The effect of thiobarbituric acid on tyrosinase: inhibition kinetics and computational simulation.

Yin, Shang-Jun,Si, Yue-Xiu,Wang, Zhi-Jiang,Wang, Su-Fang,Oh, Sangho,Lee, Sanghyuk,Sim, Seon-Mi,Yang, Jun-Mo,Qian, Guo-Ying,Lee, Jinhyuk,Park, Yong-Doo Adenine Press 2011 Journal of biomolecular structure & dynamics Vol.29 No.3

<P>Tyrosinase plays various roles in organisms and much research has focused on the regulation of tyrosinase activity. We studied the inhibitory effect of thiobarbituric acid (TBA) on tyrosinase. Our kinetic study showed that TBA inhibited tyrosinase in a reversible noncompetitive manner (K(i) 5 14.0 ± 8.5 mM and IC?????? 5 8.0 ± 1.0 mM). Intrinsic and ANS-binding fluorescences studies were also performed to gain more information regarding the binding mechanism. The results showed that no tertiary structural changes were obviously observed. For further insight, we predicted the 3D structure of tyrosinase and simulated the docking between tyrosinase and TBA. The docking simulation was successful with significant scores (binding energy for AutoDock4: -5.52 kcal/mol) and suggested that TBA was located in the active site. The 11 ns molecular dynamics simulation convinced that the four HIS residues (residue numbers: 57, 90, 250, and 282) were commonly responsible for the interaction with TBA. Our results provide a new inhibition strategy that works using an antioxidant rather than targeting the copper ions within the tyrosinase active site.</P>

Mixed-type inhibition of tyrosinase from Agaricus bisporus by terephthalic acid: computational simulations and kinetics.

Yin, Shang-Jun,Si, Yue-Xiu,Chen, Yong-Fu,Qian, Guo-Ying,L?, Zhi-Rong,Oh, Sangho,Lee, Jinhyuk,Lee, Sanghyuk,Yang, Jun-Mo,Lee, Dong-Youn,Park, Yong-Doo Kluwer Academic/Plenum 2011 The Protein Journal Vol.30 No.4

<P>Tyrosinase inhibition studies are needed due to the agricultural and medicinal applications. For probing effective inhibitors of tyrosinase, a combination of computational prediction and enzymatic assay via kinetics were important. We predicted the 3D structure of tyrosinase from Agaricus bisporus, used a docking algorithm to simulate binding between tyrosinase and terephthalic acid (TPA) and studied the reversible inhibition of tyrosinase by TPA. Simulation was successful (binding energies for Autodock4 = -1.54 and Fred2.0 = -3.19 kcal/mol), suggesting that TPA interacts with histidine residues that are known to bind with copper ions at the active site. TPA inhibited tyrosinase in a mixed-type manner with a K ( i ) = 11.01 2.12 mM. Measurements of intrinsic and ANS-binding fluorescences showed that TPA induced no changes in tertiary structure. The present study suggested that the strategy of predicting tyrosinase inhibition based on hydroxyl groups and orientation may prove useful for screening of potential tyrosinase inhibitors.</P>

Trifluoroethanol-induced changes in activity and conformation of manganese-containing superoxide dismutase.

Yin, Shang-Jun,L?, Zhi-Rong,Park, Daeui,Chung, Hae Young,Yang, Jun-Mo,Zhou, Hai-Meng,Qian, Guo-Ying,Park, Yong-Doo Humana Press 2012 Applied biochemistry and biotechnology Vol.166 No.2

<P>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.</P>

Metabolic responses and arginine kinase expression of juvenile cuttlefish (<i>Sepia pharaonis</i>) under salinity stress

Yin, Shang-Jun,Zhang, Linmeng,Zhang, Lili,Wan, Jiaxin,Song, Wei,Jiang, Xiamin,Park, Yong-Doo,Si, Yue-Xiu Elsevier 2018 INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES Vol.113 No.-

