Unique Trimer Research Articles

(Invited) Electrochemical Structure Evolution and Electronic Interactions in NaxVO2

Vanadium oxides have been highly attractive for over half a century since the discovery of the metal insulator transition near room temperatures. Here NaxVO2 is studied through a systematic comparison with other layered sodium metal oxides with early 3d transition metals. The unique trimer structure in NaxVO2 first reported by Claude Delmas is here shown to be a delicate balance between strong electronic correlations and orbital effects that can be precisely modulated by both Na compositions and atomic stackings. This unveils an opportunity to design strongly correlated materials with tailored electronic transitions through electrochemical modulations and crystallographic designs, to elegantly balance various competition effects. We think the understanding will also help further elucidate complicated electronic behaviors in other vanadium oxide systems.

Balancing orbital effects and on-site Coulomb repulsion through Na modulations in NaxVO2

Vanadium oxides have been highly attractive for over half a century since the discovery of the metal insulator transition near room temperatures. Here NaxVO2 is studied through a systematic comparison with other layered sodium metal oxides with early 3d transition metals, first disclosing a unified evolution pattern of Na density waves through in situ XRD analysis. Combining ab-initio simulations and theoretical modelings, a sodium-modulated Peierls-like transition mechanism is then proposed for the bonding formation of metal ion dimers. More importantly, the unique trimer structure in NaxVO2 is shown to be very sensitive to the onsite Coulomb repulsion value, suggesting a delicate balance between strong electronic correlations and orbital effects that can be precisely modulated by both Na compositions and atomic stackings. This unveils a unique opportunity to design strongly correlated materials with tailored electronic transitions through electrochemical modulations and crystallographic designs, to elegantly balance various competition effects. We think the understanding will also help further elucidate complicated electronic behaviors in other vanadium oxide systems.

Novel In Silico Analyses of Repetitive Spider Silk Sequences to Understand the Evolution and Mechanical Properties of Fibrous Protein Materials

The mechanical properties of spider silks have diverged as spiders have diversely speciated. Because the main components of silks are proteins, it is valuable to investigate their sequences. However, silk sequences have been regarded as difficult information to analyze due to their imbalance and imperfect tandem repeats (ITR). Here, an in silico approach is applied to systemically analyze a group of silk sequences. It is found that every time new spider groups emerge, unique trimer motifs appear. These trimer motifs are used to find additional clues of evolution and to determine relationships with mechanical properties. For the first time, crucial evidence is provided that shows silk sequences coevolved with spider species and the mechanical properties of their fibers to adapt to new living environments. This novel approach can be used as a platform for analyzing other groups of ITR-harboring proteins and to obtain information for the design of tailor-made fibrous protein materials.

Coriariin M, a trimeric hydrolysable tannin with dehydrodigalloyl and valoneoyl groups as linking units, and accompanying dimeric hydrolysable tannins from Coriaria japonica

Three oligomeric hydrolysable tannins, coriariins K, L, and M, which were previously undescribed, together with five known hydrolysable tannins were isolated from dried leaves of Coriaria japonica. Their structures were determined based on 1D and 2D NMR spectroscopy, HR-ESI-MS, and ECD spectroscopy experiments. Among the isolated compounds, coriariin M has a unique trimer structure where both dehydrodigalloyl and valoneoyl group linkages were found between the hydrolysable tannin monomers. Dimeric hydrolysable tannins coriariins K and L, having a dehydrodigalloyl group as the linking unit, were structurally related to coriariin A, the main hydrolysable tannin of this plant species. Additionally, the complexation of the eight hydrolysable tannins isolated in this study with bovine serum albumin (BSA) to form water-soluble macromolecules was analyzed using native polyacrylamide gel electrophoresis (PAGE). A comparison of the behaviors of the oligomeric hydrolysable tannins suggested the participation of the hexahydroxydiphenoyl group and the importance of the molecular sizes of the hydrolysable tannins in the formation of macromolecules.

Formation of unique trimer of nitric oxide on Cu(111).

We report that NO molecules unexpectedly prefer a trimeric configuration on Cu(111). We used scanning tunneling microscopy (STM) at 6 K, and confirmed that the NO molecule is bonded to the face-centered-cubic hollow site in an upright configuration. The individual NO molecule is imaged as a ring protrusion, which is characteristic of the doubly degenerate 2π(*) orbital. A triangular trimer is thermodynamically more favorable than the monomer and dimer, and its bonding structure was characterized by STM manipulation. This unique behavior of NO on Cu(111) is ascribed to the threefold symmetry of the surface, facilitating effective mixing of the 2π(*) orbitals in a triangular configuration.

