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《工程(英文)》 >> 2020年 第6卷 第2期 doi: 10.1016/j.eng.2018.12.012

电中性固体表面上多条肽链的吸附过程——粗粒化模拟研究

a China-Australia Joint Research Center in Future Dairy Manufacturing, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China

b Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia

收稿日期: 2018-08-07 修回日期: 2018-11-30 录用日期: 2018-12-09 发布日期: 2020-02-27

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摘要

蛋白质在固体表面的吸附过程涉及诸多复杂的分子间相互作用,因此到目前为止仍然无法做到精准调控。通过模拟计算,可以获取固-液界面分子尺度的蛋白质移动机理,从而为预测蛋白质吸附和结垢现象提供可靠的理论依据。本研究通过多尺度粗粒化模型对多条疏水的丙氨酸十二肽在金表面的聚集和吸附过程进行了分析。大约有一半(46.6%)的丙氨酸十二肽可以组成聚集体。30.0%的独立肽链会被快速地吸附到固体表面。这些在表面吸附的肽链经过一段时间的爬行,其中的一些(51.0%)能与吸附在表面的或是游离在溶液中的肽链融合,从而形成吸附在表面的聚集体。这些在固-液界面吸附的肽链使得固体表面性质发生变化。这一变化可能会进一步影响之后溶液中肽链和聚集体在金表面的吸附。本研究揭示的多条肽链吸附机理有希望为进一步研究多个蛋白质分子在固体表面的吸附机理提供理论基础。

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参考文献

[ 1 ] Bansal B, Chen XD. A critical review of milk fouling in heat exchangers. Compr Rev Food Sci Food Saf 2006;5(2):27–33. 链接1

[ 2 ] Yu W, Yang Y, Graham N. Evaluation of ferrate as a coagulant aid/oxidant pretreatment for mitigating submerged ultrafiltration membrane fouling in drinking water treatment. Chem Eng J 2016;298:234–42. 链接1

[ 3 ] Daher FB, Braybrook SA. How to let go: pectin and plant cell adhesion. Front Plant Sci 2015;6:523. 链接1

[ 4 ] Georgiadis MC, Rotstein GE, Macchietto S. Optimal design and operation of heat exchangers under milk fouling. AIChE J 1998;44(9):2099–111. 链接1

[ 5 ] Lü F, Zhou Q, Wu D, Wang T, Shao L, He P. Dewaterability of anaerobic digestate from food waste: relationship with extracellular polymeric substances. Chem Eng J 2015;262:932–8. 链接1

[ 6 ] Smollen M. Dewaterability of municipal sludge 1: a comparative study of specific resistance to filtration and capillary suction time as dewaterability parameters. Water SA 1986;12(3):127–32. 链接1

[ 7 ] Smollen M. Dewaterability of municipal sludge 2: sludge characterization and behaviour in terms of SRF and CST parameters. Water SA 1986;12(3):133–8. 链接1

[ 8 ] Cheng R, Feng F, Meng F, Deng C, Feijen J, Zhong Z. Glutathione-responsive nano-vehicles as a promising platform for targeted intracellular drug and gene delivery. J Control Release 2011;152(1):2–12. 链接1

[ 9 ] Hilgenbrink AR, Low PS. Folate receptor-mediated drug targeting: from therapeutics to diagnostics. J Pharm Sci 2005;94(10):2135–46. 链接1

[10] Hung A, Mwenifumbo S, Mager M, Kuna JJ, Stellacci F, Yarovsky I, et al. Ordering surfaces on the nanoscale: implications for protein adsorption. J Am Chem Soc 2011;133(5):1438–50. 链接1

[11] Kröner F, Hanke AT, Nfor BK, Pinkse MW, Verhaert PD, Ottens M, et al. Analytical characterization of complex, biotechnological feedstocks by pH gradient ion exchange chromatography for purification process development. J Chromatogr A 2013;1311:55–64. 链接1

[12] Hanke AT, Ottens M. Purifying biopharmaceuticals: knowledge-based chromatographic process development. Trends Biotechnol 2014;32 (4):210–20. 链接1

[13] Christian GK, Changani SD, Fryer PJ. The effect of adding minerals on fouling from whey protein concentrate: development of a model fouling fluid for a plate heat exchanger. Food Bioprod Process 2002;80(4):231–9. 链接1

[14] Michalski CB, Brackett RE, Hung YC, Ezeike GO. Use of capillary tubes and plate heat exchanger to validate US Department of Agriculture pasteurization protocols for elimination of Salmonella Enteritidis from liquid egg products. J Food Prot 1999;62(2):112–7. 链接1

[15] Imamura K, Kawasaki Y, Awadzu T, Sakiyama T, Nakanishi K. Contribution of acidic amino residues to the adsorption of peptides onto a stainless steel surface. J Colloid Interface Sci 2003;267(2):294–301. 链接1

