Y-shaped Molecule Research Articles

Small-molecule ionic liquid-based adhesive with strong room-temperature adhesion promoted by electrostatic interaction

Low-molecular-weight adhesives (LMWAs) possess many unique features compared to polymer adhesives. However, fabricating LMWAs with adhesion strengths higher than those of polymeric materials is a significant challenge, mainly because of the relatively weak and unbalanced cohesion and interfacial adhesion. Herein, an ionic liquid (IL)-based adhesive with high adhesion strength is demonstrated by introducing an IL moiety into a Y-shaped molecule replete with hydrogen bonding (H-bonding) interactions. The IL moieties not only destroyed the rigid and ordered H-bonding networks, releasing more free groups to form hydrogen bonds (H-bonds) at the substrate/adhesive interface, but also provided electrostatic interactions that improved the cohesion energy. The synthesized IL-based adhesive, Tri-HT, could directly form thin coatings on various substrates, with high adhesion strengths of up to 12.20 MPa. Advanced adhesives with electrical conductivity, self-healing behavior, and electrically-controlled adhesion could also be fabricated by combining Tri-HT with carbon nanotubes.

Zn modified XY and Goldstone models and vortex confinement transition

The modified XY model is a modification of the XY model by addition of a half-periodic term. The modified Goldstone model is a regular and continuum version of the modified XY model. The former admits a vortex molecule, that is, two half-quantized vortices connected by a domain wall, as a regular topological soliton solution to the equation of motion while the latter admits it as a singular configuration. Here we define the ${\mathbb Z}_n$ modified XY and Goldstone models as the $n=2$ case to be the modified XY and Goldstone models, respectively. We exhaust all stable and metastalble vortex solutions for $n=2,3$ and find a vortex confinement transition from an integer vortex to a vortex molecule of $n$ $1/n$-quantized vortices, depending on the ratio between the term of the XY model and the modified term. We find for the case of $n=3$, a rod-shaped molecule is the most stable while a Y-shaped molecule is metastable. We also construct some solutions for the case of $n=4$.The vortex confinement transition can be understood in terms of the ${\mathbb C}/{\mathbb Z}_n$ orbifold geometry.

Two-dimensional networks of brominated Y-shaped molecules on Au(111)

In the design of supramolecular structures, Y-shaped molecules are useful to expand the structures in three different directions. The supramolecular structures of Y-shaped molecules with three halogen-ligands on surfaces have been extensively studied, but much less are done for those with six halogen-ligands. Here, we report on the intermolecular interactions of a Y-shaped molecule, 1,3,5-Tris(3,5-dibromophenyl)benzene, with six Br-ligands studied using scanning tunneling microscopy (STM). Honeycomb-like structures were observed on Au(111), and could be explained with chiral triple-nodes made of three Br···Br halogen bonds. Molecular models were proposed based on STM images and reproduced with density-functional theory calculations. Although the molecule has six Br-ligands, only three of them form Br···Br halogen bonds because of geometrical restrictions. Our study shows that halogenated Y-shaped molecules will be useful components for building supramolecular structures.

Smectic assemblies in C₃-symmetric hexa-alkylated liquid crystals: transformation from smectogen to discogen via hydrogen bonding.

In this paper, we report a C3-symmetric liquid crystal (LC) with sixfold alkyl peripheries exhibiting an unusual smectic E-like organization in the LC state. Based on conformational considerations, the smectic assembly is attributed to the formation of an endo-type Y conformer of asymmetric triazolyl and benzylic groups that cannot be accessed in other C3-symmetric molecules exclusively showing columnar assemblies. The Y conformers form a two-dimensional oblique lattice in the aromatic layers of the ordered smectic phase. In addition, the Y-shaped molecule in the smectic phases can change into a circular shape by the 1 : 1 hydrogen-bonding interaction with a gallic acid derivative, which leads to a hexagonal columnar LC phase. The triazole-based LC design concept proves the smectic LC assembly in the C3-symmetric system, and provides the supramolecular manipulation of LC morphologies.

