This study developed a novel nanocomposite colorimetric sensor array (CSA) to distinguish between fresh and moldy maize. First, the headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC/MS) method was used to analyze volatile organic compounds (VOCs) in fresh and moldy maize samples. Then, principal component analysis and orthogonal partial least-squares discriminant analysis (OPLS-DA) were used to identify 2-methylbutyric acid and undecane as key VOCs associated with moldy maize. Furthermore, colorimetric sensitive dyes modified with different nanoparticles were employed to enhance the dye properties used in the nanocomposite CSA analysis of key VOCs. This study focused on synthesizing four types of nanoparticles: polystyrene acrylic (PSA), porous silica nanospheres (PSNs), zeolitic imidazolate framework-8 (ZIF-8), and ZIF-8 after etching. Additionally, three types of substrates, qualitative filter paper, polyvinylidene fluoride film, and thin-layer chromatography silica gel, were comparatively used to fabricate nanocomposite CSA combining with linear discriminant analysis (LDA) and K-nearest neighbor (KNN) models for real sample detection. All moldy maize samples were correctly identified and prepared to characterize the properties of the CSA. Through initial testing and nanoenhancement of the chosen dyes, four nanocomposite colorimetric sensitive dyes were confirmed. The accuracy rates for LDA and KNN models in this study reached 100%. This work shows great potential for grain quality control using CSA methods.

The modular nature and unique electronic properties of two-dimensional (2D) covalent organic frameworks (COFs) make them an attractive option for applications in catalysis, optoelectronics, and spintronics. The fabrications of such devices often involve interfaces formed between COFs and substrates. In this work, we employ the first-principlesGWapproach to accurately determine the quasiparticle electronic structure of three 2D carbonyl bridged heterotriangulene-based COFs featuring honeycomb-kagome lattice, with their properties ranging from a semi-metal to a wide-gap semiconductor. Moreover, we study the adsorption of these COFs on Au(111) surface and characterize the quasiparticle electronic structure at the heterogeneous COF/Au(111) interfaces. To reduce the computational cost, we apply the recently developed dielectric embeddingGWapproach and show that our results agree with existing experimental measurement on the interfacial energy level alignment. Our calculations illustrate how the many-body dielectric screening at the interface modulates the energies and shapes of the Dirac bands, the effective masses of semiconducting COFs, as well as the Fermi velocity of the semi-metallic COF.

Substrates have strong effects on optoelectronic properties of two-dimensional (2D) materials, which have emerged as promising platforms for exotic physical phenomena and outstanding applications. To reliably interpret experimental results and predict such effects at 2D interfaces, theoretical methods accurately describing electron correlation and electron-hole interaction such as first-principles many-body perturbation theory are necessary. In our previous work (2020Phys. Rev. B102205113), we developed the reciprocal-space linear interpolation method that can take into account the effects of substrate screening for arbitrarily lattice-mismatched interfaces at the GW level of approximation. In this work, we apply this method to examine the substrate effect on excitonic excitation and recombination of 2D materials by solving the Bethe-Salpeter equation. We predict the nonrigid shift of 1s and 2s excitonic peaks due to substrate screening, in excellent agreements with experiments. We then reveal its underlying physical mechanism through 2D hydrogen model and the linear relation between quasiparticle gaps and exciton binding energies when varying the substrate screening. At the end, we calculate the exciton radiative lifetime of monolayer hexagonal boron nitride with various substrates at zero and room temperature, as well as the one of WS2where we obtain good agreement with experimental lifetime. Our work answers important questions of substrate effects on excitonic properties of 2D interfaces.