[16] Sakiyama T, Aya A, Embutsu M, Imamura K, Nakanishi K. Protease susceptibility of b-lactoglobulin adsorbed on stainless steel surface as evidence of contribution of its specific segment to adsorption. J Biosci Bioeng 2006;101(5):434–9. 链接1

[17] Jimenez M, Delaplace G, Nuns N, Bellayer S, Deresmes D, Ronse G, et al. Toward the understanding of the interfacial dairy fouling deposition and growth mechanisms at a stainless steel surface: a multiscale approach. J Colloid Interface Sci 2013;404:192–200. 链接1

[18] Fickak A, Al-Raisi A, Chen XD. Effect of whey protein concentration on the fouling and cleaning of a heat transfer surface. J Food Eng 2011;104(3):323–31. 链接1

[19] Verheul M, Roefs SPFM. Structure of particulate whey protein gels: effect of NaCl concentration, pH, heating temperature, and protein composition. J Agric Food Chem 1998;46(12):4909–16. 链接1

[20] Xin H, Chen XD, Özkan N. Whey protein-based gel as a model material for studying initial cleaning mechanisms of milk fouling. J Food Sci 2002;67 (7):2702–11. 链接1

[21] Hagiwara T, Sakiyama T, Watanabe H. Molecular simulation of bovine blactoglobulin adsorbed onto a positively charged solid surface. Langmuir 2009;25(1):226–34. 链接1

[22] Tosaka R, Yamamoto H, Ohdomari I, Watanabe T. Adsorption mechanism of ribosomal protein L2 onto a silica surface: a molecular dynamics simulation study. Langmuir 2010;26(12):9950–5. 链接1

[23] Penna MJ, Mijajlovic M, Biggs MJ. Molecular-level understanding of protein adsorption at the interface between water and a strongly interacting uncharged solid surface. J Am Chem Soc 2014;136(14):5323–31. 链接1

[24] Xu W, Lan Z, Peng BL, Wen RF, Ma XH. Effect of surface free energies on the heterogeneous nucleation of water droplet: a molecular dynamics simulation approach. J Chem Phys 2015;142(5):054701. 链接1

[25] Zhang L, Bai S, Sun Y. Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. J Mol Graph Model 2011;29(7):906–14. 链接1

[26] Cassiano MM, Areas JAG. Study of bovine beta-casein at water/lipid interface by molecular modeling. J Mol Struct THEOCHEM 2001;539(1–3):279–88. 链接1

[27] Shen JW, Wu T, Wang Q, Pan HH. Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. Biomaterials 2008;29(5):513–32. 链接1

[28] Thyparambil AA. Structural bioinformatics based method for predicting the initial adsorbed protein orientation on a surface [dissertation]. Clemson: Clemson University; 2010. 链接1

[29] Rabe M, Verdes D, Seeger S. Understanding protein adsorption phenomena at solid surfaces. Adv Colloid Interface Sci 2011;162(1–2):87–106. 链接1

[30] Yu J, Becker ML, Carri GA. The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces. Langmuir 2012;28(2):1408–17. 链接1

[31] Baweja L, Balamurugan K, Subramanian V, Dhawan A. Effect of graphene oxide on the conformational transitions of amyloid beta peptide: a molecular dynamics simulation study. J Mol Graph Model 2015;61:175–85. 链接1

[32] Bromley EH, Krebs MR, Donald AM. Mechanisms of structure formation in particulate gels of b-lactoglobulin formed near the isoelectric point. Eur Phys J E Soft Matter 2006;21(2):145–52. 链接1

[33] Tooze J, Branden C. Introduction to protein structure. New York: Garland Pub; 1991. 链接1

[34] Verheul M, Roefs SPFM. Structure of whey protein gels, studied by permeability, scanning electron microscopy and rheology. Food Hydrocoll 1998;12(1):17–24. 链接1

[35] Eby DM, Johnson GR, Farmer BL, Pandey RB. Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations. Phys Chem Chem Phys 2011;13(3):1123–30. 链接1

[36] Pandey RB, Farmer BL. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation. J Chem Phys 2009;130(4):044906. 链接1

[37] Rouault Y, Milchev A. Monte Carlo study of living polymers with the bond- fluctuation method. Phys Rev E 1995;51(6):5905–10. 链接1

[38] Deutsch HP, Binder K. Interdiffusion and self-diffusion in polymer mixtures: a Monte Carlo study. J Chem Phys 1991;94(3):2294–304. 链接1

[39] Pandey RB, Farmer BL. Globular structure of a human immunodeficiency virus- 1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation. J Chem Phys 2010;132(12):125101. 链接1

[40] Pandey RB, Heinz H, Feng J, Farmer BL, Slocik JM, Drummy LF, et al. Adsorption of peptides (A3, Flg, Pd2, Pd4) on gold and palladium surfaces by a coarse-grained Monte Carlo simulation. Phys Chem Chem Phys 2009;11(12):1989–2001. 链接1

