Modelling of the Citrus CCD4 Family Members: In Silico Analysis of Membrane Binding and Substrate Preference

Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of β-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein–ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Å2. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.

α-Helix in Cystathionine β-Synthase Enzyme Acts as Electron Reservoir

The modulation of electron density at the Pyridoxal 5-phosphate (PLP) catalytic center, due to charge transfer across the α-Helix-PLP interface, is the determining factor for the enzymatic activities in the human Cystathionine β-Synthase (hCBS) enzyme. Applying density-based first-principle calculations in conjunction with the real space density analysis, we investigated the charge density delocalization across the entire Heme-α-Helix-PLP electron communication channels. The hydrogen bonds at the interfaces, i.e. Heme-α-Helix and α-Helix-PLP interfaces, are found to play the pivotal role in bi-directional electron transfer towards the α-Helix. Moreover, the internal hydrogen bonds of α-Helix that are crucial for its secondary structure also actively participate in the electron redistribution through the structured hydrogen bond network. α-Helix is found to accumulate the electron density at the ground state from both the cofactors and behaves as an electron reservoir for catalytic reaction at the electrophilic center of PLP.

Identification of glutamine synthetase as a contryphan-Bt binding protein by His-tag pull-down

Background: Contryphan-Bt is a D-tryptophan-containing disulfide-constrained decapeptide recently isolated from the venom of Conus betulinus. The molecular targets of contryphans are controversial, and the identification of its interacting proteins may be of great importance. Methods: His-tag pull-down assays were performed to investigate intracellular binding proteins of contryphan-Bt from rat brain lysate. Bt-Acp-[His]6, a contryphan-Bt derivative containing hexahistidine tag, was synthesized and used as the bait. As a control, Acp-[His]6 was used to exclude nonspecific bindings. Results: Glutamine synthetase was identified as a potential contryphan-Bt binding protein by pull-down assays and subsequent LC-MS/MS. The binding of contryphan-Bt to glutamine synthetase was confirmed and determined using microscale thermophoresis, with a Kd of 74.02 ± 2.8 μM. The binding did not affect glutamine synthetase activity, suggesting that the interaction site was distinct from the catalytic center. Conclusions: Glutamine synthetase was identified as a novel contryphan-Bt binding protein. This is the first report in which the conopeptide binds to an intracellular protein.

Selenium-Functionalized Corn Starch as a Biodegradable GPx Mimic with High Catalytic Performance

Selenium-functionalized starch (Se-starch80) is one of the main functional foods used for selenium supplementation. In traditional agriculture, Se-starch has some deficiencies such as long growth cycle and unstable selenium content that prevent its antioxidant performance. In this study, Se-starch was prepared by the nucleophilic addition between NaSeH and carbon-carbon double bond of octenyl succinic anhydride waxy corn starch ester (OSA starch). Some techniques such as 1HNMR, XPS, SEM-EDS, XRD and FT-IR were used to characterize the relevant samples and the results showed that the modification did not destroy the starch framework significantly and the catalytic center (negative divalent selenium) was anchored on the starch framework. The intensive distribution of catalytic center on the starch surface and the hydrophobic microenvironments derived from the OSA chains furnished the Se-starch80 with a high GPx-like catalytic activity (initial reaction rate = 3.64 μM/min). This value was about 1.5 × 105 times higher than that of a typical small-molecule GPx mimic (PhSeSePh). In addition, the Se-starch80, without any cytotoxicity, showed a saturated kinetic catalytic behavior that is similar to a typical enzyme. This work exemplifies a biodegradable selenium-functionalized polymer platform for the high-performing GPx mimic.

The structural basis for the phospholipid remodeling by lysophosphatidylcholine acyltransferase 3

As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands’ cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states. A reaction chamber was revealed in the LPCAT3 structure where the lysophosphatidylcholine and arachidonoyl-CoA were positioned in two tunnels connected near to the catalytic center. A side pocket was found expanding the tunnel for the arachidonoyl CoA and holding the main body of arachidonoyl. The structural and functional analysis provides the basis for the re-acylation of lysophosphatidylcholine and the substrate preference during the reactions.

Albumin nanoparticles loaded with hemin as peroxidase mimics for immunoassay

Contemporary immunoassays commonly used in clinical diagnostics mostly utilize enzymes, such as horseradish peroxidase, for signal generation. Numerous research is dedicated to the development of artificial peroxidase-mimicking catalysts with lower cost, high activity, better operational stability, and tunable properties. Herein we synthesized hemin-loaded bovine serum albumin (BSA) nanoparticles and applied them as catalytic labels (nanozymes) in colorimetric immunoassay of anti-tetanus antibodies. Hemin is a key part of the peroxidase catalytic center, possessing peroxidase like-activity. Albumin nanoparticles were loaded with multiple hemin molecules and decorated with Streptococcal protein G. Resulting nanozymes possessed good colloidal stability and allowed for antibody detection in blood serum. The sensitivity of antibody detection was sufficient for the assessment of post-vaccination immunity.

Improvement of thermostability and catalytic efficiency of glucoamylase from Talaromyces leycettanus JCM12802 via site-directed mutagenesis to enhance industrial saccharification applications

Background Glucoamylase is an important industrial enzyme in the saccharification of starch into glucose. However, its poor thermostability and low catalytic efficiency limit its industrial saccharification applications. Therefore, improving these properties of glucoamylase is of great significance for saccharification in the starch industry. Results In this study, a novel glucoamylase-encoding gene TlGa15B from the thermophilic fungus Talaromyces leycettanus JCM12802 was cloned and expressed in Pichia pastoris. The optimal temperature and pH of recombinant TlGa15B were 65 ℃ and 4.5, respectively. TlGa15B exhibited excellent thermostability at 60 ℃. To further improve thermostability without losing catalytic efficiency, TlGa15B-GA1 and TlGa15B-GA2 were designed by introducing disulfide bonds and optimizing residual charge–charge interactions in a region distant from the catalytic center. Compared with TlGa15B, mutants showed improved optimal temperature, melting temperature, specific activity, and catalytic efficiency. The mechanism underlying these improvements was elucidated through molecular dynamics simulation and dynamics cross-correlation matrices analysis. Besides, the performance of TlGa15B-GA2 was the same as that of the commercial glucoamylase during saccharification. Conclusions We provide an effective strategy to simultaneously improve both thermostability and catalytic efficiency of glucoamylase. The excellent thermostability and high catalytic efficiency of TlGa15B-GA2 make it a good candidate for industrial saccharification applications.

The effect of microwave stabilization on the properties of whole wheat flour and its further interpretation by molecular docking

In order to stabilize the whole wheat flour and extend its shelf life, microwave was employed to heat the wheat bran to inactivate the lipase in this paper. The effects of microwave heating of wheat bran on the lipase activities, gluten properties, dough properties and storage stability of the stabilized whole wheat flour, and the quality of steamed bread made of stabilized whole wheat flour were investigated. Furthermore, molecular docking was applied to interpret the mechanism. The results showed that microwave can reduce lipase activity, maintain the quality of whole wheat flour dough and steamed bread, and retard rancidity. The molecular docking results displayed that the conformation of the amino acids chains near the lipase catalytic center changed, which made the substrate difficult to enter the catalytic center and prevented the hydrolysis of the fat substrate.