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Background: We investigated melanogenesis- and anti-apoptosis-related melanoma factors in melanoma cells (TXM1, TXM18, A375P, and A375SM). Objective: To find melanoma associated hub factor, high-throughput screening-based techniques integrating with bioinformatics were investigated. Methods: Array CGH analysis was conducted with a commercial system. Total genomic DNAs prepared individually from each cell line with control DNA were properly labeled with Cy3-dCTP and Cy5-dCTP and hybridizations and subsequently performed data treatment by the log2 green (G; test) to red (R; reference) fluorescence ratios (G/R). Gain or loss of copy number was judged by spots with log2-transformed ratios. PPI mapping analysis of detected candidate genes based on the array CGH results was conducted using the human interactome in the STRING database. Energy minimization and a short Molecular Dynamics (MD) simulation using the implicit solvation model in CHARMM were performed to analyze the interacting residues between YWHAZ and YWHAB. Results: Three genes (BMP-4, BFGF, LEF-1) known to be involved in melanogenesis were found to lose chromosomal copy numbers, and Chr. 6q23.3 was lost in all tested cell lines. Ten hub genes (CTNNB1, PEX13, PEX14, PEX5, IFNG, EXOSC3, EXOSC1, EXOSC8, UBC, and PEX10) were predicted to be functional interaction factors in the network of the 6q23.3 locus. The apoptosis-associated genes E2F1, p50, BCL2L1, and BIRC7 gained, and FGF2 lost chromosomal copy numbers in the tested melanoma cell lines. YWHAB, which gained chromosomal copy numbers, was predicted to be the most important hub protein in melanoma cells. Molecular dynamics simulations for binding YWHAB and YWHAZ were conducted, and the complex was predicted to be energetically and structurally stable through its 3 hydrogen-bond patterns. The number of interacting residues is 27. Conclusion: Our study compares genome-wide screening interactomics predictions for melanoma factors and offers new information for understanding melanogenesis- and anti-apoptosis-associated mechanisms in melanoma. Especially, YWHAB was newly detected as a core factor in melanoma cells.

Arginine kinase is a crucial phosphagen kinase in invertebrates, which is associated to the environmental stress response, plays a key role in cellular energy metabolism. In this study, we investig...

During hibernation of Pelodiscus sinensis, sperm mature and are stored in the epididymis. We investigated seasonal changes in the morphology of epithelial cells of the epididymis of P. sinensis and changes in expression of cytoplasmic creatine kinase (CK). We found that the epididymal epithelium proliferates rapidly to form multiple layers from June to September, while the epididymal epithelial cells are arranged in a single layer from October to May. From the March before the mating period to the end of the mating period in September, a large amount of neutral glycoprotein is secreted in the epididymal epithelium and in the sperm aggregation area; after October, the glycoprotein in the epididymis decreases. At sperm maturation, cytoplasmic CK is expressed abundantly in the villous epithelium, which is formed by proliferation of epididymal epithelial cells. During hibernation and reproduction, the epididymal epithelium of P. sinensis exhibits different proliferation and secretion patterns as the animal adapts to two types of sperm storage. Cytoplasmic CK may participate in regulating the energy metabolism of the epididymal epithelium; it is an important enzyme for regulating sperm maturation.

Hydrogen sulfide (H2S) has been proven to be a multifunctional signaling molecule in plants. In this study, we attempted to explore the effects of H2S on the climacteric fruit tomato during postharvest storage. H2S fumigation for 1 d was found to delay the peel color transition from green to red and decreased fruit firmness induced by ethylene. Further investigation showed that H2S fumigation downregulated the activities and gene expressions of cell wall–degrading enzymes pectin lyase (PL), polygalacturonase (PG), and cellulase. Furthermore, H2S fumigation downregulated the expression of ethylene biosynthesis genes SlACS2 and SlACS3. Ethylene treatment for 1 d was found to induce the expression of SlACO1, SlACO3, and SlACO4 genes, whereas the increase was significantly inhibited by H2S combined with ethylene. Furthermore, H2S decreased the transcript accumulation of ethylene receptor genes SlETR5 and SlETR6 and ethylene transcription factors SlCRF2 and SlERF2. The correlation analysis suggested that the fruit firmness was negatively correlated with ethylene biosynthesis and signaling pathway. The current study showed that exogenous H2S could inhibit the synthesis of endogenous ethylene and regulate ethylene signal transduction, thereby delaying fruit softening and the ripening process of tomato fruit during postharvest storage.

The inhibition of α-glucosidase is used as a key clinical approach to treat type 2 diabetes mellitus and thus, we assessed the inhibitory effect of α-ketoglutaric acid (AKG) on α-glucosidase with both an enzyme kinetic assay and computational simulations. AKG bound to the active site and interacted with several key residues, including ASP68, PHE157, PHE177, PHE311, ARG312, TYR313, ASN412, ILE434 and ARG439, as detected by protein-ligand docking and molecular dynamics simulations. Subsequently, we confirmed the action of AKG on α-glucosidase as mixed-type inhibition with reversible and rapid binding. The relevant kinetic parameter IC

Pyrogallol is naturally found in aquatic plant and has been proposed as a substrate of tyrosinase. In this study, we evaluated the dual effect of pyrogallol on tyrosinase as an inhibitor in the presence of L‑DOPA simultaneously via integrating methods of enzyme kinetics and computational molecular dynamics (MD) simulations. Pyrogallol was found to be a reversible inhibitor of tyrosinase in the presence of L‑DOPA and its induced mechanism was the parabolic non-competitive inhibition type (IC50 = 0.772 ± 0.003 mM and Ki = 0.529 ± 0.022 mM). Kinetic measurements by real-time interval assay showed that pyrogallol induced rapid inactivation process composing with slight activations at the low dose. Spectrofluorimetry studies showed that pyrogallol mainly induced regional changes in the active site of tyrosinase accompanying with hydrophobic disruption at high dose. The computational MD simulations further revealed that pyrogallol could interact with several residues near the tyrosinase active site pocket such as HIS61, HIS85, HIS259, ASN260, HIS263, VAL283, and ALA296. Our study provides insight into the mechanism by which hydroxyl group composing pyrogallol inhibit tyrosinase and pyrogallol is a potential natural anti-pigmentation agent.

