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Yang A, Zhang J, Lv G, Chen J, Guo L, Liu Y, Zheng Y, Wang L. Chemical profiling and arginine kinase inhibitory activity of Angelica dahurica leaves. Heliyon 2024; 10:e27589. [PMID: 38509962 PMCID: PMC10950578 DOI: 10.1016/j.heliyon.2024.e27589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/25/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Angelica dahurica is a medicinal herb of the Umbelliferae family. The dried root of A. dahurica, also known as Angelicae dahuricae Radix, is widely used in clinical treatment. However, the aboveground part of A. dahurica which accounted for over 70% of the total plant was abandoned in the field. In order to develop the value of the aboveground part of A. dahurica, the chemical constituents and arginine kinase (AK) inhibitory activity of A. dahurica leaves were studied. 85 volatile components were identified from A. dahurica leaves by GC-MS; 39 non-volatile components including sugars, amino acids and organic acids were identified by pre-column derivatization GC-MS analysis; and 7 coumarins were qualitatively and quantitatively analyzed by HPLC. Then, an inhibitory enzyme-linked immunosorbent assay (iEIA) was applied for evaluation of AK inhibitory activity. The extracts of A. dahurica leaves exhibited well inhibitory effects on AK. Further, potential AK inhibitors were screened by grey relational analysis and their inhibitory activities were validated by iEIA. l-aspartic acid exhibited strongest inhibitory effect on AK with its IC50 value was 0.558 mM, which was much lower than that of chlorpheniramine (6.644 mM). The obtained chemical profiles displayed chemical diversity of A. dahurica leaves and will provide data support for the future development and utilization of A. dahurica leaves. The screened potential AK inhibitors from A. dahurica leaves could be candidates for development of antiallergic substances or insecticides.
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Affiliation(s)
- Aitong Yang
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200, China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, 050200, China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200, China
| | - Junyan Zhang
- Cangzhou Hospital of Integrated Traditional Chinese and Western Medicine, Cangzhou, 061000, China
| | - Guangying Lv
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200, China
| | - Jiabao Chen
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200, China
| | - Long Guo
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200, China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, 050200, China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200, China
| | - Yan Liu
- Tianjin Tasly Chinese Medicine Resources Technology Development Co., Ltd., Tianjin, China
| | - Yuguang Zheng
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, 050200, China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200, China
- Hebei Chemical and Pharmaceutical College, Shijiazhuang, 050026, China
| | - Lei Wang
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200, China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, 050200, China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200, China
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Yin SJ, Lee HY, Wang W, Lee J, Park YD. Characterization and activity-folding relationship of serine protease from Antarctic krill ( Euphausia superba). J Biomol Struct Dyn 2022:1-14. [PMID: 35612882 DOI: 10.1080/07391102.2022.2080115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Euphausia superba (Antarctic krill) serine protease (ESP) was investigated to gain insights into the activity-structural relationship, folding behavior, and regulation of the catalytic function. We purified ESP from the krill muscle and characterized biochemical distinctions via enzyme kinetics. Studies of inhibition kinetics and unfolding in the presence of a serine residue modifier, such as phenylmethanesulfonyl fluoride, were conducted. Structural characterizations were measured by spectrofluorimetry, including 1-anilinonaphthalene-8-sulfonate dye labeling for hydrophobic residues. The computational simulations such as docking and molecular dynamics were finally conducted to detect key residues and folding behaviors in a nano-second range. The kinetic parameters of ESP were measured as KmBANH = 0.97 ± 0.15 mM and kcat/KmBANH = 4.59 s-1/mM. The time-interval kinetics measurements indicated that ESP inactivation was transformed from a monophase to a biphase process to form a thermodynamically stable state. Spectrofluorimetry measurements showed that serine is directly connected to the regional folding of ESP. Several osmolytes such as proline and glycine only partially protected the inactive form of ESP by serine modification. Computational molecular dynamics and docking simulations showed that three serine residues (Ser183, Ser188, and Ser207) and Cys184, Val206, and Gly209 are key residues of catalytic functions. Our study revealed the functional roles of serine residues as key residues of catalytic function at the active site and of the structural conformation as key folding factors, where ESP displays a flexible property of active site pocket compared to the overall structure.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, P. R. China
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB school of Bioscience, University of Science and Technology (UST), Daejeon, Korea
| | - Wei Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, P. R. China
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB school of Bioscience, University of Science and Technology (UST), Daejeon, Korea
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, P. R. China.,Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P.R. China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P.R. China
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Yin SJ, Lee J, Lim G, Chen Z, Qian GY, Si YX, Park YD. A study of Pb 2+ induced unfolding and aggregation of arginine kinase from Euphausia superba: kinetics and computational simulation integrating study. J Biomol Struct Dyn 2021; 40:8206-8215. [PMID: 33847251 DOI: 10.1080/07391102.2021.1908168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