Contacting a Conjugated Molecule with a Surface Dangling Bond Dimer on a Hydrogenated Ge(001) Surface Allows Imaging of the Hidden Ground Electronic State

Fabrication of single-molecule logic devices requires controlled manipulation of molecular states with atomic-scale precision. Tuning molecule-substrate coupling is achieved here by the reversible attachment of a prototypical planar conjugated organic molecule to dangling bonds on the surface of a hydrogenated semiconductor. We show that the ground electronic state resonance of a Y-shaped polyaromatic molecule physisorbed on a defect-free area of a fully hydrogenated surface cannot be observed by scanning tunneling microscopy (STM) measurements because it is decoupled from the Ge bulk states by the hydrogen-passivated surface. The state can be accessed by STM only if the molecule is contacted with the substrate by a dangling bond dimer. The reversibility of the attachment processes will be advantageous in the construction of surface atomic-scale circuits composed of single-molecule devices interconnected by the surface dangling bond wires.

Antibodies 2.0

Antibodies 2.0

对称Y型分子向列相液晶的相变

Based on the V-shaped molecule of biaxial nematic liquid crystal,a model of symmetric Y-shaped molecule is developed.In this model the Y-shaped molecule is Abstracted to three linked rod-like arms.Using a simple biaxial molecular interaction model in nematic liquid crystal,the interaction energy between two molecules is obtained by the superposition of all rod-to-rod interactions.With the mean field approximation,the free energy of the system is derived and the result shows that the free energy is the function of order parameters.The relationship between the Y-shaped molecule and its ability to form a biaxial nematic phase is established.And phase transitions from isotropic to uniaxial nematic(NI phase transition) and from uniaxial to biaxial nematic(IB phase transition) are obtained.

Photocrosslinking Detects a Compact, Active Structure of the Hammerhead Ribozyme

The hammerhead ribozyme has been intensively studied for approximately 15 years, but its cleavage mechanism is not yet understood. Crystal structures reveal a Y-shaped molecule in which the cleavage site is not ideally aligned for an S(N)2 reaction and no RNA functional groups are positioned appropriately to perform the roles of acid and base or other functions in the catalysis. If the ribozyme folds to a more compact structure in the transition state, it probably does so only transiently. We have used photocrosslinking as a tool to trap hammerhead ribozyme-substrate complexes in various stages of folding. Results suggest that the two substrate residues flanking the cleavage site approach and stack upon two guanosines (G8 and G12) in domain 2, moving 10-15 A closer to domain 2 than they appear in the crystal structure. Most crosslinks obtained with the nucleotide analogues positioned in the ribozyme core are catalytically inactive; however, one cobalt(III) hexaammine-dependent crosslink of an unmodified ribozyme retains catalytic activity and confirms the close stacking of cleavage site residue C17 with nucleotide G8 in domain 2. These findings suggest that residues involved in the chemistry of hammerhead catalysis are likely located in that region containing G8 and G12.

Synthesis, X-ray structure, and magnetic properties of interconnected ferromagnetic molecular bowls by hydrogen bonds

Ferromagnetic molecular bowls, [(μ 3-OH)Cu 3(L)]Cl 0.5(ClO 4) 4.5·1.5H 2O ( A), were interconnected by the hydrogen bonding interactions with sodium 1,3,5-benzenetricarboxylate (Na 3BTC), and a dimer of molecular bowl {[Cu 3(L)(μ 3-OH)] 2(C 9H 3O 6)}(ClO 4) 6·Cl·8H 2O ( 1) was isolated. In the structure, two molecular bowls are connected to a BTC 3− ion via the μ 3-hydroxo groups by the hydrogen-bonding interactions, which gives rise to a Y-shaped nano-sized molecule (12.1×19.1×19.9 Å 3). Each molecular bowl in 1 shows similar bond distances and angles to those of A, especially around the Cu II ions and the central oxygen atom. Variable temperature magnetic susceptibility data indicate that compound 1 has magnetic parameters of g=2.03, J=37.8 cm −1 and zJ′=−0.50 cm −1 and R=1.54×10 −5. Three Cu(II) ions within a molecular bowl exhibit relatively strong ferromagnetic interaction, but a weak antiferromagnetic interaction occurs between the two Cu 3 units connected to a BTC 3−.