Herbivores gastrointestinal microbiota is of tremendous interest for mining novel lignocellulosic enzymes for bioprocessing. We previously reported a set of potential carbohydrate-active enzymes from the metatranscriptome of the Hu sheep rumen microbiome. In this study, we isolated and heterologously expressed two novel glucanase genes, Cel5A-h38 and Cel5A-h49, finding that both recombinant enzymes showed the optimum temperatures of 50 °C. Substrate-specificity determination revealed that Cel5A-h38 was exclusively active in the presence of mixed-linked glucans, such as barley β-glucan and Icelandic moss lichenan, whereas Cel5A-h49 (EC 3.2.1.4) exhibited a wider substrate spectrum. Surprisingly, Cel5A-h38 initially released only cellotriose from lichenan and further converted it into an equivalent amount of glucose and cellobiose, suggesting a dual-function as both endo-β-1,3-1,4-glucanase (EC 3.2.1.73) and exo-cellobiohydrolase (EC 3.2.1.91). Additionally, we performed enzymatic hydrolysis of sheepgrass (Leymus chinensis) and rice (Orysa sativa) straw using Cel5A-h38, revealing liberation of 1.91 ± 0.30 mmol/mL and 2.03 ± 0.09 mmol/mL reducing sugars, respectively, including high concentrations of glucose and cellobiose. These results provided new insights into glucanase activity and lay a foundation for bioconversion of lignocellulosic biomass.

The expression and localization of different isoforms of creatine kinase in Pelodiscus sinensis (PSCK) were studied to reveal the role of PSCK isozymes (PSCK-B, PSCK-M, PSCK-S) under bacterial infection-induced immunologic stress. The computational molecular dynamics simulations predicted that PSCK-S would mostly possess a kinase function in a structural aspect when compared to PSCK-B and PSCK-M. The assay of biochemical parameters such as total superoxide dismutase (T-SOD), lactate dehydrogenase (LDH), malondialdehyde (MDA), catalase (CAT), and the content of ATP were measured along with total PSCK activity in different tissue samples under bacterial infection. The expression detections of PSCK isozymes in vitro and in vivo were overall well-matched where PSCK isozymes were expressed differently in P. sinensis tissues. The results showed that PSCK-B mostly contributes to the spleen, followed by the liver and myocardium; PSCK-M mostly contributes to the liver, followed by the myocardium and skeletal muscle, while PSCK-S contributes to the spleen and is uniquely expressed in skeletal muscle. Our study suggests that the various alterations of PSCK isozymes in tissues of P. sinensis are prone to defense the bacterial infection and blocking energetic imbalance before severe pathogenesis turned on in P. sinensis.

Background: Fibrinolytic protease from Euphausia superba (EFP) was isolated. Objective: Biochemical distinctions, regulation of the catalytic function, and the key residues of EFP were investigated. Methods: The serial inhibition kinetic evaluations coupled with measurements of fluorescence spectra in the presence of 4-(2-aminoethyl) benzene sulfonyl fluoride hydrochloride (AEBSF) was conducted. The computational molecular dynamics (MD) simulations were also applied for a comparative study. Results: The enzyme behaved as a monomeric protein with a molecular mass of about 28.6 kD with Km BApNA = 0.629 ± 0.02 mM and kcat/Km BApNA = 7.08 s-1/mM. The real-time interval measurements revealed that the inactivation was a first-order reaction, with the kinetic processes shifting from a monophase to a biphase. Measurements of fluorescence spectra showed that serine residue modification by AEBSF directly caused conspicuous changes of the tertiary structures and exposed hydrophobic surfaces. Some osmolytes were applied to find protective roles. These results confirmed that the active region of EFP is more flexible than the overall enzyme molecule and serine, as the key residue, is associated with the regional unfolding of EFP in addition to its catalytic role. The MD simulations were supportive to the kinetics data. Conclusion: Our study indicated that EFP has an essential serine residue for its catalyst function and associated folding behaviors. Also, the functional role of osmolytes such as proline and glycine that may play a role in defense mechanisms from environmental adaptation in a krill’s body was suggested.

The function of acetaldehyde dehydrogenase 1 (ALDH1) has been gradually elucidated in several diseases, especially in various cancers. However, the role of ALDH1 in skin-related diseases has been mostly unknown. Previously, we found that ALDH1 is involved in the pathogenesis of atopic dermatitis (AD). In this study, we used high-throughput screening (HTS) approaches to identify critical factors associated with ALDH1 in human keratinocytes to reveal its functions in skin. We overexpressed ALDH1 in human HaCaT keratinocytes and then conducted serial HTS studies, a DNA microarray and antibody array integrated with bioinformatics algorithms. Together, those tests identified several novel genes associated with the function of ALDH1 in keratinocytes, as well as AD, including CTSG and CCL11. In particular, GNB3, GHSR, TAS2R9, FFAR1, TAS2R16, CCL21, GPR32, NPFFR1, GPR15, FBXW12, CCL19, EDNRA, FFAR3, and RXFP3 proteins were consistently detected as hub proteins in the PPI maps. By integrating the datasets obtained from these HTS studies and using the strengths of each method, we obtained new insights into the functional role of ALDH1 in skin keratinocytes. The approach used here could contribute to the clinical understanding of ALDH1-associated applications for the treatment of AD.Communicated by Ramaswamy H. Sarma.

