Detection of Maize Mold Based on a Nanocomposite Colorimetric Sensor Array under Different Substrates

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.

Quasiparticle electronic structure of two-dimensional heterotriangulene-based covalent organic frameworks adsorbed on Au(111)

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.

Substrate effect on excitonic shift and radiative lifetime of two-dimensional materials

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.

Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms

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.

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family

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.

Development of a Plate-Based Screening Assay to Investigate the Substrate Specificity of the PRMT Family of Enzymes

There are nine protein arginine methyltransferases (PRMTs 1-9) expressed in humans that vary in both subcellular localization and substrate specificity. The variation in substrate specificity between isozymes leads to competing effects that result in either activation or repression of tumor suppressor genes. Current methods used to study substrate specificity for these enzymes utilize radioisotopic labeling of substrates, mass spectrometry analysis of complex samples, or coupled assays that monitor cofactor degradation. Herein, we report the development of a rapid, nonradioactive, and sensitive method for screening multiple peptides in parallel to gain insight into the substrate specificity of PRMT enzymes. Our assay provides a major advantage over other high-throughput screening assays (e.g., ELISA, AlphaScreen chemiluminescence) by eliminating the need for purification of individual peptides and provides a timesaving, cost-effective alternative to the traditional PRMT assays. A one-bead one-compound (OBOC) peptide library was synthesized and subsequently screened against PRMT1 in a 96-well plate. This screen resulted in identification of a novel PRMT1 substrate with kinetic parameters similar to histone H4-21 (e.g., the best-known PRMT1 peptide substrate).

A continuous fluorescence assay for the characterization of Nudix hydrolases

The common substrate structure for the functionally diverse Nudix protein superfamily is nucleotide-diphosphate-X, where X is a large variety of leaving groups. The substrate specificity is known for less than 1% of the 29,400 known members. Most activities result in the release of an inorganic phosphate ion or of a product bearing a terminal phosphate moiety. Reactions have typically been monitored by a modification of the discontinuous Fiske-SubbaRow assay, which is relatively insensitive and slow. We report here the development of a continuous fluorescence assay that enables the rapid and accurate determination of substrate specificities in a 96-well format. We used this novel assay to confirm the reported substrate characterizations of MutT and NudD of Escherichia coli and to characterize DR_1025 of Deinococcus radiodurans and MM_0920 of Methanosarcina mazei. Novel findings enabled by the new assay include the following. First, in addition to the well-characterized hydrolysis of 8-oxo-dGTP at the α-β position, MutT cleaves at the β-γ phosphate bond at a rate of 3% of that recorded for hydrolysis at the α-β position. Second, MutT also catalyzes the hydrolysis of 5-methyl-dCTP. Third, 8-oxo-dGTP was observed to be the best substrate for DR_1025 of the 41 compounds screened.