Engineering of a Staphylokinase-based Fibrinolytic Agent with Antithrombotic Activity and Targeting Capability toward Thrombin-rich Fibrin and Plasma Clots

Current clinically approved thrombolytic agents have significant drawbacks including reocclusion and bleeding complications. To address these problems, a staphylokinase-based thrombolytic agent equipped with antithrombotic activity from hirudin was engineered. Because the N termini for both staphylokinase and hirudin are required for their activities, a Y-shaped molecule is generated using engineered coiled-coil sequences as the heterodimerization domain. This agent, designated HE-SAKK, was produced and assembled from Bacillus subtilis via secretion using an optimized co-cultivation approach. After a simple in vitro treatment to reshuffle the disulfide bonds of hirudin, both staphylokinase and hirudin in HE-SAKK showed biological activities comparable with their parent molecules. This agent was capable of targeting thrombin-rich fibrin clots and inhibiting clot-bound thrombin activity. The time required for lysing 50% of fibrin clot in the absence or presence of fibrinogen was shortened 21 and 30%, respectively, with HE-SAKK in comparison with staphylokinase. In plasma clot studies, the HE-SAKK concentration required to achieve a comparable 50% clot lysis time was at least 12 times less than that of staphylokinase. Therefore, HE-SAKK is a promising thrombolytic agent with the capability to target thrombin-rich fibrin clots and to minimize clot reformation during fibrinolysis.

Formatting antibody fragments to mediate specific therapeutic functions.

Monoclonal antibodies are increasingly being used as therapeutic agents in a wide range of indications, including oncology, inflammation and infectious disease. In most cases the basis of the therapeutic function is the high degree of specificity and affinity the antibody-based drug has for its target antigen. However, the mechanism of action (MOA), the way the drug takes advantage of this specificity to mediate a therapeutic effect, varies considerably from drug to drug. Three basic potential categories of MOAs exist: antagonists, agonists and specific delivery mechanisms to target an active function to a particular cell type. The latter functions include selective cell killing, based on Fc-mediated events, recruitment of effector cells, and drug or radioisotope delivery. The majority of these mechanisms are not necessarily optimally mediated by an IgG structure; clearly, in the case of antibody-dependent cellular cytotoxicity or complement-mediated lysis, Fc is required. However, Fab fragments (the fragment comprising one antigen-binding arm of the Y-shaped IgG molecule) can be formatted to mediate most mechanisms and have the advantage that valency and half-life can be controlled to simplify the drug and address only the mechanism required. Moreover, Fab fragments can be produced in microbial expression systems which address manufacturing issues such as scale of supply and cost of goods.

PII: S0969-2126(01)00700-6

PII: S0969-2126(01)00700-6

Crystal Structure of Colicin E3: Implications for Cell Entry and Ribosome Inactivation

Colicins kill E. coli by a process that involves binding to a surface receptor, entering the cell, and, finally, intoxicating it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3, reported here in a binary complex with its immunity protein (IP), reveals a Y-shaped molecule with the receptor binding domain forming a 100 Å long stalk and the two globular heads of the translocation domain (T) and the catalytic domain (C) comprising the two arms. Active site residues are D510, H513, E517, and R545. IP is buried between T and C. Rather than blocking the active site, IP prevents access of the active site to the ribosome.

Substitutions of the Glutamine Residue in the ubiquitous GGQ tripeptide in human eRF1 do not entirely abolish the release factor activity

Translation termination in eukaryotes takes place on the ribosome and requires the presence of a stop codon (any of the three) and of the eRF1 protein--a class-1 polypeptide chain release factor--at the ribosomal A site (reviewed in [1, 2]). Primary [3] and 3D [4] structures of human eRF1 have been established, making it possible to study the functioning of this protein. Regardless of the species, all class1 release factors share a common tripeptide GGQ, absolutely conserved in Eukarya, Archaea, and Prokarya [5]. This tripeptide occupies the minidomain "tip" at one of the extremities of the Y-shaped human eRF1 molecule [4].