The pharaoh cuttlefish Sepia pharaonis is particularly sensitive to environmental changes in its breeding environment. The breeding of S. pharaonis larvae was carried out in different salinities for 48h, and the changes in survival rate, histological structure, energy metabolism, and anti-oxidative stress parameters were investigated and correlated with arginine kinase (AK) expression changes in muscle and liver tissues. The suitable salinity for larvae cultivation ranged from 24 to 30‰, and the survival rate showed a significant decline at 21‰ salinity. Histological observations of muscle and liver showed that changes in salinity and osmotic pressure had an adverse effect on tissue structure. Measurements of glycogen and lactic acid levels suggested that S. pharaonis could dynamically adjust energy metabolism to provide additional energy under unsuitable salinity. The protein levels and enzyme activities of AK in muscle significantly increased at 21‰ salinity. The results were consistent with prompt replenishment of phosphoarginine stores during salinity stress to maintain a dynamic ATP balance, suggesting that AK plays an important role in the regulation of energy metabolism. This study provides insight into metabolic changes during salinity stress and sheds light on the functional role of AK in S. pharaonis.

Agouti signaling protein (ASP) is a secreted paracrine protein that has been widely reported to function in melanogenesis and obesity and could potentially be a core protein that regulates the color and fatty phenotype of P. sinensis. In this study, we screened out interacting proteins of ASP by combined co-immunoprecipitation mass spectrometry (CoIP-MS), yeast two hybrid (Y2H) analysis, and computational predictions. We performed docking of ASP with its well-known receptor melanocortin receptor 4 (MC4R) to predict the binding capacity and to screen out actual ASP interacting proteins, CoIP-MS was performed where identified 32 proteins that could bind with ASP and Y2H confirmed seven proteins binding with ASP directly. CoIP-MS and Y2H screening results including PPI prediction revealed that vitronectin (VTN), apolipoprotein A1 (APOA1), apolipoprotein B (APOB), and filamin B (FLNB) were the key interacting proteins of ASP. VTN, APOA1, and APOB are functional proteins in lipid metabolism and various skin disorders, suggesting ASP may function in lipid metabolism through these partners. This study provided protein-protein interaction information of ASP, and the results will promote further research into the diverse roles of ASP, as well as its binding partners, and their function in different strains of P. sinensis.

Mannooligosaccharides are released by mannan-degrading endo-β-1,4-mannanase and are known as functional additives in human and animal diets. To satisfy demands for biocatalysis and bioprocessing in crowed environments, in this study, we employed a recently developed enzyme-engineering system, isopeptide bond-mediated molecular cyclization, to modify a mesophilic mannanase from Bacillus subtilis. The results revealed that the cyclized enzymes showed enhanced thermostability and ion stability and resilience to aggregation and freeze-thaw treatment by maintaining their conformational structures. Additionally, by using the SpyTag/SpyCatcher system, we generated a mannanase-xylanase bifunctional enzyme that exhibited a synergistic activity in substrate deconstruction without compromising substrate affinity. Interestingly, the dual-enzyme ring conformation was observed to be more robust than the linear enzyme but inferior to the single-enzyme ring conformation. Taken together, these findings provided new insights into the mechanisms of molecular cyclization on stability improvement and will be useful in the production of new functional oligosaccharides and feed additives.

Because serum is an optimal source to identify proteins derived from diseased-tissue compartments, serum proteomics has been applied for the discovery and analysis of biomarkers related to human disease. The general 2D-PAGE method is suitable for acidic and neutral proteome separation while highly basic proteins remain unresolved. In this study, we optimized basic proteome fractionation by integrating several methods such as, Micro-Rotofor isoelectric focusing (IEF) fractionation, acetic acid-urea polyacrylamide gel electrophoresis (A-U PAGE) separation, and mass spectrometry analysis for identifying basic proteins in patient sera. The sera samples were obtained from patients with atopic dermatitis (AD) to establish the model method introduced in the present study. We successfully identified the specific presence of a C3 complement component fragment protein and C4A fragment protein in AD patient-derived sera. Highly basic proteins in serum are very difficult to detect due to their separation properties. Thus, the integrated proteomic method approaches described here could be applicable for the detection of basic proteins associated with other diseases.

Arginine kinase is an essential enzyme which is closely related to energy metabolism in marine invertebrates. Arginine kinase provides a significant role in quick response to environmental change and stress. In this study, we simulated a tertiary structure of Sepia pharaonis arginine kinase (SPAK) based on the gene sequence and conducted the molecular dynamics simulations between SPAK and Zn(2+). Using these results, the Zn(2+) binding sites were predicted and the initial effect of Zn(2+) on the SPAK structure was elucidated. Subsequently, the experimental kinetic results were compared with the simulation results. Zn(2+) markedly inhibited the activity of SPAK in a manner of non-competitive inhibitions for both arginine and ATP. We also found that Zn(2+) binding to SPAK resulted in tertiary conformational change accompanying with the hydrophobic residues exposure. These changes caused SPAK aggregation directly. We screened two protectants, glycine and proline, which effectively prevented SPAK aggregation and recovered the structure and activity. Overall, our study suggested the inhibitory effect of Zn(2+) on SPAK and Zn(2+) can trigger SPAK aggregation after exposing large extent of hydrophobic surface. The protective effects of glycine and proline against Zn(2+) on SPAK folding were also demonstrated.

Hydroxysafflor yellow A (HSYA) is found in the flower of Carthamus tinctorius. We evaluated the effects of hydroxysafflor yellow A (HSYA) on tyrosinase kinetics and computationally simulated the interaction between HSYA and tyrosinase. HSYA was found to be a mixed-type, reversible inhibitor of tyrosinase, with a Ki of 0.285 ± 0.040 mM. Kinetic measurements of intrinsic and ANS-binding fluorescence showed that HSYA induced changes in the tertiary structure of tyrosinase. HSYA showed a relatively strong binding affinity for tyrosinase and one possible binding site was identified. To gain further insight into the HSYA/tyrosinase interaction, we performed computational docking and molecular dynamics simulations. These experiments indicated that HSYA can interact with several residues near the tyrosinase active site. Our study provides insight into the mechanism by which chalcone compounds such as flavonoids inhibit tyrosinase. Since HSYA inhibits tyrosinase and is also an antioxidant, HSYA is a potential natural antipigmentation agent.