<P><B>Abstract</B></P> <P>The pharaoh cuttlefish <I>Sepia pharaonis</I> is particularly sensitive to environmental changes in its breeding environment. The breeding of <I>S</I>. <I>pharaonis</I> 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 <I>S</I>. <I>pharaonis</I> 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 <I>S</I>. <I>pharaonis</I>.</P>

Analysis of the peptides detected in atopic dermatitis and various inflammatory diseases patients-derived sera

Yin, Shang-Jun,Cho, Ick-Hyun,Yang, Hee Seung,Park, Yong-Doo,Yang, Jun-Mo Elsevier 2018 International journal of biological macromolecules Vol.106 No.-

<P><B>Abstract</B></P> <P>Serum proteomics has been applied for the discovery and analysis of biomarkers related to human disease. Serum is an optimal source to identify proteins derived from diseased-tissue compartments. We recently established an integrative method to analyze highly basic proteins that remain unresolved by the general 2D-PAGE method. In this follow-up study, we successfully detected several disease-associated proteins from sera samples obtained from patients with atopic dermatitis (AD). After proteomic analyses, target proteins were validated from AD patient-derived sera using ELISA or Western blotting methods We detected zinc finger CCHC domain containing 10 (ZCCHC10), peptidoglycan recognition protein L (PGRP-L), kininogen, α-1-antitrypsin, and hornerin proteins that are dysregulated in AD patient sera samples, which suggest effective approaches to methodologically analyze the serum proteome. Thus, the integrated proteomic method approach described here could be applicable for the detection of proteins associated with other human diseases. Our present study provides new insights into optimized serum proteomic techniques to understand systemic events of AD.</P>

The inhibitory effect of pyrogallol on tyrosinase activity and structure: Integration study of inhibition kinetics with molecular dynamics simulation

Xiong, Shang-Ling,Lim, Gyu Tae,Yin, Shang-Jun,Lee, Jinhyuk,Si, Yue-Xiu,Yang, Jun-Mo,Park, Yong-Doo,Qian, Guo-Ying Elsevier 2019 INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES Vol.121 No.-

<P><B>Abstract</B></P> <P>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 (<I>IC</I> <SUB>50</SUB> = 0.772 ± 0.003 mM and <I>K</I> <SUB>i</SUB> = 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.</P>

Serum Macrophage Migration Inhibitory Factor as a Biomarker of Active Pulmonary Tuberculosis

Zhong-bo Shang,Jun Wang,Shou-gang Kuai,Yin-yin Zhang,Qin-fang Ou,Hao Pei,Li Hua Huang 대한진단검사의학회 2018 Annals of Laboratory Medicine Vol.38 No.1

Background: Macrophage migration inhibitory factor (MIF), a pro-inflammatory cytokine with chemokine-like functions, has been shown to play a central role in several acute and chronic inflammatory diseases. However, limited information is available regarding the use of MIF as an inflammatory pathway marker in patients with tuberculosis. This study aimed to investigate the association of MIF with IFN-γ and TNF-α in active pulmonary tuberculosis (APTB) following anti-tuberculosis treatment. Methods: The MIF, TNF-α, and IFN-γ serum levels were determined in 47 patients with APTB by cytokine-specific ELISA at four phases: prior to anti-tuberculosis drug treatment (baseline), and following 2, 4, and 6 months of treatment. In addition, we measured the MIF, TNF-α, and IFN-γ serum levels in 50 health controls. Results: MIF serum levels were significantly elevated (P<0.05) in patients with APTB prior to treatment compared with that in control subjects, and TNF-α ≥449.7 pg/mL was associated with high MIF levels (≥13.1 ng/mL). MIF levels were significantly reduced (P<0.01) following 2, 4, and 6 months of treatment, with variations in TNF-α and IFN-γ serum levels. MIF levels were positively correlated with the paired TNF-α level at baseline (r=0.1103, P=0.0316) and following 6 months of treatment (r=0.09569, P=0.0364).Conclusions: A reduction in the MIF serum levels in patients with APTB following anti-tuberculosis treatment may positively affect host immune protection against Mycobacterium tuberculosis infection. Thus, serum MIF levels may constitute a useful marker for assessing therapy effectiveness in patients with APTB.

