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Zhang X, Xu J, Tian X, Wang Y, Liao X, Zhao L. Mechanisms of persimmon pectin methyl esterase activation by high pressure processing based on chemical experiments and molecular dynamics simulations. Food Chem 2024; 432:137239. [PMID: 37683335 DOI: 10.1016/j.foodchem.2023.137239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
High pressure processing (HPP) was found to have a kinase effect on persimmon pectin methyl esterase (PME), while the mechanism remains unclear. In this study, chemical experiments and molecular dynamics (MD) simulations were used to reveal its mechanisms. Persimmon PME was first extracted and purified using ion exchange columns with 81.89% purity. After 500 MPa/5 min, PME activity increased 11.3%, the α-helix and β-folding decreased 10.8% and 6.1% compared to the 0.1 MPa group, respectively. MD results showed that HPP decreased the volume, increased the number of hydrogen bonds between PME and pectin. Under high pressure, Asp-157, Asp-136 and Gln-135 in the enzyme activity center remained stable, while the positions of Arg-225 and Gln-113 changed a lot. The conformation of the substrate binding channel also changed. The secondary structure and volume changes of the HPP-treated PME affected the active center and substrate channels, ultimately altering the activity.
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Affiliation(s)
- Xinyue Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China
| | - Jiayue Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China
| | - Xuezhi Tian
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, 100083 Beijing, China.
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Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022; 13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023] Open
Abstract
Insulin is a peptide hormone known for chiefly regulating glucose level in blood among several other metabolic processes. Insulin remains the most effective drug for treating diabetes mellitus. Insulin is synthesized in the pancreatic β-cells where it exists in a compact hexameric architecture although its biologically active form is monomeric. Insulin exhibits a sequence of conformational variations during the transition from the hexamer state to its biologically-active monomer state. The structural transitions and the mechanism of action of insulin have been investigated using several experimental and computational methods. This review primarily highlights the contributions of molecular dynamics (MD) simulations in elucidating the atomic-level details of conformational dynamics in insulin, where the structure of the hormone has been probed as a monomer, dimer, and hexamer. The effect of solvent, pH, temperature, and pressure have been probed at the microscopic scale. Given the focus of this review on the structure of the hormone, simulation studies involving interactions between the hormone and its receptor are only briefly highlighted, and studies on other related peptides (e.g., insulin-like growth factors) are not discussed. However, the review highlights conformational dynamics underlying the activities of reported insulin analogs and mimetics. The future prospects for computational methods in developing promising synthetic insulin analogs are also briefly highlighted.
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Affiliation(s)
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, United States
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The effects of high pressure treatment on the structural and digestive properties of myoglobin. Food Res Int 2022; 156:111193. [DOI: 10.1016/j.foodres.2022.111193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/22/2022]
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Huang Y, Zhang X, Suo H. Interaction between β-lactoglobulin and EGCG under high-pressure by molecular dynamics simulation. PLoS One 2021; 16:e0255866. [PMID: 34932559 PMCID: PMC8691620 DOI: 10.1371/journal.pone.0255866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
The binding between β-lactoglobulin and epigallocatechin gallate (EGCG) under the pressure of 600 MPa was explored using molecular docking and molecular dynamics (MD) simulation. EGCG bound mainly in two regions with site 1 in internal cavity of the β-barrel and site 2 on the surface of protein. 150 ns MD was performed starting from the structure with the optimal binding energy at the two sites in molecular docking, respectively. It was found that the protein fluctuated greatly when small molecule bound to site 2 at 0.1 MPa, and the protein fluctuation and solvent accessible surface area became smaller under high-pressure. The binding of small molecules made the protein structure more stable with increasing of α-helix and β-sheet, while high-pressure destroyed α-helix of protein. The binding energy of small molecules at site 1was stronger than that at site 2 under 0.1 MPa, with stronger van der Waals and hydrophobic interaction at site 1 while more hydrogen bonds were present at site 2. The binding energy of both sites weakened under high-pressure, especially at site 1, causing the binding force to be weaker at site 1 than that at site 2 under high-pressure.
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Affiliation(s)
- Yechuan Huang
- College of Bioengineering, Jingchu University of Technology, Jingmen, PR China
- * E-mail: ,
| | - Xicai Zhang
- College of Bioengineering, Jingchu University of Technology, Jingmen, PR China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, PR China
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