Arginine kinase is closely associated with adaptation to environmental stresses such as high salinity and heavy metal ion levels in marine invertebrates. In this study, the effects of Cd(2+) on the cuttlefish Sepia pharaonis' arginine kinase (SPAK) were investigated. SPAK was isolated from the muscles of S. pharaonis and upon further purification, showed a single band on SDS-PAGE. Cd(2+) effectively inactivated SPAK, and the double-reciprocal kinetics indicated that Cd(2+) induced non-competitive inhibition of arginine and ATP. Spectrofluorometry results showed that Cd(2+) induced tertiary structure changes in SPAK with the exposure of hydrophobic surfaces that directly induced SPAK aggregation. The addition of osmolytes, glycine, and proline successfully blocked SPAK aggregation and restored the conformation and activity of SPAK. Molecular dynamics simulations involving SPAK and Cd(2+) showed that Cd(2+) partly blocks the entrance of ATP to the active site, and this result is consistent with the experimental results showing Cd(2+)-induced inactivation of SPAK. These results demonstrate the effect of Cd(2+) on SPAK enzymatic function and unfolding, including aggregation and the protective effects of osmolytes on SPAK folding. This study provides concrete evidence of the toxicity of Cd(2+) in the context of the metabolic enzyme SPAK, and it illustrates the toxic effects of heavy metals and detoxification mechanisms in cuttlefish.

We simulated the 3D structure of arginine kinase from Exopalaemon carinicauda (ECAK) on the basis of homology modeling. Computational molecular dynamics simulations between ECAK and Cr3+ were conducted to elucidate the functional role of Cr3+ on ECAK structure and catalysis. As a result, the binding mechanism of Cr3+ to ECAK along with binding sites and structural changes were predicted. To confirm the simulation results, kinetic studies of Cr3+-mediated aggregation of ECAK were subsequently conducted. We found that Cr3+ significantly induced ECAK aggregation with a multi-phase kinetic process at a high dose of Cr3+. The spectrofluorimetric results showed that Cr3+-induced tertiary structural changes in ECAK caused extensive exposure of hydrophobic surfaces, which could be a triggering factor for inducing ECAK aggregation. Our study provides new information concerning the effect of Cr3+ on ECAK's enzymatic function and unfolding, including aggregation, which might be toxic or act as a negative regulator.

We built a 3D structure of arginine kinase from Exopalaemon carinicauda (ECAK) on the basis of the ORF gene sequence to conduct molecular dynamics simulations between ECAK and Pb2+. As a result, the binding mechanism of Pb2+ to ECAK was predicted from the binding sites, and the structural change was elucidated. To confirm the simulated results, the Pb2+-mediated inhibition and aggregation of ECAK were subsequently conducted. We found that Pb2+ partially inactivated the activity of ECAK with relatively strong binding. The spectrofluorimetry results showed that Pb2+ induced tertiary structural changes of ECAK, with the substantial exposure of hydrophobic surfaces directly induced by ECAK aggregation. The ECAK aggregation process induced by Pb2+ occurred with multi-phase kinetics. The addition of osmolytes did not protect ECAK from Pb2+ inactivation. Because AK plays an important role in the cellular energy metabolism of invertebrates, our study suggests new information about the effect of Pb2+ on ECAK's enzymatic function and unfolding, including aggregation, which may be toxic to invertebrates or may act as a negative regulator.

Arginine kinase plays an important role in invertebrate cellular energy metabolism. We investigated the effects of Cu 2+ on the enzymatic activity, unfolding and aggregation of Euphausia superba arginine kinase (ESAK). Cu 2+ inhibited the activity of ESAK (IC 50 = 0.050 ± 0.002 mM) following first-order kinetics consistent with the transition from a monophasic to a biphasic reaction. Double-reciprocal Lineweaver–Burk plots indicated that Cu 2+ induced non-competitive inhibition of arginine and ATP. Spectrofluorimetry results showed that Cu 2+ induced tertiary structural changes in ESAK with exposure of hydrophobic surfaces and directly induced ESAK aggregation. The addition of osmolytes such as glycine and proline successfully blocked ESAK aggregation, recovering the conformation and activity of ESAK. Computational simulations indicated that the ATP/ADP binding site locations overlap with the Cu 2+ interacting residues, inferring that Cu 2+ binding can block ESAK enzyme catalysis with ATP/ADP cofactor binding via modulating structural conformation. Our study demonstrates the effect of Cu 2+ on ESAK enzymatic function and folding mechanisms that might provide important insights into other metabolic enzymes of invertebrates in extreme climatic marine environments.

Investigations of energy-related enzymatic properties may provide valuable information about the mechanisms that are involved in the adaptation to extreme climatic environments. The protective effects of osmolytes on the thermal denaturation and aggregation of arginine kinase from E. superba (ESAK) was investigated. When the concentration of glycine, proline and glycerol increased, the relative activation was significantly enhanced, while the aggregation of ESAK during thermal denaturation was decreased. Spectrofluorometry results showed that the presence of these three osmolytes significantly decreased the tertiary structural changes of ESAK and that thermal denaturation directly induced ESAK aggregation. The results demonstrated that glycine, proline and glycerol not only prevented ESAK from inactivation and unfolding but also inhibited aggregation by stabilizing the ESAK conformation. We measured the ORF gene sequence of ESAK by RACE, and built the 3D structure of ESAK and osmolytes by homology models. The results showed that the docking energy was relatively low and that the clustering groups were spread to the surface of ESAK, indicating that osmolytes directly protect the surface of the protein. Our study provides important insight into the protective effects of osmolytes on ESAK folding.

Arginine kinase (AK) is a key metabolic enzyme for maintaining energy balance in invertebrates and studies on AK from Euphausia superba might provide important insights into the metabolic enzymes in extreme climatic marine environments. A folding study of the AK from E. superba (ESAK) has not yet been reported. To gain insights into the structural and folding mechanisms of ESAK, the denaturants guanidine HCl and urea were applied in this study. We purified ESAK from the muscle of E. superba and evaluated the inhibition kinetics with structural unfolding studies under various conditions. The results revealed that ESAK was almost completely inactivated when using 1.0 M guanidine HCl and 8.25 M urea. The kinetics, characterized via time-interval measurements, showed that the inactivations by guanidine HCl and urea were first-order reactions, with the kinetic processes shifting from monophases to biphases as concentrations increased. Measurements of intrinsic and ANS (anilinonaphthalene-8-sulfonate)-binding fluorescences showed that guanidine HCl and urea induced conspicuous changes in tertiary structures and followed the regular unfolding mechanisms. Our study provides information regarding the folding of this muscle-derived metabolic enzyme and expands our knowledge and understanding of invertebrate metabolisms.