An integrated study of tyrosinase inhibition by rutin: progress using a computational simulation.

Si, Yue-Xiu,Yin, Shang-Jun,Oh, Sangho,Wang, Zhi-Jiang,Ye, Sen,Yan, Li,Yang, Jun-Mo,Park, Yong-Doo,Lee, Jinhyuk,Qian, Guo-Ying Adenine Press 2012 Journal of biomolecular structure & dynamics Vol.29 No.5

<P>Tyrosinase inhibition studies have recently gained the attention of researchers due to their potential application values. We simulated docking (binding energies for AutoDock Vina: -9.1 kcal/mol) and performed a molecular dynamics simulation to verify docking results between tyrosinase and rutin. The docking results suggest that rutin mostly interacts with histidine residues located in the active site. A 10 ns molecular dynamics simulation showed that one copper ion at the tyrosinase active site was responsible for the interaction with rutin. Kinetic analyses showed that rutin-mediated inactivation followed a first-order reaction and mono- and biphasic rate constants occurred with rutin. The inhibition was a typical competitive type with K(i) = 1.100.25 mM. Measurements of intrinsic and ANS-binding fluorescences showed that rutin showed a relatively strong binding affinity for tyrosinase and one possible binding site that could be a copper was detected accompanying with a hydrophobic exposure of tyrosinase. Cell viability testing with rutin in HaCaT keratinocytes showed that no toxic effects were produced. Taken together, rutin has the potential to be a potent anti-pigment agent. The strategy of predicting tyrosinase inhibition based on hydroxyl group number and computational simulation may prove useful for the screening of potential tyrosinase inhibitors.</P>

The Inhibitory Effects of Cu(2+) on Exopalaemon carinicauda Arginine Kinase via Inhibition Kinetics and Molecular Dynamics Simulations.

Si, Yue-Xiu,Lee, Jinhyuk,Yin, Shang-Jun,Gu, Xiao-Xu,Park, Yong-Doo,Qian, Guo-Ying Humana Press 2015 Applied biochemistry and biotechnology Vol.176 No.4

<P>We studied the Cu2+-mediated inhibition and aggregation of Exopalaemon carinicauda arginine kinase ( ECAK). We found that Cu2+ significantly inactivated ECAK activity and double-reciprocal kinetics demonstrated that Cu2+ induced noncompetitive inhibition of arginine and ATP ( IC50=2.27 +/- 0.16 mu M; K-i for arginine=13.53 +/- 3.76; K-i for ATP=4.02 +/- 0.56). Spectrofluorometry results showed that Cu2+ induced ECAK tertiary structural changes including the exposure of hydrophobic surfaces that directly induced ECAK aggregation. The addition of osmolytes such as glycine and proline successfully blocked ECAK aggregation induced by Cu2+ and recovered ECAK activity. We built a 3D structure for ECAK using the ECAK ORF gene sequence. Molecular dynamics ( MD) and docking simulations between ECAK and Cu2+ were conducted to elucidate the binding mechanisms. The results showed that Cu2+ blocked the entrance to the ATP active site; these results are consistent with the experimental result that Cu2+ induced ECAK inactivation. Since arginine kinase ( AK) plays an important role in cellular energy metabolism in invertebrates, our study can provide new information about the effect of Cu2+ on ECAK enzymatic function and unfolding, including aggregation, and the protective effects of osmolytes on ECAK folding to better understand the role of the invertebrate ECAK metabolic enzyme in marine environments.</P>

An OMICS-based study of the role of C3dg in keratinocytes: RNA sequencing, antibody-chip array, and bioinformatics approaches

Zhang, Li-Li,Kwak, Hyunchang,Yin, Shang-Jun,Lee, Bit-Na,Chang, Ye-Jin,Hahn, Myong-Joon,Yang, Jun-Mo,Lee, Jae-Rin,Park, Yong-Doo Elsevier 2019 INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES Vol.133 No.3