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分子模拟技术在食品分子互作中的应用研究进展

  • 王娟娟 ,
  • 李海平
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  • (天津市食品生物技术重点实验室,天津商业大学 生物技术与食品科学学院,天津,300134)
第一作者:硕士研究生(李海平副教授为通信作者,E-mail:hhppli@163.com)

收稿日期: 2021-10-08

  修回日期: 2021-10-27

  网络出版日期: 2022-08-19

基金资助

国家自然基金面上项目(31171674);2021年天津市研究生科研创新项目(2021YJSS298)

Application progress of molecular simulation technology in food molecular interaction

  • WANG Juanjuan ,
  • LI Haiping
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  • (Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China)

Received date: 2021-10-08

  Revised date: 2021-10-27

  Online published: 2022-08-19

摘要

分子模拟技术是近年来探究食品组分之间、食品组分与机体之间、食品组分与环境之间互作机理和构效关系的一种新兴技术,因其能打破科学实验存在的盲目、耗时、费力等局限性,在食品领域的应用日益广泛。该文从分子模拟的概念出发,首先介绍了分子对接、分子动力学和量子力学3种分子模拟技术的基本原理,重点综述了分子对接技术(基于AutoDock和Discovery Studio软件)、分子动力学技术(基于GROMACS和Materials Studio软件)和量子力学技术(基于Gaussian软件)在食品功能机制、食品毒素检测、食品活性分子递送、食品加工贮藏、食品包装和食品添加剂中的应用现状,最后对其发展趋势与应用前景进行展望,旨在为食品领域科研人员选择适合研究体系的分子模拟技术提供理论依据,为分子模拟技术在食品领域更广阔的应用提供参考。

本文引用格式

王娟娟 , 李海平 . 分子模拟技术在食品分子互作中的应用研究进展[J]. 食品与发酵工业, 2022 , 48(14) : 292 -302 . DOI: 10.13995/j.cnki.11-1802/ts.029564

Abstract

In recent years, molecular simulation technology has great potential in exploring the interaction mechanism and structure-activity relationship between food components, food components and/or body and surroundings.It could effectively overcome the blindness, time-consumption and great labor in scientific experiments and is widely used in food science. The basic principles of three molecular simulation techniques, including molecular docking, molecular dynamics and quantum mechanics, were explored. The application status of molecular docking technology (based on AutoDock and Discovery Studio software), molecular dynamics technology (based on GROMACS and Materials Studio software) and quantum mechanics technology (based on Gaussian software) in food function mechanism, food toxin detection, food active molecule delivery, food processing and storage, food packaging and food additives were expounded emphatically. Finally, its development trend and application prospects havealso been described, which could provide a theoretical base for the selection of suitable molecular simulation technologies for food researchers, and provide references for its further application in food science.