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 investigated the Pb2+-induced inhibition and aggregation of Euphausia superba arginine kinase (ESAK) and found that significantly inactivated ESAK in a dose-dependent manner (IC50 = 0.058 ± 0.002 mM). Spectrofluorimetry results showed that Pb2+ induced tertiary structural changes via the internal polarity increased and the non-polarity decreased in ESAK and directly induced ESAK aggregation. The ESAK aggregation process induced by Pb2+ occurred with multi-phase kinetics. The addition of osmolytes did not show protective effect on Pb2+-induced inactivation of ESAK. The computational molecular dynamics (MD) simulation showed that three Pb2+ interrupt the entrance of the active site of ESAK and it could be the reason on the loss of activity of ESAK. Several important residues of ESAK were detected that were importantly contributed the conformation and catalytic function of ESAK. Our study showed that Pb2+-induced misfolding of ESAK and the complete loss of activity irreversibly, which cannot be recovered by osmolytes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Sciences and Technology, Daejeon, Korea
| | - Gyutae Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Zhongfa Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Yue-Xiu Si
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, P.R. China
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China.,Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P.R. China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P. R. China
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Wang ZJ, Ma W, Yang JM, Kang Y, Park YD. Effects of Cu2+ on alkaline phosphatase from Macrobrachium rosenbergii. Int J Biol Macromol 2018; 117:116-123. [DOI: 10.1016/j.ijbiomac.2018.05.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]
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Yin SJ, Zhang L, Zhang L, Wan J, Song W, Jiang X, Park YD, Si YX. Metabolic responses and arginine kinase expression of juvenile cuttlefish (Sepia pharaonis) under salinity stress. Int J Biol Macromol 2018. [PMID: 29524487 DOI: 10.1016/j.ijbiomac.2018.03.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Linmeng Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Lili Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jiaxin Wan
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Wei Song
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xiamin Jiang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710, Republic of Korea.
| | - Yue-Xiu Si
- College of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou 310053, PR China.
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Si YX, Lee J, Cheng JG, Yin SJ, Park YD, Qian GY, Jiang XM. Kinetics for Zinc Ion Induced Sepia Pharaonis Arginine Kinase Inactivation and Aggregation. Protein Pept Lett 2017; 23:508-17. [PMID: 27030550 PMCID: PMC5427814 DOI: 10.2174/0929866523666160331144049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 02/12/2016] [Accepted: 03/16/2016] [Indexed: 11/22/2022]
Abstract
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 Zn2+. Using these results, the Zn2+ binding sites were predicted and the initial effect of Zn2+ on the SPAK structure was elucidated. Subsequently, the experimental kinetic results were compared with the simulation results. Zn2+ markedly inhibited the activity of SPAK in a manner of non-competitive inhibitions for both arginine and ATP. We also found that Zn2+ 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 Zn2+ on SPAK and Zn2+ can trigger SPAK aggregation after exposing large extent of hydrophobic surface. The protective effects of glycine and proline against Zn2+ on SPAK folding were also demonstrated.
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Affiliation(s)
| | | | | | | | | | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, P.R China.
| | - Xia-Min Jiang
- School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China.
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Xu Y, Lee J, Lü ZR, Mu H, Zhang Q, Park YD. Integration of Inhibition Kinetics and Molecular Dynamics Simulations: A Urea-Mediated Folding Study on Acetaldehyde Dehydrogenase 1. Appl Biochem Biotechnol 2016; 179:1101-14. [PMID: 27000059 DOI: 10.1007/s12010-016-2052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/14/2016] [Indexed: 11/21/2022]
Abstract
Understanding the mechanism of acetaldehyde dehydrogenase 1 (ALDH1) folding is important because this enzyme is directly involved in several types of cancers and other diseases. We investigated the urea-mediated unfolding of ALDH1 by integrating kinetic inhibition studies with computational molecular dynamics (MD) simulations. Conformational changes in the enzyme structure were also analyzed using intrinsic and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence measurements. Kinetic studies revealed that the direct binding of urea to ALDH1 induces inactivation of ALDH1 in a manner of mixed-type inhibition. Tertiary structural changes associated with regional hydrophobic exposure of the active site were observed. The urea binding regions on ALDH1 were predicted by docking simulations and were partly shared with active site residues of ALDH1 and with interface residues of the oligomerization domain for tetramer formation. The docking results suggest that urea prevents formation of the ALDH1 normal shape for the tetramer state as well as entrance of the substrate into the active site. Our study provides insight into the structural changes that accompany urea-mediated unfolding of ALDH1 and the catalytic role associated with conformational changes.
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Affiliation(s)
- Yingying Xu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China.,School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 Beisanhuan Dong Road, Beijing, 100029, People's Republic of China
| | - Jinhyuk Lee
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea.,Department of Nanobiotechnology and Bioinformatics, University of Sciences and Technology, Daejeon, 305-350, South Korea
| | - Zhi-Rong Lü
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China
| | - Hang Mu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China
| | - Qian Zhang
- School of Preclinical Medicine, Beijing University of Chinese Medicine, 11 Beisanhuan Dong Road, Beijing, 100029, People's Republic of China.
| | - Yong-Doo Park
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, 314006, People's Republic of China. .,College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, People's Republic of China.
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