A novel catalyst with a yolk-shell structure was designed to overcome the leaching of noble metals in heterogeneous catalysis. Through a template method, palladium (Pd) nanoparticles were encapsulated by hollow spherical covalent organic frameworks (COFs) consisting of 2,4,6-trihydroxybenzene-1,3,5-tricarbaldehyde (Tp) and p-phenylenediamine (Pa). The final catalyst with a yolk-shell structure was denoted as (Pd/C)@TpPa COFs. The unique morphology and chemical structure of this novel composite (Pd/C)@TpPa COFs were confirmed by a transmission electron microscope (TEM), a laser particle analyzer, X-ray diffraction (XRD), and N2 adsorption and desorption. Subsequently, to demonstrate its catalytic performance brought by structural design, this novel catalyst was applied to catalyze the Suzuki reaction. Interestingly, this catalyst exhibited a brilliant size cutoff efficiency for aryl benzene amounting to 100% and achieved a high conversion with only 0.05 mol% Pd loading. Besides, this catalyst could be readily recovered via filtration and reused for at least five consecutive cycles without any significant loss in its activity.

2-phenylethanol (2-PE) is a value-added compound widely used in industry due to its rose-like odor and antibacterial properties that can be bioproduced using wastes as raw materials. This study presents the valorization of nine agro-industrial wastes as potential substrates for 2-PE production using an isolated 2-PE producer Pichia kudriavzevii, and the solid-state fermentation (SSF) technology as an alternative approach. The assessed substrates comprised wastes of varied traits such that each of them provided different characteristics to the fermentation. Thus, by using a principal component analysis (PCA), it was possible to identify the most significant characteristics associated with the substrates affecting the 2-PE production. Results show that L-phenylalanine biotransformation was more efficient than de novo synthesis for producing 2-PE. Besides, from the evaluated set, the maximum 2-PE production was achieved with red apple pomace, reaching 1.7 and 25.2 mg2PE per gram of used waste through de novo and L-phenylalanine biotransformation, respectively. In that scenario, volumetric productivity and precursor yield were 39.6 mg2PE L-1h-1 and 0.69 g2PE per gram of L-phenylalanine added, respectively. From the PCA, it was identified that the reducing sugars content of the substrate, the air-filled porosity of the bed and the L-phenylalanine availability were the most critical parameters (associated with the substrates) influencing the microbial activity and 2-PE production. These results suggest that the desirable traits a solid media needs for promoting 2-PE production via SSF could be reached by using a combination of wastes in a synergistic approach.

Promiscuous enzymes can be modified by protein engineering, which enables the catalysis of non-native substrates. γ-lactamase Sspg from Sulfolobus solfataricus is an enzyme with high activity, high stability, and pronounced tolerance of high concentrations of the γ-lactam substrate. These characteristics suggest Sspg as a robust enzymatic catalyst for the preparation of optically pure γ-lactam. This study investigated the modification of this enzyme to expand its application toward resolving chiral esters. γ-Lactamase-esterase conversion was performed by employing a three-step method: initial sequence alignment, followed by substrate screening, and protein engineering based on the obtained substrate-enzyme docking results. This process of fine-tuning of chemical groups on substrates has been termed \"substrate screening.\" Steric hindrance and chemical reactivity of the substrate are major concerns during this step, since both are determining factors for the enzyme-substrate interaction. By employing this three-step method, γ-lactamase Sspg was successfully converted into an esterase with high enantioselectivity towards phenylglycidate substrates (E value > 300). However, since both wild-type Sspg and Sspg mutants did not hydrolyze para-nitrophenyl substrates (pNPs), this esterase activity was termed \"atypical esterase activity.\" The γ-lactamase activity and stability of the Sspg mutants were not severely compromised. The proposed method can be applied to find novel multi-functional enzyme catalysts within existing enzyme pools.

