Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability

Mammalian cytochrome P450 enzymes often metabolize many pharmaceuticals and other xenobiotics, a feature that is valuable in a biotechnology setting. However, extant P450 enzymes are typically relatively unstable, with T50 values of ∼30–40 °C. Reconstructed ancestral cytochrome P450 enzymes tend to have variable substrate selectivity compared with related extant forms, but they also have higher thermostability and therefore may be excellent tools for commercial biosynthesis of important intermediates, final drug molecules, or drug metabolites. The mammalian ancestor of the cytochrome P450 1B subfamily was herein characterized structurally and functionally, revealing differences from the extant human CYP1B1 in ligand binding, metabolism, and potential molecular contributors to its thermostability. Whereas extant human CYP1B1 has one molecule of α-naphthoflavone in a closed active site, we observed that subtle amino acid substitutions outside the active site in the ancestor CYP1B enzyme yielded an open active site with four ligand copies. A structure of the ancestor with 17β-estradiol revealed only one molecule in the active site, which still had the same open conformation. Detailed comparisons between the extant and ancestor forms revealed increases in electrostatic and aromatic interactions between distinct secondary structure elements in the ancestral forms that may contribute to their thermostability. To the best of our knowledge, this represents the first structural evaluation of a reconstructed ancestral cytochrome P450, revealing key features that appear to contribute to its thermostability.

Mechanical scarification, seed origin, and substrate influence on germination of Samanea tubulosa

ABSTRACTSamanea tubulosa is an important species mainly to its uses in reforestation projects and as a wood and fruit resource. This species seed dormancy and other scarce germination information have been limiting the adequate seedling production process. Thus, this study tried to understand how seed origin, mechanical scarification, and substrate could influence the seedling production process. The population affected the time required for germination and germination speed, probably due to high genetic variability. Whereas mechanical scarification did not present statistical differences in the control treatment, with seeds in the natural condition, indicating that seed dormancy could be variable. Substrate promoted significant differences in germination rate. The population seems to affect, but not preclude seedling production. Mechanical scarification did not provide a relevant enhancement of germination. Vermiculite presented a significantly higher germination rate than the organic-based substrate.

Effects of spatially-varying substrate anchoring on instabilities and dewetting of thin nematic liquid crystal films

We investigate (theoretically and numerically) free surface evolution of nematic liquid crystal films in the presence of variable substrate anchoring.

Self-organized reactivation maintains and reinforces memories despite synaptic turnover

Long-term memories are believed to be stored in the synapses of cortical neuronal networks. However, recent experiments report continuous creation and removal of cortical synapses, which raises the question how memories can survive on such a variable substrate. Here, we study the formation and retention of associative memory in a computational model based on Hebbian cell assemblies in the presence of both synaptic and structural plasticity. During rest periods, such as may occur during sleep, the assemblies reactivate spontaneously, reinforcing memories against ongoing synapse removal and replacement. Brief daily reactivations during rest-periods suffice to not only maintain the assemblies, but even strengthen them, and improve pattern completion, consistent with offline memory gains observed experimentally. While the connectivity inside memory representations is strengthened during rest phases, connections in the rest of the network decay and vanish thus reconciling apparently conflicting hypotheses of the influence of sleep on cortical connectivity.

Reflection phase analysis of reflectarray antenna based on paper substrate materials

<span>This article presents an analysis of reflection loss and reflection phase behavior of a novel microstrip reflectarray antenna, embedded on paper substrate material. Two different paper substrates were first analyzed for dielectric material properties. A detailed analysis of scattering parameters of rectangular patch element with variable substrate heights has been carried out. Rectangular patch elements fabricated using adhesive copper tape over the paper substrate, show that a wide bandwidth is achieved compared to available conventional substrate materials. Fabricated patch elements over paper substrate material show a broadband frequency response of 340 and 290 MHz. It has also been demonstrated that the measured reflection phase ranges for both the substrate cover 310º and 294º at low phase gradients of 0.12 and 0.24 º/MHz respectively.</span>

Stabilizing a homoclinic stripe

For a large class of reaction–diffusion systems with large diffusivity ratio, it is well known that a two-dimensional stripe (whose cross-section is a one-dimensional homoclinic spike) is unstable and breaks up into spots. Here, we study two effects that can stabilize such a homoclinic stripe. First, we consider the addition of anisotropy to the model. For the Schnakenberg model, we show that (an infinite) stripe can be stabilized if the fast-diffusing variable (substrate) is sufficiently anisotropic. Two types of instability thresholds are derived: zigzag (or bending) and break-up instabilities. The instability boundaries subdivide parameter space into three distinct zones: stable stripe, unstable stripe due to bending and unstable due to break-up instability. Numerical experiments indicate that the break-up instability is supercritical leading to a ‘spotted-stripe’ solution. Finally, we perform a similar analysis for the Klausmeier model of vegetation patterns on a steep hill, and examine transition from spots to stripes. This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)’.

Bacteroides thetaiotaomicron generates diverse α-mannosidase activities through subtle evolution of a distal substrate-binding motif

A dominant human gut microbe, the well studied symbiont Bacteroides thetaiotaomicron (Bt), is a glyco-specialist that harbors a large repertoire of genes devoted to carbohydrate processing. Despite strong similarities among them, many of the encoded enzymes have evolved distinct substrate specificities, and through the clustering of cognate genes within operons termed polysaccharide-utilization loci (PULs) enable the fulfilment of complex biological roles. Structural analyses of two glycoside hydrolase family 92 α-mannosidases, BT3130 and BT3965, together with mechanistically relevant complexes at 1.8–2.5 Å resolution reveal conservation of the global enzyme fold and core catalytic apparatus despite different linkage specificities. Structure comparison shows that Bt differentiates the activity of these enzymes through evolution of a highly variable substrate-binding region immediately adjacent to the active site. These observations unveil a genetic/biochemical mechanism through which polysaccharide-processing bacteria can evolve new and specific biochemical activities from otherwise highly similar gene products.