Piperonylic acid is a natural molecule with a benzoic acid group and high antioxidant capacity. Based on its aromatic acid structure and antioxidant properties, we studied the effects of piperonylic acid on tyrosinase by the analysis of its inhibitory kinetics and computational simulations. Piperonylic acid reversibly inhibited tyrosinase through a mixed-type inhibitory mechanism. The time courses of the tyrosinase inhibition showed that piperonylic acid binds to tyrosinase very quickly and the inactivation processes follow first-order kinetics. The continuous substrate reactions indicated that piperonylic acid induced a tight-binding inhibition and the substrate can promote the inactivation process. The ANS-binding fluorescence of tyrosinase suggested that piperonylic acid did not detectably disrupt the tertiary structure of the enzyme. The results of the computational docking and molecular dynamics simulations showed that piperonylic acid closely interacts with three residues and it might block the active site of tyrosinase.

The protective effect of osmolytes on the thermal denaturation and aggregation of Pelodiscus sinensis muscle creatine kinase (PSCK) was investigated by a combination of spectroscopic methods and thermodynamic analysis. Our results demonstrated that the addition of osmolytes, such as glycine and proline, could prevent thermal denaturation and aggregation of PSCK in a concentration-dependent manner. When the concentration of glycine and proline increased in the denatured system, the relative activation was significantly enhanced; meanwhile, the aggregation of PSCK during thermal denaturation was decreased. Spectrofluorometer results showed that glycine and proline significantly decreased the tertiary structural changes of PSCK and that thermal denaturation directly induced PSCK aggregation. In addition, we also built the 3D structure of PSCK and osmolytes by homology models. The results of computational docking simulations showed that the docking energy was relatively low and that the clustering groups were spread to the surface of PSCK, indicating that osmolytes directly protect the surface of the protein. P. sinensis are poikilothermic and quite sensitive to the change of ambient temperature; however, there were few studies on the thermal denaturation of reptile CK. Our study provides important insight into the protective effects of osmolytes on thermal denaturation and aggregation of PSCK.

Tyrosinase (EC 1.14.18.1) is a diversely distributed enzyme in various organisms with physiological roles related to pigment production. Tyrosinase has gained the attention of researchers due to its biological functions and potential applications. In this regard, studies on the partner proteins of tyrosinase are important. In this study, we predicted the 3D structure of human tyrosinase and simulated the protein–protein interactions between tyrosinase and binding partners by using the PEIMAP algorithm. As a result, we found that tyrosinase is predicted to bind with G protein-related proteins, potassium voltage-gated channel-related proteins, and vesicle/sorting-related proteins. In particular, GIPC1, GIPC2, GIPC3, TYRP1, and DCT were predicted to primarily bind with tyrosinase. Interacting proteins (103) were secondarily bound to these 5 interacting proteins in the PEIMAP network of tyrosinase. An involvement in melanogenesis was also newly predicted by associating the predicted binding proteins. We simulated the protein–protein bindings by probing the residues of each complex facing toward the predicted site of interaction with tyrosinase. Among the interacting residues, some were predicted to dock to the active site of tyrosinase, which could affect its activity directly. Our computational predictions will be useful for elucidating the protein–protein interactions of tyrosinase and for studying its binding mechanisms and the melanin biosynthesis pathway.

In this study, we investigated validamycin A as a tyrosinase inhibitor based on its structural properties. We found that the reversible inhibition of tyrosinase by validamycin A occurred in a mixed-type manner with Ki = 5.893 ± 0.038 mM, as determined by integrating kinetics studies and computational simulations. Time-interval tyrosinase studies showed that the inhibition followed first-order kinetics with two phases. Fluorescence measurements of ANS binding showed that validamycin A induced changes in the tertiary protein structure of tyrosinase. To obtain further insight, computational docking and molecular dynamics were applied, and the results indicated that HIS85, HIS244, GLU256, HIS259, and ASN260 of tyrosinase interacted with validamycin A. This strategy of predicting tyrosinase inhibition based on hydroxyl group numbers might be useful in the design and screening of potential tyrosinase inhibitors.

Acetylsalicylic acid (ASA), generally well known as aspirin, has various biomedical functions. In this study, we revealed that ASA reversibly inhibits tyrosinase (EC 1.14.18.1) in a mixed-type manner with a Ki = 11.778 ± 2.01 mM. Time-interval kinetics showed that the inhibition followed first-order reaction kinetics. Measurements of ANS-binding fluorescence showed that ASA did not induce significant detectable changes in the hydrophobic surface of tyrosinase. For further insight, we performed molecular dynamics simulations to predict the key interactions between tyrosinase and ASA and found that the acetate and carboxylic acid groups of ASA play a critical role in binding to several residues (HIS61, HIS85, HIS94, HIS259, HIS263, and ALA286) on tyrosinase that are thought to be pivotal for docking. Our study suggested that ASA could be a useful depigmentation agent due to the structural functions of the acetic and carboxyl groups on tyrosinase.

Boldine is one of the most potent natural antioxidants and displays some important pharmacological activities, such as cytoprotective and anti-inflammatory activities. Based on its antioxidant properties, we studied the effects of boldine on l -DOPA oxidation by evaluating the inhibitory kinetics and a computational simulation between boldine and tyrosinase. Boldine reversibly inhibited tyrosinase from mushroom (Agaricus bisporus) in a mixed-type manner, with a Ki = 7.203 ± 0.933 mM. To gain insight into the inactivation process, we computed the kinetics via time-interval measurements and continuous substrate reactions. The results indicated that the inactivation induced by boldine was a first-order reaction with biphasic processes and that the substrate can promote the inactivation process. To gain further insight, we performed computational docking and molecular dynamics simulations, and the results showed that boldine can interact with several residues near the tyrosinase active site. Our study provides insight into the inhibition of tyrosinase in response to alkaloids. Based on its tyrosinase-inhibiting effect and low toxicity, boldine is a potential natural anti-pigmentation agent.