Crystal Structure of RNA Helicase from Genotype 1b Hepatitis C Virus: A FEASIBLE MECHANISM OF UNWINDING DUPLEX RNA

Crystal structure of RNA helicase domain from genotype 1b hepatitis C virus has been determined at 2.3 A resolution by the multiple isomorphous replacement method. The structure consists of three domains that form a Y-shaped molecule. One is a NTPase domain containing two highly conserved NTP binding motifs. Another is an RNA binding domain containing a conserved RNA binding motif. The third is a helical domain that contains no beta-strand. The RNA binding domain of the molecule is distinctively separated from the other two domains forming an interdomain cleft into which single stranded RNA can be modeled. A channel is found between a pair of symmetry-related molecules which exhibit the most extensive crystal packing interactions. A stretch of single stranded RNA can be modeled with electrostatic complementarity into the interdomain cleft and continuously through the channel. These observations suggest that some form of this dimer is likely to be the functional form that unwinds double stranded RNA processively by passing one strand of RNA through the channel and passing the other strand outside of the dimer. A "descending molecular see-saw" model is proposed that is consistent with directionality of unwinding and other physicochemical properties of RNA helicases.

Cloning of the mouse laminin alpha 4 cDNA. Expression in a subset of endothelium.

Endothelial cells express a 400-kDa or 240-kDa laminin alpha chain, depending on their tissue of origin or physiological state [1, 2]. Using differential display and subsequent screening of a mouse endothelial cell cDNA library we here identify the gene coding for the 240-kDa laminin chain as the laminin alpha 4 gene. The complete mouse laminin alpha 4 cDNA sequence is reported and compared with other laminin alpha chains. In situ hybridization of embryonic and new born mouse tissues revealed expression of laminin alpha 4 mRNA in a subset of endothelium, in particular aortic endothelium, endocardium and endothelium of blood vessels in the skin and in the brain. Strong laminin alpha 4 expression by aortic endothelia was confirmed by data obtained from cultured bovine aortic endothelial cells (BAEC). Isolation of laminin from BAEC conditioned medium revealed a Y-shaped molecule in rotary shadowing. Subsequent sequencing of BAEC laminin resulted in laminin alpha 4, beta 1 and gamma 1 amino acid sequences, confirming that laminin alpha 4 is one of the major laminin alpha chains expressed by aortic endothelium not only in the mouse. In addition, strong laminin alpha 4 mRNA expression occurred in peripheral nerves, cardiac muscle, fat, the dermis of the skin and lung stroma of mouse tissues. The data demonstrate a cytokine and progesterone-regulated differential expression of laminin alpha 4 mRNA in mouse endothelium, suggesting a distinct functional role for this laminin chain in endothelium.

Domain swapping: entangling alliances between proteins.

The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein association which we call domain swapping. The structure of dimeric DT has been extensively refined against data to 2.0-A resolution and a three-residue loop has been corrected as compared with our published 2.5-A-resolution structure. The monomeric DT structure has also been determined, at 2.3-A resolution. Monomeric DT is a Y-shaped molecule with three domains: catalytic (C), transmembrane (T), and receptor binding (R). Upon freezing in phosphate buffer, DT forms a long-lived, metastable dimer. The protein chain tracing discloses that upon dimerization an unprecedented conformational rearrangement occurs: the entire R domain from each molecule of the dimer is exchanged for the R domain from the other. This involves breaking the noncovalent interactions between the R domain and the C and T domains, rotating the R domain by 180 degrees with atomic movements up to 65 A, and re-forming the same noncovalent interactions between the R domain and the C and T domains of the other chain of the dimer. This conformational transition explains the long life and metastability of the DT dimer. Several other intertwined, dimeric protein structures satisfy our definition of domain swapping and suggest that domain swapping may be the molecular mechanism for evolution of these oligomers and possibly of oligomeric proteins in general.

