else\texttimes\fi{}2)$ phase were identified from a systematic search using tight-binding molecular dynamics and first-principles total-energy calculations. Our calculations showed that the low-energy $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ and $6\ifmmode\times\else\texttimes\fi{}1$ structures can be derived from the well-known honeycomb chain-channel $3\ifmmode\times\else\texttimes\fi{}1$ model. Two $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ models are found to have lower surface energies than both the $3\ifmmode\times\else\texttimes\fi{}1$ and $6\ifmmode\times\else\texttimes\fi{}1$ models, which is consistent with the experimental observation. A distinct feature of the $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ structure is the dimer formation induced by lateral displacements of Ag atoms within the same row in the $6\ifmmode\times\else\texttimes\fi{}1$ phase. Different packing patterns of the Ag dimers with the same surface area can lead to either $6\ifmmode\times\else\texttimes\fi{}2$ or $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ phase with very similar energies. Simulated scanning tunneling microscope images from our $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ structure are in excellent agreement with the experimental measurement. Moreover, the lowest-energy $\text{c}(12\ifmmode\times\else\texttimes\fi{}2)$ structure identified from our calculations also reproduces the key features in the angle-resolved photoemission measurement.

1,4-Bis(4-chlorophenylseleno)-2,5-dimethoxybenzene

The title compound, C20H16Cl2O2Se2, utilizes the symmetry of the crystallographic inversion center. Mol­ecular chains are formed through symmetric C—H⋯Cl inter­actions around inversion centers, mimicking the commonly observed symmetric hydrogen-bonded dimer pattern often found in carboxylic acids.

Sp1-mediated transcription regulation of TAF-Iα gene encoding a histone chaperone

TAF-I, one of histone chaperones, consists of two subtypes, TAF-Iα and TAF-Iβ. The histone chaperone activity of TAF-I is regulated by dimer patterns of these subtypes. TAF-Iβ is expressed ubiquitously, while the expression level of TAF-Iα with less activity than TAF-Iβ differs among cell types. It is, therefore, assumed that the expression level of TAF-Iα in a cell is important for the TAF-I activity level. Here, we found that TAF-Iα and TAF-Iβ genes are under the control of distinct promoters. Reporter assays and gel shift assays demonstrated that Sp1 binds to three regions in the TAF-Iα promoter and two or all mutaions of the three Sp1 binding regions reduced the TAF-Iα promoter activity. ChIP assays demonstrated that Sp1 binds to the TAF-Iα promoter in vivo. Furthermore, the expression level of TAF-Iα mRNA was reduced by knockdown of Sp1 using siRNA method. These studies indicated that the TAF-Iα promoter is under the control of Sp1.

Structural Analysis of B-Box 2 from MuRF1: Identification of a Novel Self-Association Pattern in a RING-like Fold

The B-box motif is the defining feature of the TRIM family of proteins, characterized by a RING finger-B-box-coiled coil tripartite fold. We have elucidated the crystal structure of B-box 2 (B2) from MuRF1, a TRIM protein that supports a wide variety of protein interactions in the sarcomere and regulates the trophic state of striated muscle tissue. MuRF1 B2 coordinates two zinc ions through a cross-brace alpha/beta-topology typical of members of the RING finger superfamily. However, it self-associates into dimers with high affinity. The dimerization pattern is mediated by the helical component of this fold and is unique among RING-like folds. This B2 reveals a long shallow groove that encircles the C-terminal metal binding site ZnII and appears as the defining protein-protein interaction feature of this domain. A cluster of conserved hydrophobic residues in this groove and, in particular, a highly conserved aromatic residue (Y133 in MuRF1 B2) is likely to be central to this role. We expect these findings to aid the future exploration of the cellular function and therapeutic potential of MuRF1.