α-Glucosidase (EC 3.2.1.20) is a critical enzyme with clinical relevance to type 2 diabetes mellitus. Therefore, research on this enzyme's inhibition is important. In the present study, we investigated Zn 2+ -induced inhibition and the structural changes of α-glucosidase. α-Glucosidase activity was significantly inhibited by Zn 2+ in a dose-dependent manner. The inhibition followed a multi-phase kinetic process with a first-order reaction. Zn 2+ inhibited α-glucosidase in a parabolic mixed-type reaction ( K i = 0.102 ± 0.001 mM) and directly induced the unfolding of α-glucosidase, resulting in a slight hydrophobic exposure. We also performed 10 ns molecular dynamics simulations on α-glucosidase and Zn 2+ . The simulations suggest that ten Zn 2+ ions possibly interact with 57 α-glucosidase residues. The molecular dynamics simulations also confirmed the binding mechanism of Zn 2+ to α-glucosidase and suggest that the Zn 2+ binding sites are not located in the glucose binding pocket of α-glucosidase. Our study provides insights into the mechanism of Zn 2+ -induced unfolding of α-glucosidase and inhibition of ligand binding and suggests that Zn 2+ could act as a potent inhibitor of α-glucosidase for the treatment of type 2 diabetes mellitus.

Arginine kinase plays an important role in cellular energy metabolism and is closely related to the environmental stress response in marine invertebrates. We studied the Cu(2+)-mediated inhibition and aggregation of Sepia pharaonis arginine kinase (SPAK) and found that Cu(2+) markedly inhibited the SPAK activity along with mixed-type inhibition against the arginine substrate and noncompetitive inhibition against the ATP cofactor. Spectrofluorimetry results showed that Cu(2+) induced a tertiary structure change in SPAK, resulting in exposure of the hydrophobic surface and increased aggregation. Cu(2+)-mediated SPAK aggregation followed first-order kinetics consistent with monophasic and a biphasic processes. Addition of osmolytes, including glycine and proline, effectively blocked SPAK aggregation and restored SPAK activity. Our results demonstrated the effects of Cu(2+) on SPAK catalytic function, conformation, and aggregation, as well as the protective effects of osmolytes on SPAK folding. This study provided important insights into the role of Cu(2+) as a negative effector of the S. pharaonis metabolic enzyme AK and the possible responses of cephalopods to unfavorable environmental conditions.

Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) is an important bioactive target for the design of environmentally benign herbicides. On the basis of previous virtual screening, 50 asymmetric aryl disulfides containing [1,2,4]triazole groups were synthesized and characterized by (1)H NMR, HRMS, and crystal structure. Compounds I-a, I-b, and I-p show Ki values of 1.70, 4.69, and 5.57 μM, respectively, for wild type Arabidopsis thaliana AHAS (AtAHAS) and low resistance against mutant type AtAHAS W574L. At 100 mg L(-1) concentration, compounds I-a, II-a, and II-b exhibit 86.6, 81.7, and 87.5% in vivo rape root growth inhibition. CoMFA steric and electrostatic contour maps were established, and a possible binding mode was suggested from molecular docking, which provide valuable information to understand the key structural features of these disulfide compounds. To the authors' knowledge, this is the first comprehensive case suggesting that asymmetric aryl disulfides are novel AHAS inhibitors.

Fucoidan is a complex sulfated polysaccharide extracted from brown seaweed and has a wide variety of biological activities. In this study, we investigated the inhibitory effect of fucoidan on tyrosinase via a combination of inhibition kinetics and computational simulations. Fucoidan reversibly inhibited tyrosinase in a mixed-type manner. Time-interval kinetics showed that the inhibition was processed as first order with biphasic processes. For further insight, we simulated dockings with various sizes of molecular models (monomer to decamer) of fucoidan and showed that the best binding energy change results were obtained from the pentamer (-1.89 kcal/mol) and the hexamer (-1.97 kcal/mol) models of AutoDock Vina. The molecular dynamics simulation confirmed the binding mechanisms between tyrosinase and fucoidan and suggested that fucoidan mostly interacts with several residues including copper ions located in the active site. Our study suggests that fucoidan might be a potential natural antipigment agent.

A new chromone polymorchromone B was isolated and characterized from the roots of Angelica polymorpha Maxim, a commonly used traditional Chinese medicine. On the basis of spectroscopic analysis, including IR, HR-ESI-MS, 1D and 2D NMR spectral data, and hydrolysis followed by chromatographic analysis, the structure of the new chromone was elucidated as 5-hydroxy-2-[(angeloyloxy)methyl]-2'-(dimethyl)-3'-(2S,3S-epoxy-2-methylbutanoate)-dihydropyran [3',2':6,7]chromone. Moreover, it was found that polymorchromone B showed remarkable cytotoxic activity against A-549 cell lines.

Tyrosinase inhibitors have potential applications in medicine, cosmetics and agriculture to prevent hyperpigmentation or browning effects. Some of the flavonoids mostly found in herbal plants and fruits are revealed as tyrosinase inhibitors. We studied the inhibitory effects of one such flavonoid, hesperetin, on mushroom tyrosinase using inhibition kinetics and computational simulation. Hesperetin reversibly inhibited tyrosinase in a competitive manner with K i = 4.03 ± 0.26 mM. Measurements of ANS-binding fluorescence showed that hesperetin induced the hydrophobic disruption of tyrosinase. For further insight, we used the docking algorithms to simulate binding between tyrosinase and hesperetin. Simulation was successful (binding energies for Dock6.3: −34.41 kcal/mol and for AutoDock4.2: −5.67 kcal/mol) and showed that a copper ion coordinating with 3 histidine residues (HIS61, HIS85, and HIS259) within the active site pocket was chelated via hesperetin binding. Our study provides insight into the inhibition of tyrosinase in response to flavonoids. A combination of inhibition kinetics and computational prediction may facilitate the identification of potential natural tyrosinase inhibitors such as flavonoids and the prediction of their inhibitory mechanisms.

