Weak Substrate Interaction Research Articles

Substrate Affinity Versus Catalytic Efficiency: Ancestral Sequence Reconstruction of tRNA Nucleotidyltransferases Solves an Enzyme Puzzle.

In tRNA maturation, CCA-addition by tRNA nucleotidyltransferase is a unique and highly accurate reaction. While the mechanism of nucleotide selection and polymerization is well understood, it remains a mystery why bacterial and eukaryotic enzymes exhibit an unexpected and surprisingly low tRNA substrate affinity while they efficiently catalyze the CCA-addition. To get insights into the evolution of this high-fidelity RNA synthesis, the reconstruction and characterization of ancestral enzymes is a versatile tool. Here, we investigate a reconstructed candidate of a 2 billion years old CCA-adding enzyme from Gammaproteobacteria and compare it to the corresponding modern enzyme of Escherichia coli. We show that the ancestral candidate catalyzes an error-free CCA-addition, but has a much higher tRNA affinity compared with the extant enzyme. The consequence of this increased substrate binding is an enhanced reverse reaction, where the enzyme removes the CCA end from the mature tRNA. As a result, the ancestral candidate exhibits a lower catalytic efficiency in vitro as well as in vivo. Furthermore, the efficient tRNA interaction leads to a processive polymerization, while the extant enzyme catalyzes nucleotide addition in a distributive way. Thus, the modern enzymes increased their polymerization efficiency by lowering the binding affinity to tRNA, so that CCA synthesis is efficiently promoted due to a reduced reverse reaction. Hence, the puzzling and at a first glance contradicting and detrimental weak substrate interaction represents a distinct activity enhancement in the evolution of CCA-adding enzymes.

Growth Order-Dependent Strain Variations of Lateral Transition Metal Dichalcogenide Heterostructures

Understanding the heterojunction of a lateral heterostructured transition metal dichalcogenide (hTMD) is important in order to take advantage of the combined optoelectronic properties of individual TMDs for various applications but, however, is hampered by mingled effects from lattice mismatch and substrate interaction. Here, we systematically investigated the strain occurring at lateral hTMDs consisting of molybdenum disulfide (MoS2) and molybdenum diselenide (MoSe2) prepared by chemical vapor deposition. Comparison of homologous TMDs and hTMDs from controlled growth order revealed systematic change in photoluminescence behavior depending on substrate interaction and relative lattice mismatch. Near the heterojunction, a TMD with a larger lattice constant (a) exhibits photoluminescence (PL) red-shift, whereas a TMD with smaller a shows an opposite trend owing to lattice-induced strain. These effects are augmented in a subtractive or additive manner by tensile strain from the substrate interaction. Moreover, comparison of PLs revealed that the shell region grown from the core edges exhibits weak substrate interaction contrasted by that of a shell region independently grown on a shell. This study provides detailed understandings of the heterojunction at a lateral hTMD for various applications.

Thermal expansion in single-walled carbon nanotubes and graphene: Nonequilibrium Green’s function approach

The nonequilibrium Green's function method is applied to investigate the coefficient of thermal expansion (CTE) in single-walled carbon nanotubes (SWCNT) and graphene. It is found that atoms expand about 1% from equilibrium positions even at $T=0\text{ }\text{K}$, resulting from the interplay between quantum zero-point motion and nonlinear interaction. The CTE in SWCNT of different sizes is studied and analyzed in terms of the competition between various vibration modes. As a result of this competition, the axial CTE is positive in the whole temperature range, while the radial CTE is negative at low temperatures. In graphene, the CTE is very sensitive to the substrate. Without substrate, CTE has large negative region at low temperatures and very small value at high-temperature limit, and the value of CTE at 300 K is $\ensuremath{-}6\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}6}\text{ }{\text{K}}^{\ensuremath{-}1}$ which is very close to a recent experimental result, $\ensuremath{-}7\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}6}\text{ }{\text{K}}^{\ensuremath{-}1}$ [Nat. Nanotechnol. 10, 1038 (2009)]. A very weak substrate interaction (about 0.06% of the in-plane interaction) can largely reduce the negative CTE region and greatly enhance the value of CTE. If the substrate interaction is strong enough, the CTE will be positive in whole temperature range and the saturate value at high temperatures reaches $2.0\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}\text{ }{\text{K}}^{\ensuremath{-}1}$.

Electronic coupling of optical excitations in organic/inorganic semiconductor hybrid structures

The epitaxial growth of small conjugated molecules on ZnO-based surfaces is studied. A weak substrate interaction allows for the preparation of organic layers with well-defined morphology and electronically intact interfaces without the need for extra passivation. Nonradiative energy transfer from inorganic quantum wells to various molecules is identified by optical spectroscopy. The strength of the dipole–dipole mediated coupling between Wannier and Frenkel excitons is as large as 2 meV. In hybrid structures with type-II energy level alignment, charge separation occurs at the organic/inorganic interface as well. These findings render organic/ZnO hybrid structures interesting for light-emitting as well as photovoltaic applications benefiting from favorable properties of both material classes.

Scanning tunneling microscopy of Ag growth on GaAs(110) at 300 K: From clusters to crystallites.

Scanning-tunneling-microscopy (STM) studies of Ag overlayer growth on GaAs(110) at 300 K show cluster nucleation at low coverage followed by conversion to nanocrystallites with distinct facets. Clusters formed by depositions below \ensuremath{\sim}0.5 monolayer (ML) Ag exhibit no apparent preferential substrate orientation, and individual atoms within the clusters cannot be resolved. These are three-dimensional (3D) clusters, as shown by calculations of cluster volumes and areas based on the STM images, and they contain up to \ensuremath{\sim}250 atoms. Continued deposition yields new small clusters in addition to the growth of existing clusters and the coalescing of clusters in close proximity. By \ensuremath{\sim}5 ML deposition the Ag structures exhibit crystalline order and expose {111} facets. The evolution from clusters to crystallites also involves a preferential orientation so that [11\ifmmode\bar\else\textasciimacron\fi{}0] of Ag is parallel to [11\ifmmode\bar\else\textasciimacron\fi{}0] of GaAs(110) and the Ag overlayer (111) plane is tilted 25\ifmmode^\circ\else\textdegree\fi{} around the [11\ifmmode\bar\else\textasciimacron\fi{}0] direction of GaAs(110). The overlayer derived from these 3D crystallites is then highly irregular, and contact with the partially relaxed GaAs(110) surface is achieved through regularly stepped Ag(110) planes. These results demonstrate weak substrate interaction and cooperative Ag rearrangement to minimize surface energies, even at 300 K.