Serine peptidases of the prolyl oligopeptidase (POP) family are of substantial therapeutic importance because of their involvement in diseases such as diabetes, cancer, neurological diseases, and autoimmune disorders. Proper annotation and knowledge of substrate specificity mechanisms in this family are highly valuable. Although endopeptidase, dipeptidyl peptidase, tripeptidyl peptidase, and acylaminoacyl peptidase activities have been reported previously, here we report the first instance of carboxypeptidase activity in a POP family member. We determined the crystal structures of this carboxypeptidase, an S9C subfamily member from Deinococcus radiodurans, in its active and inactive states at 2.3-Å resolution, providing an unprecedented view of assembly and disassembly of the active site mediated by an arginine residue. We observed that this residue is poised to bind substrate in the active structure and disrupts the catalytic triad in the inactive structure. The assembly of the active site is accompanied by the ordering of gating loops, which reduces the effective size of the oligomeric pore. This prevents the entry of larger peptides and constitutes a novel mechanism for substrate screening. Furthermore, we observed structural adaptations that enable its carboxypeptidase activity, with a unique loop and two arginine residues in the active site cavity orienting the peptide substrate for catalysis. Using these structural features, we identified homologs of this enzyme in the POP family and confirmed the presence of carboxypeptidase activity in one of them. In conclusion, we have identified a new type within POP enzymes that exhibits not only unique activity but also a novel substrate-screening mechanism.

Three threonine aldolases (TAs) were cloned and overexpressed in Escherichia coli (Aeromonas jandaeil-allo-threonine aldolase, E. colil-threonine aldolase and Thermotoga maritimal-allo-threonine aldolase). A Design of Experiments strategy was used to identify optimal reaction conditions for each enzyme. These conditions were used to characterize the substrate- and stereoselectivity of each TA toward a panel of aldehyde acceptors. In general, the A. jandaei TA performed best, and six representative conversions were scaled up 10-fold in order to develop downstream steps for product isolation. One key improvement was to treat the crude reaction product with Bacillus subtilis glycine oxidase, which eliminated residual starting material and significantly simplified product isolation. NMR studies were used to identify the major and minor diastereomers from the preparative-scale reactions and the absolute configurations for three representative cases.

The nearly 50,000 known Nudix proteins have a diverse array of functions, of which the most extensively studied is the catalyzed hydrolysis of aberrant nucleotide triphosphates. The functions of 171 Nudix proteins have been characterized to some degree, although physiological relevance of the assayed activities has not always been conclusively demonstrated. We investigated substrate specificity for eight structurally characterized Nudix proteins, whose functions were unknown. These proteins were screened for hydrolase activity against a 74-compound library of known Nudix enzyme substrates. We found substrates for four enzymes with kcat /Km values >10,000 M-1  s-1 : Q92EH0_LISIN of Listeria innocua serovar 6a against ADP-ribose, Q5LBB1_BACFN of Bacillus fragilis against 5-Me-CTP, and Q0TTC5_CLOP1 and Q0TS82_CLOP1 of Clostridium perfringens against 8-oxo-dATP and 3\'-dGTP, respectively. To ascertain whether these identified substrates were physiologically relevant, we surveyed all reported Nudix hydrolytic activities against NTPs. Twenty-two Nudix enzymes are reported to have activity against canonical NTPs. With a single exception, we find that the reported kcat /Km values exhibited against these canonical substrates are well under 105 M-1  s-1 . By contrast, several Nudix enzymes show much larger kcat /Km values (in the range of 105 to >107 M-1  s-1 ) against noncanonical NTPs. We therefore conclude that hydrolytic activities exhibited by these enzymes against canonical NTPs are not likely their physiological function, but rather the result of unavoidable collateral damage occasioned by the enzymes\' inability to distinguish completely between similar substrate structures. Proteins 2016; 84:1810-1822. © 2016 Wiley Periodicals, Inc.

Elucidation of the key determinants for the phosphorylation site specificities of protein kinases facilitates identification of their physiological substrates, and serves to better define their critical roles in the signaling networks that underlie a multitude of cellular activities. Albeit with some apparent limitations, such as the lack of contextual information for secondary substrate-binding sites, the synthetic peptide-based approach has been adopted widely for the kinase specificity profiling studies, especially when they are used in an array format, which permits the screening of large numbers of potential peptide substrates in parallel. In this chapter, we present detailed protocols for determining protein kinase substrate specificity using an approach that involves both peptide microarrays and macroarrays. In particular, SPOT synthesis on macroarrays can be used to follow up on in silico predictions of protein kinase substrate specificity with predictive algorithms.