Nanoporous copper with nano-scale pore size was synthesized by dealloying Mn-Cu precursor alloy using a free corrosion method. The effects of heat treatment of Mn-Cu precursors on alloy phase, morphology and composition of the resultant nanoporous copper were investigated. It is revealed that the compositions distribute homogeneously in the bulk Mn-Cu precursors, which consequently results in a more fully dealloying for forming nanoporous copper. The alloy phase changes from Cu0.49Mn0.51 and Cu0.21Mn0.79 of non-thermally treated precursor to Cu0.33Mn0.67 of heat treated alloy. The residual Mn content in nanoporous copper is decreased from 12.97% to 2.04% (molar fraction) made from the precursor without and with 95 h heat treatment. The typical pore shape of nanoporous copper prepared by dealloying the precursor without the heat treatment is divided into two different zones: the uniform bi-continuous structure zone and the blurry or no pore structure zone. Nanoporous copper is of a uniform sponge-like morphology made from the heat-treated precursor, and the average ligament diameter is 40 nm, far smaller than that from the non-thermally treated precursor, in which the average ligament diameter is estimated to be about 70 nm.

Superoxide dismutase (SOD, EC 1.15.1.1) plays an important role in antioxidant defense in organisms exposed to oxygen. However, there is a lack of research into the regulation of SOD activity and structural changes during folding, especially for SOD originating from extremophiles. We studied the inhibitory effects of trifluoroethanol (TFE) on the activity and conformation of manganese-containing SOD (Mn-SOD) from Thermus thermophilus. TFE decreased the degree of secondary structure of Mn-SOD, which directly resulted in enzyme inactivation and disrupted the tertiary structure of Mn-SOD. The kinetic studies showed that TFE-induced inactivation of Mn-SOD is a first-order reaction and that the regional Mn-contained active site is very stable compared to the overall structure. We further simulated the docking between Mn-SOD and TFE (binding energy for Dock 6.3, -9.68 kcal/mol) and predicted that the LEU9, TYR13, and HIS29 residues outside of the active site interact with TFE. Our results provide insight into the inactivation of Mn-SOD during unfolding in the presence of TFE and allow us to describe ligand binding via inhibition kinetics combined with computational predictions.

Triangular silver nanoplates in aqueous solvent and on the surface of quartz substrate have been synthesized by seed-mediated growth approach in the presence of tannin. It was found that both the amount of tannin and the small triangular silver nanoplate seeds added to the growth solution are the key factors to modulation absorption band of triangular silver nanoplates. The optical in-plane dipole surface plasmon resonance (SPR) bands of these Ag nanoplates can be tuned from 608 nm to 980 nm via tannin deoxidization method. The formation mechanism of triangular silver nanoplates was proposed. The tannin deoxidization method realizes a convenient modulation of the absorption band of Ag nanostructures within the visible near-infrared (IR) region both in aqueous solvent and on substrates under mild conditions.

Superoxide dismutase (SOD, EC 1.15.1.1) plays an important antioxidant defense role in organisms exposed to oxygen. Copper- and zinc-containing SOD (Cu/Zn-SOD) catalysis and the change in folding behavior of this enzyme in response to inactivators are therefore of interest. We studied the inhibitory effects of trifluoroethanol (TFE) on the activity and conformation of a Cu/Zn-SOD from Bos taurus. We found that TFE inactivated the enzyme and disrupted the tertiary and secondary structures of Cu/Zn-SOD. Kinetic studies showed that TFE-induced inactivation of Cu/Zn-SOD follows first-order reaction kinetics and that TFE binding sites are distinct from the copper- and zinc-containing active site. These structural changes occurred prior to enzyme activity loss. A computational docking simulation of Cu/Zn-SOD and TFE (binding energy of Dock 6.3: -11.52 kcal/mol) suggested that THR37, ASP40, and GLU119, which are located near the active site, interact with TFE. Evaluation of the ligand binding kinetics of Cu/Zn-SOD during unfolding in the presence of TFE combined with computational prediction allowed us to gain insight into the inactivation of Cu/Zn-SOD.

Superoxide dismutase (SOD, EC 1.15.1.1) plays an important antioxidant defense role in skins exposed to oxygen. We studied the inhibitory effects of Al3+ on the activity and conformation of manganese-containing SOD (Mn-SOD). Mn-SOD was significantly inactivated by Al3+ in a dose-dependent manner. The kinetic studies showed that Al3+ inactivated Mn-SOD follows the first-order reaction. Al3+ increased the degree of secondary structure of Mn-SOD and also disrupted the tertiary structure of Mn-SOD, which directly resulted in enzyme inactivation. We further simulated the docking between Mn-SOD and Al3+ (binding energy for Dock 6.3: −14.07 kcal/mol) and suggested that ASP152 and GLU157 residues were predicted to interact with Al3+, which are not located in the Mn-contained active site. Our results provide insight into the inactivation of Mn-SOD during unfolding in the presence of Al3+ and allow us to describe a ligand binding via inhibition kinetics combined with the computational prediction.

The model compounds of androgenic steroid-bismetalloporphyrins 3a—3d and androgenic monometalloporphyrins 2a—2d have been synthesized. Catalytic study in two-phase condition on epoxidation of styrene under the catalysis of model catalysts shows that the catalytic performances of steroid-bismetalloporphyrin is superior to steroid-metalloporphyrin and the corresponding simple metalloporphyrin. The excellent catalytic property of steriod-bismetalloporphyrin can be rationalized as the hydrophobic action of steroid framework and the cooperative action of two metalloporphyrins in catalysis.

Synthesis of (+)-altholactone has been achieved starting from L-tartaric acid using (2S, 3R,4R,5R)-2-hydroxymethyl-3,4-bis(memoxymethoxy)-5-phenyltetrahydrofuran as key intermediate. The key epoxy ring was introduced by monoperoxyphthalate (MMPP) in high stereoselectivity (8.4:1).