参考文献

[1] AURÉLIEN G, VINCENT Z, OLIVIER M.SwissDock, a protein-small molecule docking web service based on EADock DSS[J].Nucleic Acids Research, 2011, 39(2):270-277.
[2] TAO X, HUANG Y K, WANG C, et al.Recent developments in molecular docking technology applied in food science:A review[J].International Journal of Food Science & Technology, 2020, 55(1):33-34.
[3] 吕鹏飞, 单晨旭, 曲广淼, 等.腰果酚聚氧乙烯醚磺酸钠在癸烷-水体系的分子动力学模拟[J].油田化学, 2017, 34(1):126-131.
LYU P F, SHAN C X, QU G M et al.Molecular dynamics simulation of cardanol polyoxyethylene ether sulfonate in decane-water interface[J].Oilfield Chemistry, 2017, 34(1):126-131.
[4] 洪祥宇, 徐亨宇, 崔风路, 等.分子模拟在非常规油气开发中的应用[J].计算力学学报, 2021, 38(3):313-320.
HONG X Y, XU X Y, CUI F L, et al.Application of molecular simulation in unconventional oil and gas development[J].Chinese Journal of Computational Mechanics, 2021, 38(3):313-320.
[5] DÜREN T, BAE Y S, SNURR R Q.Using molecular simulation to characterise metal-organic frameworks for adsorption applications[J].Chemical Society Reviews, 2009, 38(5):1 237-1 247.
[6] 王伟华, 雷红涛, 孙远明.分子模拟技术在小分子免疫检测方法研究中的应用[J].现代食品科技, 2010, 26(1):102-108.
WANG W H, LEI H T, SUN Y M.Application of molecular modeling technique in development of small molecular immunity examination methods[J].Modern Food Science & Technology, 2010, 26(1):102-108.
[7] 段爱霞, 陈晶, 刘宏德, 等.分子对接方法的应用与发展[J].分析科学学报, 2009, 25(4):473-477.
[8] ROY S, NARANG B K, GUPTA M K, et al.Molecular docking studies on isocytosine analogues as xanthine oxidase inhibitors[J].Drug Research, 2018, 68(7):395-402.
[9] 张宝花, 徐顺.GROMACS软件并行计算性能分析[J].计算机系统应用, 2016, 25(12):16-23.
ZHANG B H, XU S.Parallel computing performance analysis on GROMACS software[J].Computer System Application, 2016, 25(12):16-23.
[10] FENG T, LI M M, ZHOU J J, et al.Application of molecular dynamics simulation in food carbohydrate research—A review[J].Innovative Food Science and Emerging Technologies, 2015, 31:1-13.
[11] 洪祥宇, 徐亨宇, 崔风路, 等.分子模拟在非常规油气开发中的应用[J].计算力学学报, 2021, 38(3):313-320.
HONG X Y, XU H Y, CUI F L, et al.Application of molecular simulation in unconventional oil and gas development[J].Chinese Journal of Computational Mechanics, 2021, 38(3):313-320.
[12] 崔丹丹, 刘科梅, 刘源, 等.量子化学计算在天然抗氧化物研究中的应用[J].食品安全质量检测学报, 2019, 10(2):320-327.
CUI D D, LIU K M, LIU Y, et al.Application of quantum chemistry in the study of free radical scavenging activity by natural antioxidants[J].Journal of Food Safety & Quality, 2019, 10(2):320-327.
[13] YUE Y Y, ZHAO S F, SUN Y Y, et al.Effects of plant extract aurantio-obtusin on pepsin structure—Spectroscopic characterization and docking simulation[J].Journal of Luminescence, 2017, 187:333-339.
[14] ZHAO J, HUANG L, SUN C Y, et al.Studies on the structure-activity relationship and interaction mechanism of flavonoids and xanthine oxidase through enzyme kinetics, spectroscopy methods and molecular simulations[J].Food Chemistry, 2020, 323:126807.
[15] XIE F, ZHANG W, GONG S X, et al.Investigating lignin from Canna edulis ker residues induced activation of α-amylase:Kinetics, interaction, and molecular docking[J].Food Chemistry, 2019, 271:62-69.
[16] BILAL S, HASSAN M M, REHMAN M F U, et al.An insect acetylcholinesterase biosensor utilizing WO3/g-C3 N4 nanocomposite modified pencil graphite electrode for phosmet detection in stored grains[J].Food Chemistry, 2021, 346:128894.
[17] SADEGHI A S, MOHSENZADEH M, ABNOUS K, et al.Development and characterization of DNA aptamers against florfenicol:Fabrication of a sensitive fluorescent aptasensor for specific detection of florfenicol in milk[J].Talanta, 2018, 182:193-201.