LeishmaniaTDR1 structure, a unique trimeric glutathione transferase capable of deglutathionylation and antimonial prodrug activation

Thiol-dependent reductase I (TDR1), an enzyme found in parasitic Leishmania species and Trypanosoma cruzi, is implicated in deglutathionylation and activation of antimonial prodrugs used to treat leishmaniasis. The 2.3Å resolution structure of TDR1 reveals a unique trimer of subunits each containing two glutathione-S-transferase (GST) domains. The similarities of individual domains and comparisons with GST classes suggest that TDR1 evolved by gene duplication, diversification, and gene fusion; a combination of events previously unknown in the GST protein superfamily and potentially explaining the distinctive enzyme properties of TDR1. The deglutathionylation activity of TDR1 implies that glutathione itself has regulatory intracellular roles in addition to being a precursor for trypanothione, the major low mass thiol present in trypanosomatids. We propose that activation of antiparasite Sb(V)-drugs is a legacy of the deglutathionylation activity of TDR1 and involves processing glutathione adducts with concomitant reduction of the metalloid to active Sb(III) species.

One-step synthesis of solid sulfonic acid catalyst and its application in the acetalization of glycerol: crystal structure of cis-5-hydroxy-2-phenyl-1,3-dioxane trimer

AbstractA one-pot method was employed to immobilize sulfonic acid onto silica obtained from rice husk ash using 3-(mercaptopropyl)trimethoxysilane to form a solid catalyst denoted as RHASO3H. BET measurements of the catalyst showed the surface area to be 340 m2 g−1 with the average pore volume of 0.24 mL g−1 and the pore diameter of 2.9 nm. Acidity test of cation exchange capacity and pyridine adsorption studies revealed the presence of Brønsted acid sites on the catalyst surface. The catalyst was used in the acetalization reaction of glycerol with benzaldehyde. Under optimized conditions, the reaction showed the maximum conversion of 78 % after 8 h with 67 % selectivity towards the five membered ring isomer. Variation in the glycerol concentration had a significant effect on the reactants conversion. A single crystal X-ray study of one of the products proved the existence of a unique trimer formed by hydrogen bonding by the six-membered cis-isomer. The catalyst was several times recycled without any loss of its catalytic activity.

Solid state stacked trimers of 1,10-phenanthroline in a supramolecular tubular motif of C-methyl calix[4]resorcinarene

The self-assembly of bidentate ligand, 1,10-phenanthroline with C-methyl calix[4]resorcinarene (CMCR) in presence of coumarin results in a unique trimer stacking arrangement of phenanthroline molecules in a nanotubular motif generated by the supramolecular assembly of the host.

Induction of alpha-helix in the beta-sheet protein tumor necrosis factor-alpha: acid-induced denaturation.

Acid-induced unfolding of proteins often results in an intermediate structure, called the molten globule structure or "A" state, which retains at least partial secondary structure but lacks a rigid tertiary structure. Acid-induced unfolding has been studied extensively for alpha-helical proteins, while few studies have been done on proteins containing only beta-strands. Tumor necrosis factor-alpha (TNF-alpha) is a trimer in which the individual subunits consist of antiparallel beta-sheet, organized into a jellyroll beta-sandwich. We have found previously [Narhi et al. (1996) Biochemistry 35, 11447-11453] that thermal denaturation of TNF-alpha results in an aggregate which contains a substantial amount of alpha-helix and that the addition of trifluoroethanol induces alpha-helix in both murine and human TNF-alpha. Here we show that acid also can induce alpha-helix in these proteins. At acidic pH (below 4), both human and murine TNF-alpha convert to a monomeric form, as determined by sedimentation and diffusion constants obtained from sedimentation velocity experiments. The sedimentation coefficient indicated that this monomer was only slightly expanded relative to the native state. Near-UV circular dichroic (CD) analysis showed a loss of tertiary structure. These structural features coincide with the notion that the acid-induced structure of TNF-alpha is a molten globule. What is unique in this protein is that TNF-alpha acquires alpha-helical structure, which is not present in the native structure as determined by both CD and Fourier transform infrared spectroscopy. Even more surprising is that TNF-alpha at pH 3.3 undergoes a very gradual noncooperative change in secondary structure upon heating, which results in an increase in alpha-helical content. At pH 2.2 in the absence of salt, TNF-alpha shows considerable alpha-helix, although heating does not change the spectrum. At pH 2.2, physiological salt decreases the amount of alpha-helix at ambient temperature, and upon heating, we see the noncooperative increase in alpha-helix as observed at pH 3.3 with low salt. The addition of salt at low pH induces reassociation but to a range of oligomers rather than a unique trimer structure. This acid-induced formation of an alpha-helical monomer of TNF-alpha may be related to its known interaction with lipid bilayers.