Class I terpene synthases generate the structural core of bioactive terpenoids. Deciphering structure-function relationships in the reactive closed complex and targeted engineering is hampered by highly dynamic carbocation rearrangements during catalysis. Available crystal structures, however, represent the open, catalytically inactive form or harbor nonproductive substrate analogs. Here, we present a catalytically relevant, closed conformation of taxadiene synthase (TXS), the model class I terpene synthase, which simulates the initial catalytic time point. In silico modeling of subsequent catalytic steps allowed unprecedented insights into the dynamic reaction cascades and promiscuity mechanisms of class I terpene synthases. This generally applicable methodology enables the active-site localization of carbocations and demonstrates the presence of an active-site base motif and its dominating role during catalysis. It additionally allowed in silico-designed targeted protein engineering that unlocked the path to alternate monocyclic and bicyclic synthons representing the basis of a myriad of bioactive terpenoids.computational biology | closed complex modeling | protein engineering | terpene synthases | terpene synthase catalysis

The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value ≤ 1e −70 ) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.chain-elongation | prenyltransferase T he five-carbon molecules isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) are the fundamental building blocks for isoprenoid compounds. Beginning with DMAPP, a series of polyprenyl diphosphates with C 10 (geranyl diphosphate, GPP), C 15 (farnesyl diphosphate, FPP), C 20 (geranylgeranyl diphosphate, GGPP), C 25 (farnesylgeranyl diphosphate, FGPP), and higher molecular weight isoprenoid chains are synthesized by polyprenyl transferases (PTSs). With only a few exceptions, PTSs provide substrates for all but a few branch point enzymes for the biosynthesis of the more than 55,000 known isoprenoid metabolites, including monoterpenes, sesquiterpenes, diterpenes, sterols, carotenoids, ubiquinones, and prenylated proteins and peptides fulfilling essential roles in cells (Fig. S1) (1, 2).There are two distinct classes of PTSs, E-PTS forming trans bonds and Z-PTS forming cis bonds throughout chain elongation. The carbon skeletons of the great majority of isoprenoid metabolites are derived from products of E-PTSs, which share a common protein fold and two functionally important Asp-rich (DDXXD) motifs (1, 3, 4). E-PTSs synthesize linear allylic diphosphates ranging f...

Anatase TiO2 films are grown on Si (100) by atomic layer deposition. Three different interlayers (Si3N4, Al2O3, and Ti-rich SiOx) between the TiO2 films and the Si substrate have been considered. The band alignment of the titanium oxide films with the silicon substrate is investigated by x-ray photoelectron spectroscopy (XPS), internal photoemission (IPE) spectroscopy, and optical absorption (OA) measurements. XPS analysis indicates that TiO2∕Si heterojunctions with different interlayers (ILs) have different valence-band offsets (VBOs). A VBO value of 2.56±0.09eV is obtained for the TiO2∕Ti-rich SiOx∕Si sample. Similarly, we obtain a VBO value of 2.44±0.09 and 2.73±0.10eV for the TiO2∕Si3N4∕Si and TiO2∕Al2O3∕Si samples, respectively. According to IPE and OA measurements, the band gap of the as-grown TiO2 films is 3.3±0.1eV for all the samples. Combining the XPS and IPE data, the conduction band offset values at the TiO2∕Si heterojunction are found to be −0.2±0.1, −0.4±0.1, and −0.5±0.1eV for the TiO2∕Si3N4∕Si, TiO2∕Ti-rich SiOx∕Si, and TiO2∕Al2O3∕Si samples, respectively. According to our experimental results, the band alignment of a TiO2 film with the underlying Si (100) substrate is clearly affected by the presence of an IL, suggesting the possibility to tune the band structure of a TiO2∕Si heterojunction by selecting the proper IL.

We study the electrical properties of thin TiO2 films made by atomic layer deposition (ALD) on p-doped silicon in an electrolyte-oxide-silicon (EOS) configuration. The electrolyte contact of the TiO2∕Si heterostructure allows measurements of the differential capacitance for a wide range of bias voltages as they cannot be performed in a metal-oxide-silicon structure because of extensive leakage currents. In the accumulation region of p-silicon, we find a saturation of capacitance that decreases with oxide thickness, indicating an insulator with a dielectric constant of 34. In the inversion region of p-silicon, the capacitance increases in two steps far beyond the saturation capacitance. We assign this effect to the presence of electrons in TiO2 which is controlled by the bias voltage and by immobile positive charges at the TiO2∕Si interface: When the Fermi energy in p-silicon is raised to the level of the low lying conduction band of TiO2, electrons accumulate in two layers near the TiO2∕Si interface and at the electrolyte/TiO2 interface with a concomitantly enhanced differential capacitance. As a control, we study HfO2 films also made by ALD. We obtain a dielectric constant of 15 from the capacitance in the accumulation region of p-silicon. For HfO2 with a high lying conduction band, the capacitance decreases as expected in the inversion region for the high-frequency limit of silicon. The electrical characterization of TiO2 and HfO2 in EOS junctions opens future applications of high-κ materials in bioelectronics for efficient capacitive interaction of silicon chips and living cells.