[18] POÓR M, KUNSÁGI-MÁTÉ S, BÁLINT M, et al.Interaction of mycotoxin zearalenone with human serum albumin[J].Journal of Photochemistry and Photobiology B:Biology, 2017, 170:16-24.
[19] POÓR M, LEMLI B, BÁLINT M, et al.Interaction of citrinin with human serum albumin[J].2015, 7(12):5 155-5 166.
[20] 王小凤, 申慧婷, 孙小玲, 等.金枪鱼(Thunnus sp.)胰腺酶解液对H2O2诱导的胰岛素瘤细胞(INS-1)氧化损伤的保护作用[J].海洋与湖沼, 2019, 50(5):1 146-1 153.
WANG X F, SHEN H T, SUN X L,et al.In-Silico analysis and in vivo tests of anti-oxidation effect of tuna pancreas hydrolysate on ins-1 cell[J].Oceanologia et Limnologia Sinica, 2019, 50(5):1 146-1 153.
[21] HAN J J, HUANG Z B, TANG S S, et al.The novel peptides ICRD and LCGEC screened from tuna roe show antioxidative activity via Keap1/Nrf2-ARE pathway regulation and gut microbiota modulation[J].Food Chemistry, 2020, 327:127094.
[22] 王锐, 张迪雅, 李晔, 等.金枪鱼暗色肉酶解优势肽鉴定及其体外抗氧化和血管紧张素转换酶抑制活性分析[J].食品科学, 2020, 41(23):91-99.
WANG R, ZHANG D Y, LI Y, et al.Identification of dominant peptides from hydrolyzed tuna dark muscle and their antioxidant and angiotensin-converting enzyme inhibitory activities[J].Food Science, 2020, 41(23):91-99.
[23] 董丽莎, 李妍妍, 张红燕, 等.黑线鳕鱼皮胶原蛋白胰蛋白酶酶解多肽对UVB诱导HaCaT光损伤的抑制作用[J].食品科学, 2018, 39(10):185-192.
DONG L S, LI Y Y, ZHANG H Y, et al.Inhibitory effects of peptides derived from tryptic hydrolysate of skin collagen from melanogrammus aeglefinus on uvb-induced photodamage in hacat cells[J].Food Science,2018, 39(10):185-192.
[24] WU H X, LIU Y L, GUO M R, et al.A virtual screening method for inhibitory peptides of Angiotensin I-converting enzyme[J].Journal of Food Science, 2014, 79(9):C1635-C1642.
[25] WU Q Y, JIA J Q, YAN H, et al.A novel angiotensin-I converting enzyme (ACE) inhibitory peptide from gastrointestinal protease hydrolysate of silkworm pupa (Bombyx mori) protein:Biochemical characterization and molecular docking study[J].Peptides, 2015, 68:17-24.
[26] ALGHAMDI H A, CAMPBELL L J, EUSTON S R.Molecular dynamics simulation of the adsorption of mung bean defensin VrD1 to a phospholipid bilayer[J].Food Structure, 2019, 21:100117.
[27] ZARE D, ALLISON J R, MCGRATH K M.Molecular dynamics simulation of β-lactoglobulin at different oil/water interfaces[J].Biomacromolecules, 2016, 17(5):1 572-1 581.
[28] JAKOBTORWEIHEN S, HEUER J, WALUGA T.A novel approach to calculate protein adsorption isotherms by molecular dynamics simulations[J].Journal of Chromatography A, 2020, 1620:460940.
[29] 于晶, 扈莹莹, 温荣欣, 等.植物源抗冻蛋白作用机制及其在食品中的应用[J].食品科学, 2019, 40(23):305-312.
YU J, HU Y Y, WEN R X, et al.A review of the mechanism of action of plant antifreeze proteins and their application in food[J].Food Science, 2019, 40(23):305-312.
[30] MEISTER K, MOLL C J, CHAKRABORTY S, et al.Molecular structure of a hyperactive antifreeze protein adsorbed to ice[J].The Journal of Chemical Physics, 2019, 150(13):131101.
[31] KUMARI S, MUTHACHIKAVIL A V, TIWARI J K, et al.Computational study of differences between antifreeze activity of type-III antifreeze protein from ocean pout and its mutant[J].Langmuir, 2020, 36(9):2 439-2 448.
[32] LÓPEZ C A, DE VRIES A H, MARRINK S J.Amylose folding under the influence of lipids[J].Carbohydrate Research, 2012, 364:1-7.
[33] CHENG L L, FENG T, ZHANG B Y, et al.A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water[J].Carbohydrate Polymers, 2018, 196:56-65.
[34] GÓRNAS P, NEUNERT G, BACZYŃSKI K, et al.Beta-cyclodextrin complexes with chlorogenic and caffeic acids from coffee brew:Spectroscopic, thermodynamic and molecular modelling study[J].Food Chemistry, 2009, 114(1):190-196.