The crystal structure of diphtheria toxin

The crystal structure of the diphtheria toxin dimer at 2.5 A resolution reveals a Y-shaped molecule of three domains. The catalytic domain, called fragment A, is of the alpha + beta type. Fragment B actually consists of two domains. The transmembrane domain consists of nine alpha-helices, two pairs of which are unusually apolar and may participate in pH-triggered membrane insertion and translocation. The receptor-binding domain is a flattened beta-barrel with a jelly-roll-like topology. Three distinct functions of the toxin, each carried out by a separate structural domain, can be useful in designing chimaeric proteins, such as immunotoxins, in which the receptor-binding domain is substituted with antibodies to target other cell types.

Structure of the lipophosphoglycan from Leishmania major.

The major cell surface glycoconjugate of the parasitic protozoan Leishmania major is a heterogeneous lipophosphoglycan. It has a tripartite structure, consisting of a phosphoglycan (Mr 5,000-40,000), a variably phosphorylated hexasaccharide glycan core, and a lysoalkylphosphatidylinositol (lysoalkyl-PI) lipid anchor. The structures of the phosphoglycan and the hexasaccharide core were determined by monosaccharide analysis, methylation analysis, fast atom bombardment-mass spectrometry, one- and two-dimensional 500-MHz (correlated spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA] 1H NMR spectroscopy, and exoglycosidase digestions. The phosphoglycan consists of eight types of phosphorylated oligosaccharide repeats which have the general structure, [formula: see text] where R = H, Galp(beta 1-3), Galp(beta 1-3)Galp(beta 1-3), Arap(alpha 1-2)Galp(beta 1-3), Glcp(beta 1-3)Galp(beta 1-3), Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3), Arap(alpha 1-2)Galp(beta 1-3)Galp(beta 1-3), or Arap(alpha 1-2)Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3), and where all the monosaccharides, including arabinose, are in the D-configuration. The average number of repeat units/molecule (n) is 27. Data are presented which suggest that the nonreducing terminus of the phosphoglycan is capped exclusively with the neutral disaccharide Manp(alpha 1-2)Manp alpha 1-. The structure of the glycan core was determined to be, [formula: see text] where approximately 60% of the mannose residues distal to the glucosamine are phosphorylated and where the inositol is part of the lysoalkyl-PI lipid moiety containing predominantly 24:0 and 26:0 alkyl chains. The unusual galactofuranose residue is in the beta-configuration, correcting a previous report where this residue was identified as alpha Galf. Although most of the phosphorylated repeat units are attached to the terminal galactose 6-phosphate of the core to form a linear lipophosphoglycan (LPG) molecule, some of the mannose 6-phosphate residues may also be substituted to form a Y-shaped molecule. The L. major LPG is more complex than the previously characterized LPG from Leishmania donovani, although both LPGs have the same repeating backbone structure and glycolipid anchor. Finally we show that the LPG anchor is structurally related to the major glycolipid species of L. major, indicating that some of these glycolipids may have a function as precursors to LPG.

Structure of a mouse immunoglobulin G that lacks the entire CH1 domain: protein sequencing and small-angle x-ray scattering studies

The structure of a short-chain IgG2a antibody, which is a member of the family of mouse anti-dansyl switch variant antibodies with identical variable regions but different heavy-chain constant regions [Dangl, J.L., Parks, D. R., Oi, V. T., & Herzenberg, L. A. (1982) Cytometry 2, 395-401], is reported. Amino acid sequencing analyses have demonstrated that in the short-chain IgG2a antibody the entire CH1 domain is deleted whereas the hinge region remains intact. Small-angle X-ray scattering data were collected for the short-chain IgG2a antibody and compared with those for the switch variant IgG1, IgG2a, and IgG2b antibodies with the normal heavy chain. It has been concluded that deletion of the CH1 domain results in a large structural change and the short-chain IgG2a antibody possesses an elongated molecular shape with a much smaller hinge angle as compared with the normal IgG2a antibody that is a Y-shaped molecule.