目的 研究单克隆抗体依那西普融合蛋白二聚体在不同状态下的动力学稳定性和热力学稳定性,为其活性保护的研究奠定基础。方法 利用Gromacs 4.6分子模拟软件和Amber99sb-ildn分子力场以及拉伸模拟和伞状采样的方法,获取依那西普抗体蛋白的解离自由能和解离拉力的变化。结果 研究结果表明,依那西普抗体蛋白在真空中的解离自由能是在水溶液中的10.05倍,其在真空中解离的平均作用力是在水溶液中的3.03倍。溶剂化环境对于抗体蛋白的稳定性具有显著的影响,而真空冷冻干燥可以提高其结构的稳定性。结论 拉伸模拟过程中,最大拉力简单易得,且影响因素少,可以用最大拉力表征抗体蛋白二聚体的活性结构稳定性。
Abstract
OBJECTIVE To investigate the stability of etanercept in vacuum and water to lay foundation for study on its bioactiveprotection. METHODS Umbrella sampling and steered molecular dynamics simulation aqueous solution adopted to study the dissociation process of dimer etanercept with Gromacs software and amber99sb-ildn force field. RESULTS Potential of mean forcel(PMF) free energy of etanercept dissociation in vacuum was approximately three times of that in aqueous solution. And the maximum barrier force of etanercept dissociation in vacuum was approximately ten times of that in aqueous solution. The solvation environment had effect on the stability of antibody protein. Freeze-drying in vacuum could improve the stability of antibody protein. CONCLUSION In the process of steered molecular dynamics simulation, the pulling force can be got easily and is less affected by other factors, which can be used to characterize the stability of active structure of antibody protein dimer.
关键词
拉伸模拟 /
伞状采样 /
依那西普 /
活性结构稳定性 /
自由能
{{custom_keyword}} /
Key words
steered molecular dynamic;umbrella sampling /
active structure stability /
etanercept /
potential of mean forcel
{{custom_keyword}} /
中图分类号：
R944
{{custom_clc.code}}
({{custom_clc.text}})
{{custom_sec.title}}
{{custom_sec.title}}
{{custom_sec.content}}
参考文献
[1] SHEN L L, SHEN J H, LUO X M, et al. Steered molecular dynamics simulation on the binding of NNRTI to HIV-1 RT[J]. Biophys J, 2003, 84(6):3547-3563.
[2] SCHMIDT R K, TEO B, BRADY J W. Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamic simulations[J]. J Phys Chem, 1995, 99 (29):11339-11343.
[3] SOUAILLE M, ROUX B. Extension to the weighted histogram analysis method:combining umbrella sampling with free energy calculations [J]. Comput Phys Commun, 2001, 135(1):40-57.
[4] SHANKAR K, ROSENBERG J M, DJAMAL B, et al. The weighted histogram analysis method for free energy calculation on biomolecules [J]. J Comput Chem, 1992, 13(8):1011-1021.
[5] MEASE P J, GOFFE B S, METZ J, et al. Etanercept in the treatment of psoriatic arthritis and psoriasis:a randomised trial [J]. Lancent, 2000, 356(9227):385-389.
[6] HEIJDE D V D, SILVA J C D, DOUGADOS M, et al. Etanercept 50 mg once weekly is as effective as 25 mg twice weekly in patients with ankylosing spondylitis [J]. Ann Rheum Dis, 2006, 65(12):1572-1577.
[7] WONG M, ZIRING D, KORIN Y, et al. TNF-α blockade in human diseases:mechanisms and future directions[J]. Clin Immunol, 2008, 126(2):121-136.
[8] GOFFE B, CATHER J C. Etanercept:an overview [J]. J Am Acad Dermatol, 2003, 49(2):105-111.
[9] VAN D S D, LINDAHL E, HESS B, et al. GROMACS:fast, flexible, and free[J]. J Comput Chem, 2005, 26(16):1701-1718.
[10] KRESTEN L, STEFANO P, KIM P. Improved side-chain torsion potential for the Amber ff99SB protein force field[J]. Proteins, 2010, 78(8):1950-1958.
[11] PRICE D, BROOKS C L. A modified TIP3P water potential for simulation with Ewald summation[J]. J Phys Chem, 2004, 121(20):10096-10103.
[12] BATCHO P F, CASE D A, SCHLICK T. Optimized paticle-mesh ewald/multipul-time step integration for molecular dynamics simulations[J]. J Chem Phys, 115(9):4003-4018.
[13] HESS B. P-LINCS:a parallel linear constraint solver for molecular simulation[J]. J Chem Theory Comput, 2007, 4(1):116-122.
[14] ANDERSEN H C. Molecular dynamics simulation at constant pressure and temperature [J]. J Chem Phys, 1980, 72(4):2384-2393.
[15] BUSSI G, DONADIO D, PARRINNELLO M. Canonical sampling through velocity rescaling[J]. J Chem Phys, 2007, 126(1):14101-14107.
[16] BEREBDSEN H J C, POSTMA J M P, GUNSTEREN W F, et al. Molecular dynamic with coupling to an external bath[J]. J Chem Phys, 1984, 81(8):3684-3690.
[17] NILGES M, CLORE G M, GRONENBORN A M. Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing calculation [J]. Febs Lett, 1988, 229(2):129-136.
[18] XU Y C, SHEN J H, LUO X M, et al. Simulating ligand-receptor interaction by steered molecular dynamics [J]. Sci Sin(Chimica)(中国科学 B辑化学), 2004, 34(3):177-187.
[19] PARK S, SCHULTEN K. Calculating potential of mean force from steered molecular dynamics simulation[J]. J Chem Phys, 2004, 120(13):5946-5961.
[20] YUAN Z, SAGUI C. Secondary structure assignment for conformationally irregular peptides:comparision between DSSP, STRIDE and KAKSI[J]. J Mol Graph Model, 2015, 55(1):72-84.
[21] OUALI M, KING R D. Cascaded multiple classifiers for secondary structure prediction[J]. Protein Sci, 2000, 9(6):1162-1176.
[22] KUMAR V, SHARMA V K, KALONIA D S. In situ precipitation and vacuum drying of interferon alpha-2a:development of a single-step process for obtaining dry, stable protein formulation[J]. Int J Pharm, 2009, 366(1-2):88-98.
{{custom_fnGroup.title_cn}}
脚注
{{custom_fn.content}}
基金
国家自然科学基金资助项目(51076108); 上海市重点学科资助项目(T0503,P0502);上海市自然科学基金资助项目(12ZR1420400);上海市“创新行动计划”国际科技合作资助项目(12430702000);上海市联盟计划项目和上海理工大学人文社会科学基金资助项目(14YZ092)
{{custom_fund}}
PDF(1733 KB)
