High-Temperature Tolerance Protein Engineering through Deep Evolution.

Protein engineering aimed at increasing temperature tolerance through iterative mutagenesis and high-throughput screening is often labor-intensive. Here, we developed a deep evolution (DeepEvo) strategy to engineer protein high-temperature tolerance by generating and selecting functional sequences using deep learning models. Drawing inspiration from the concept of evolution, we constructed a high-temperature tolerance selector based on a protein language model, acting as selective pressure in the high-dimensional latent spaces of protein sequences to enrich those with high-temperature tolerance. Simultaneously, we developed a variant generator using a generative adversarial network to produce protein sequence variants containing the desired function. Afterward, the iterative process involving the generator and selector was executed to accumulate high-temperature tolerance traits. We experimentally tested this approach on the model protein glyceraldehyde 3-phosphate dehydrogenase, obtaining 8 variants with high-temperature tolerance from just 30 generated sequences, achieving a success rate of over 26%, demonstrating the high efficiency of DeepEvo in engineering protein high-temperature tolerance.

[Theoretical analysis and practical applications of the catalytic mechanism of flavonoid 6-hydroxylase].

Insufficient catalytic efficiency of flavonoid 6-hydroxylases in the fermentative production of scutellarin leads to the formation of at least about 18% of by-products. Here, the catalytic mechanisms of two flavonoid 6-hydroxylases, CYP82D4 and CYP706X, were investigated by molecular dynamics simulations and quantum chemical calculations. Our results show that CYP82D4 and CYP706X have almost identical energy barriers at the rate-determining step and thus similar reaction rates, while the relatively low substrate binding energy of CYP82D4 may facilitate product release, which is directly responsible for its higher catalytic efficiency. Based on the study of substrate entry and release processes, the catalytic efficiency of the L540A mutation of CYP82D4 increased by 1.37-fold, demonstrating the feasibility of theoretical calculations-guided engineering of flavonoid 6-hydroxylase. Overall, this study reveals the catalytic mechanism of flavonoid 6-hydroxylases, which may facilitate the modification and optimization of flavonoid 6-hydroxylases for efficient fermentative production of scutellarin.

Origin and evolution of the main starch biosynthetic enzymes.

Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.

Effects of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of proton pump inhibitors.

Proton pump inhibitors (PPIs) are used widely for the treatment of acid-related disorders. Despite their excellent efficacy and tolerance, the pharmacodynamics and pharmacokinetics of PPIs are affected by each patient's CYP2C19 and gastric H+,K+-ATPase genotype. The aim of this review was to analyze the effect of genetic polymorphisms on the pharmacodynamic and pharmacokinetic properties of PPIs. The gastric acid-suppressive effect of PPIs is affected by both gastric H+,K+-ATPase and CYP2C19 polymorphisms, although gastric H+,K+-ATPase polymorphisms may have larger effects. Ilaprazole and rabeprazole show relatively small differences in the pharmacokinetic and pharmacodynamic properties and clinical efficacy among the different CYP2C19 genotypes. Compared with oral administration, the intravenous infusion of PPIs is less affected by CYP2C19 polymorphism. At the same dose, each enantiomer has less variation among different CYP2C19 genotypes than a racemate mixture.

Atomically precise bottom-up synthesis of π-extended [5]triangulene.

The zigzag-edged triangular graphene molecules (ZTGMs) have been predicted to host ferromagnetically coupled edge states with the net spin scaling with the molecular size, which affords large spin tunability crucial for next-generation molecular spintronics. However, the scalable synthesis of large ZTGMs and the direct observation of their edge states have been long-standing challenges because of the molecules' high chemical instability. Here, we report the bottom-up synthesis of π-extended [5]triangulene with atomic precision via surface-assisted cyclodehydrogenation of a rationally designed molecular precursor on metallic surfaces. Atomic force microscopy measurements unambiguously resolve its ZTGM-like skeleton consisting of 15 fused benzene rings, while scanning tunneling spectroscopy measurements reveal edge-localized electronic states. Bolstered by density functional theory calculations, our results show that [5]triangulenes synthesized on Au(111) retain the open-shell π-conjugated character with magnetic ground states.

Conformationally Flexible Bis(9-fluorenylidene)porphyrin Diradicaloids.

A stable 5,10-bis(9-fluorenylidene)porphyrin (Por-Fl) diradicaloid was synthesized. It shows a quinoidal, saddle-shaped geometry in the single crystal but can be thermally populated to a triplet diradical both in solution and in the solid state. Coordination with the Ni2+ ion (Por-Fl-Ni) does not significantly change the contorted conformation but reduces the singlet-triplet gap. Heat-induced geometric change can explain the observed paramagnetic properties as well as unusual hysteresis in SQUID measurements. On the other hand, protonation (Por-Fl-2H+ ) dramatically changes the conformation while maintains the closed-shell electronic structure. Our studies demonstrate how heat, coordination, and protonation affect the geometry, diradical character, and physical properties of conformationally flexible open-shell singlet diradicaloids.