[41] Yesylevskyy SO, Schäfer LV, Sengupta D, Marrink SJ. Polarizable water model for the coarse-grained Martini force field. PLoS Comput Biol 2010;6(6): e1000810. 链接1

[42] Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. The Martini coarse-grained force field: extension to proteins. J Chem Theory Comput 2008;4(5):819–34. 链接1

[43] de Jong DH, Singh G, Bennett WF, Arnarez C, Wassenaar TA, Schäfer LV, et al. Improved parameters for the Martini coarse-grained protein force field. J Chem Theory Comput 2013;9(1):687–97. 链接1

[44] Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. The Martini force field: coarse grained model for biomolecular simulations. J Phys Chem B 2007;111(27):7812–24. 链接1

[45] Stark AC, Andrews CT, Elcock AH. Toward optimized potential functions for protein–protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the Martini coarse-grained force field. J Chem Theory Comput 2013;9(9):4176–85. 链接1

[46] Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV. Mixing Martini: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B 2013;117(13):3516–30. 链接1

[47] Gobbo C, Beurroies I, de Ridder D, Eelkema R, Marrink SJ, De Feyter S, et al. Martini model for physisorption of organic molecules on graphite. J Phys Chem C 2013;117:15623–31. 链接1

[48] López CA, Bellesia G, Redondo A, Langan P, Chundawat SP, Dale BE, et al. Martini coarse-grained model for crystalline cellulose microfibers. J Phys Chem B 2015;119(2):465–73. 链接1

[49] Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26(16):1781–802. 链接1

[50] Parrinello M, Rahman A. Crystal structure and pair potentials: a moleculardynamics study. Phys Rev Lett 1980;45:1196. 链接1

[51] Qiu R, Xiao J, Chen XD. Further understanding of the biased diffusion for peptide adsorption on uncharged solid surfaces that strongly interact with water molecules. Colloids Surf A Physicochem Eng Asp 2017;518:197–207. 链接1

[52] Sheikholeslami S, Pandey RB, Dragneva N, Floriano W, Rubel O, Barr SA, et al. Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach. J Chem Phys 2014;140(20):204901. 链接1

[53] Pandey RB, Heinz H, Feng J, Farmer BL. Biofunctionalization and immobilization of a membrane via peptide binding (CR3-1, S2) by a Monte Carlo simulation. J Chem Phys 2010;133(9):095102. 链接1

[54] Pandey RB, Farmer BL. Conformational response to solvent interaction and temperature of a protein (Histone h3.1) by a multi-grained Monte Carlo simulation. PLoS ONE 2013;8(10):e76069. 链接1

[55] Pandey RB, Farmer BL. Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials. PLoS ONE 2012;7(11):e49352. 链接1

[56] Foo GM, Pandey RB. Electro-deposition of polymer chains on an adsorbing wall: density profiles and wall coverage. J Chem Phys 1997;107(23):10260–7. 链接1

[57] Foo GM, Pandey RB. Conformation and dynamics of polymer chains on dirty surfaces: a discrete-to-continuum approach. J Chem Phys 1998;109(3):1162–9. 链接1

[58] Pandey RB, Heinz H, Farmer BL, Drummy LF, Jones SE, Vaia RA, et al. Layer of clay platelets in a peptide matrix: binding, encapsulation, and morphology. J Polym Sci B Polym Phys 2010;48(24):2566–74. 链接1

[59] Foo GM, Pandey RB. Effects of field on temperature-induced segregation and folding of polymer chains. J Chem Phys 1999;110(12): 5993–7. 链接1

[60] Pandey RB, Kuang Z, Farmer BL, Kim SS, Naik RR. Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach. Soft Matter 2012;8(35):9101–9. 链接1

[61] Pandey RB, Kuang Z, Farmer BL. A hierarchical coarse-grained (all-atom-to-allresidue) computer simulation approach: self-assembly of peptides. PLoS ONE 2013;8(8):e70847. 链接1

[62] Heinz H, Vaia RA, Farmer BL, Naik RR. Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12–6 and 9–6 Lennard-Jones potentials. J Phys Chem C 2008;112(44):17281–90. 链接1

[63] Ozboyaci M, Kokh DB, Wade RC. Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations. Phys Chem Chem Phys 2016;18(15):10191–200. 链接1

[64] King JL, Jukes TH. Non-Darwinian evolution. Science 1969;164(3881):788–98. 链接1

[65] Xiao J, Huang Y. Microstructure-property-quality-correlated paint design: an LMC-based approach. AIChE J 2009;55:132–49. 链接1

[66] Carmesin I, Kremer K. The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions. Macromolecules 1988;21(9):2819–23. 链接1

[67] Kuszewski J, Gronenborn AM, Clore GM. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J Am Chem Soc 1999;121(10):2337–8. 链接1

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