[35] BHOPATKAR D, FENG T, CHEN F, et al.Self-assembled nanoparticle of common food constituents that carries a sparingly soluble small molecule[J].Journal of Agricultural and Food Chemistry, 2015, 63(17):4 312-4 319.
[36] BALASUBRAMANIAN S, DEVI A, SINGH K K, et al.Application of glass transition in food processing[J].Critical Reviews in Food Science and Nutrition, 2016, 56(6):919-936.
[37] ZHOU G H, ZHAO T H, WAN J, et al.Predict the glass transition temperature and plasticization of β-cyclodextrin/water binary system by molecular dynamics simulation[J].Carbohydrate Research, 2015, 401:89-95.
[38] 周国辉, 刘成梅, 万婕, 等.分子动力学模拟水分对小分子糖玻璃态转变温度及扩散性质的影响[J].现代食品科技, 2014, 30(9):154-160.
ZHOU G H, LIU C M, WAN J,et al.Effect of moisture content on glass transition temperature and diffusion properties of low-molecular-weight sugars by molecular dynamics simulation[J].Modern Food Science & Technology, 现代食品科技, 2014, 30(9):154-160.
[39] 邱福生, 任力, 王家鸣, 等.分子动力学模拟预测壳聚糖的玻璃化转变温度[J].化工学报, 2012, 63(7):2 285-2 289.
QIU F S, REN L, WANG J M, et al.Prediction of glass transition temperature of chitosan through molecular dynamics simulation[J].CIESC Journa, 2012, 63(7):2 285-2 289.
[40] LIU Y J, CAI Y X, JIANG X Y, et al.Molecular interactions, characterization and antimicrobial activity of curcumin-chitosan blend films[J].Food Hydrocolloids, 2016, 52:564-572.
[41] SUN L N, LU L X, PAN L, et al.Development of active low-density polyethylene (LDPE) antioxidant packaging films:Controlled release effect of modified mesoporous silicas[J].Food Packaging and Shelf Life, 2021, 27:100616.
[42] HASSANZADEH K, AKHTARI K, HASSANZADEH H, et al.The role of structural CH compared with phenolic OH sites on the antioxidant activity of oleuropein and its derivatives as a great non-flavonoid family of the olive components:A DFT study[J].Food Chemistry, 2014, 164:251-258.
[43] 王兰娇, 李大婧, 张良聪, 等.利用密度泛函理论分析蓝莓花色苷抗氧化活性[J].食品科学, 2020, 41(17):53-59.
[44] SARKAR A, MIDDYA T R, JANA A D.A QSAR study of radical scavenging antioxidant activity of a series of flavonoids using DFT based quantum chemical descriptors—The importance of group frontier electron density[J].Journal of Molecular Modeling, 2012, 18(6):2 621-2 631.
[45] YADAV R, AWASTHI N, SHUKLA A, et al.Modeling the hydroxylation of estragole via human liver cytochrome P450[J].Journal of Molecular Modeling, 2021, 27(7):199.
[46] DUARTE L M, PASCHOAL D, IZUMI C M S, et al.Simultaneous determination of aspartame, cyclamate, saccharin and acesulfame-K in powder tabletop sweeteners by FT-Raman spectroscopy associated with the multivariate calibration:PLS, iPLS and siPLS models were compared[J].Food Research International, 2017, 99(1):106-114.
[47] DUAN X K, YAO Y, LI J W, et al.Detection of acesulfame potassium in mouthwash based on surface-enhanced Raman spectroscopy[J].Optical Engineering, 2018, 57(5):057102.
[48] ZHAN F C, DING S, XIE W Y, et al.Towards understanding the interaction of β-lactoglobulin with capsaicin:Multi-spectroscopic, thermodynamic, molecular docking and molecular dynamics simulation approaches[J].Food Hydrocolloids, 2020, 105:105767.
[49] GENG S, JIANG Z J, MA H J, et al.Interaction mechanism of flavonoids and bovine β-lactoglobulin:Experimental and molecular modelling studies[J].Food Chemistry, 2020, 312:126066.
[50] CUI F C, YANG K C, LI Y Q.Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation[J].PLoS One, 2015, 10(5):e0125848.
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