Background: The heat produced by exposure to infrared radiation (IR) has been demonstrated to modulate the expression of tropoelastin and fibrillin-1, the two main components of elastic fibers in human skin in vivo. However, the effect of IR range of radiations on tropoelastin and fibrillin-1 expression has not been thoroughly investigated. Methods: Eighteen volunteers were enrolled in this study involving three trials. Time-dependent, dose-dependent and cumulative effects of IR were investigated, respectively. Tropoelastin and fibrillin-1 expression was measured by immunohistochemical staining on skin biopsy samples from volunteers. In addition, we also measured tropoelastin mRNA expression by a real-time RT-polymerase chain reaction. Results: A single dose of IR (2 minimal heating dose) induced a time-dependent increase in tropoelastin expression at the protein level. An inverse correlation was found between the alterations of tropoelastin and fibrillin-1. Furthermore, IR was found to increase tropoelastin expression in a dose-dependent manner at both the mRNA and the protein level. Repeated low doses of IR increased tropoelastin expression and decreased fibrillin-1 expression at the protein level in the dermis. Meanwhile, the number of both fibers along the dermal–epidermal junction was increased. Conclusion: IR can alter the expression of tropoelastin and fibrillin-1, which may result in abnormal elastic fiber formation.

4H-Imidazol-4-ones 4 or 4(3H)-quinazolinones 8 were synthesized by base catalytic reactions of 2-mercaptobenzothiazole with carbodiimides 2 or 6, respectively, which were obtained via aza-Wittig reaction of iminophosphorane 1 or 5 with aromatic isocyanates. 4 and 8 exhibited fungicidal activity.

2-Dialkylamino-4H-imidazolin-4-ones 6 were rapidly synthesized by a solution-phase parallel synthetic method, which includes Aza-Wittig reaction of iminophosphorane 3 with aromatic isocynate to give carbodiimide 4 and subsequent reaction of 4 with various aliphatic secondary amine in a parallel fashion.

To gain insight into the structural and folding mechanisms of Antarctic krill alkaline phosphatase (ALP), the enzyme was properly purified by (NH4)2SO4 fractionation and by both Sephadex G-75 and DEAE anion exchange chromatography. The purified enzyme (62.6 kDa; 2.62 unit/mg) was unstable at temperatures exceeding 30°C. Denaturants, such as sodium dodecyl sulfate (SDS), guanidine HCl, and urea, were applied to evaluate the folding mechanism, including kinetics and thermodynamics, of krill ALP. Sodium dodecyl sulfate elicited no significant effect on ALP activity even at excessively high concentrations (300 mM), whereas guanidine HCl and urea effectively inactivated the enzyme at concentrations of 2 and 3.5 M, respectively. Kinetic studies showed that the enzymatic inhibition by guanidine HCl and urea represented a first-order reaction that was a monophasic unfolding process. This process was found to be associated with conformational changes without significant transient free-energy changes. Additionally, the overall structural changes occurred proximally to the active site pocket. Our study provides new insight into ALP of the Antarctic krill, which lives in extreme environmental conditions.

(+) and (−)-Goniofufurones, (+) and (−)-8-epi-goniofufurones have been synthesized from d -(−) and l -(+)-tartaric acids by the addition of ethyl lithiopropiolate to a chiral aldehyde intermediate as a key step, in which LDA is the best base compared to n-BuLi plus Lewis acid YCl3 (cat.).

The regulation of enzymatic activity and unfolding studies of arginine kinase (AK) from various invertebrates have been the focus of investigation. To gain insight into the structural and folding mechanisms of AK from Euphausia superba (ESAK), we purified ESAK from muscle properly. The enzyme behaved as a monomeric protein with a molecular mass of about 40 kDa and had pH and temperature optima of 8.0 and 30 °C, respectively. The K m Arg and K m ATP for the synthesis of phosphoarginine were 0.30 and 0.47 mM, respectively, and k cat / K m A r g was 282.7 s−1/mM. A study of the inhibition kinetics of structural unfolding in the denaturant sodium dodecyl sulfate (SDS) was conducted. The results showed that ESAK was almost completely inactivated by 1.0 mM SDS. The kinetics analyzed via time-interval measurements revealed that the inactivation was a first-order reaction, with the kinetic processes shifting from a monophase to biphase as SDS concentrations increased. Measurements of intrinsic and 1-anilinonaphthalene-8-sulfonate-binding fluorescence showed that SDS concentrations lower than 5 mM did not induce conspicuous changes in tertiary structures, while higher concentrations of SDS exposed hydrophobic surfaces and induced conformational changes. These results confirmed that the active region of AK is more flexible than the overall enzyme molecule.

We studied the effects of Zn(2+) on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn(2+) inactivated the activity of PSCK (IC(50) = .079 ± .004 mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn(2+) induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn(2+) directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn(2+) bind to PSCK and one Zn(2+) is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn(2+) with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn(2+) on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.

We studied the inhibitory effects of isorhamnetin on mushroom tyrosinase by inhibition kinetics and computational simulation. Isorhamnetin reversibly inhibited tyrosinase in a mixed-type manner at Ki=0.235±0.013 mM. Measurements of intrinsic and 1-anilinonaphthalene-8-sulfonate(ANS)-binding fluorescence showed that isorhamnetin did not induce significant changes in the tertiary structure of tyrosinase. To gain insight into the inactivation process, the kinetics were computed via time-interval measurements and continuous substrate reactions. The results indicated that inactivation induced by isorhamnetin was a first-order reaction with biphasic processes. To gain further insight, we simulated docking between tyrosinase and isorhamnetin. Simulation was successful (binding energies for Dock6.3: -32.58 kcal/mol, for AutoDock4.2: -5.66 kcal/mol, and for Fred2.2: -48.86 kcal/mol), suggesting that isorhamnetin interacts with several residues, such as HIS244 and MET280. This strategy of predicting tyrosinase interaction in combination with kinetics based on a flavanone compound might prove useful in screening for potential natural tyrosinase inhibitors.