海藻糖和氨基酸之间相互作用的分子动力学模拟

doi:10.3866/PKU.WHXB201405151

物理化学学报 >> 2014, Vol. 30 >> Issue (7): 1239-1246.doi: 10.3866/PKU.WHXB201405151

海藻糖和氨基酸之间相互作用的分子动力学模拟

白姝^1,2, 常颖¹, 刘小娟¹, 刘夫锋^1,2

1. 天津大学化工学院生物工程系, 系统生物工程教育部重点实验室, 天津 300072;
2. 天津化学化工协同创新中心, 天津 300072

收稿日期:2014-03-04 修回日期:2014-05-14 发布日期:2014-06-30
通讯作者: 刘夫锋 E-mail:fufengliu@tju.edu.cn
基金资助:
国家自然科学基金（20906068）和中国博士后科学基金（2013M530115，2012T50241）资助项目

Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations

BAI Shu^1,2, CHANG Ying¹, LIU Xiao-Juan¹, LIU Fu-Feng^1,2

1. Key Laboratory of Systems Bioengineering of the Ministry of Education, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China;
2. Collaborative Innovation Center of Chemical Science and Engineering Tianjin, Tianjin 300072, P. R. China

Received:2014-03-04 Revised:2014-05-14 Published:2014-06-30
Contact: LIU Fu-Feng E-mail:fufengliu@tju.edu.cn
Supported by:
The project was supported by the National Natural Science Foundation of China (20906068) and China Postdoctoral Science Foundation (2013M530115, 2012T50241).

摘要/Abstract

摘要：

虽然海藻糖已经广泛用于蛋白质稳定性研究，但海藻糖稳定蛋白质的作用机理尚不清晰. 本文利用全原子分子动力学模拟研究了20种常见氨基酸和海藻糖之间的分子机理. 结果表明，所有氨基酸，尤其是极性和带电氨基酸，均优先与水分子结合. 相反，仅有疏水性氨基酸与海藻糖发生相互作用，尤其是芳香族和疏水性氨基酸的侧链更易于和海藻糖接触. 所有氨基酸的主链与水分子接触的趋势一致. 虽然氨基酸和海藻糖与水之间均形成氢键，但氨基酸和海藻糖之间的氢键相互作用要弱于氨基酸和水之间的氢键相互作用. 上述分子模拟的结果对于海藻糖稳定蛋白质作用机理的解析及高效蛋白质稳定剂的理性设计具有非常重要的理论指导意义.

关键词: 海藻糖, 渗透剂, 分子动力学模拟, 蛋白质稳定性, 氢键

Abstract:

Although trehalose is used as a protein stabilizer, the mechanism by which this stability is induced is not fully understood at present. In this study, we investigated the interactions between trehalose and all 20 common amino acids using all-atom molecular dynamics simulations. It is found that all the amino acids exhibit a preference for contact with water, especially the polar and charged amino acids. Conversely, only the hydrophobic amino acids were found to have a slight preference for contact with trehalose molecules. This tendency is most pronounced in the case of contact between trehalose and aromatic or hydrophobic side chains, whereas the backbones of each amino acids all show similar propensities for contact with water. Furthermore, hydrogen bonds between amino acids and trehalose were found to be significantly weaker than those between amino acids and water, although both trehalose and water can interact with the amino acids via hydrogen bonds. These findings are important with regard to the exploration of the molecular mechanism of protein stability induced by trehalose and the rational design of highly efficient protein stabilizers.

Key words: Trehalose, Osmolyte, Molecular dynamics simulation, Protein stability, Hydrogen bond

MSC2000:

O641

白姝, 常颖, 刘小娟, 刘夫锋. 海藻糖和氨基酸之间相互作用的分子动力学模拟[J]. 物理化学学报, 2014, 30(7): 1239-1246.

BAI Shu, CHANG Ying, LIU Xiao-Juan, LIU Fu-Feng. Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations[J]. Acta Phys. -Chim. Sin., 2014, 30(7): 1239-1246.

参考文献

(1) Richards, A. B.; Krakowka, S.; Dexter, L. B.; Schmid, H.; Wolterbeek, A. P.;Waalkens-Berendsen, D. H.; Shigoyuki, A.; Kurimoto, M. Food Chem. Toxicol. 2002, 40, 871. doi: 10.1016/S0278-6915(02)00011-X
(2) Singer, M. A.; Lindquist, S. Trends Biotechnol. 1998, 16, 460. doi: 10.1016/S0167-7799(98)01251-7
(3) Crowe, J. H.; Crowe, L. M.; Carpenter, J. F.;Wistrom, A. C. Biochem. J. 1987, 242, 1.
(4) Ohtake, S.;Wang, Y. J. J. Pharm. Sci. 2011, 100, 2020. doi: 10.1002/jps.22458
(5) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2012, 116, 7040. doi: 10.1021/jp300171h
(6) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. Biochem. Eng. J. 2013, 70, 188. doi: 10.1016/j.bej.2012.11.004
(7) Liu, F. F.; Ji, L.; Zhang, L.; Dong, X. Y.; Sun, Y. J. Chem. Phys. 2010, 132, 225103. doi: 10.1063/1.3453713
(8) Liu, F. F.; Ji, L.; Dong, X. Y. Acta Phys. -Chim. Sin. 2010, 26, 2813. [刘夫锋, 纪络, 董晓燕. 物理化学学报, 2010, 26, 2813.]
(9) Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y. Biochem. Eng. J. 2013, 79, 120. doi: 10.1016/j.bej.2013.07.007
(10) Dong, X. Y.; Liu, J. H.; Liu, F. F.; Sun, Y. Biochem. Eng. J. 2009, 43, 321. doi: 10.1016/j.bej.2008.10.015
(11) Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y. J. Phys. Chem. B 2009, 113, 11320. doi: 10.1021/jp905580j
(12) Liu, F. F.; Dong, X. Y.; Sun, Y. Acta Phys. -Chim. Sin. 2010, 26, 1643. [刘夫锋, 董晓燕, 孙彦. 物理化学学报, 2010, 26, 1643.]
(13) Bolen, D.W.; Rose, G. D. Annu. Rev. Biochem. 2008, 77, 339. doi: 10.1146/annurev.biochem.77.061306.131357
(14) Lins, R. D.; Pereira, C. S.; Hunenberger, P. H. Proteins 2004, 55, 177. doi: 10.1002/prot.10632
(15) Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton,W. A. Science 1992, 256, 1796. doi: 10.1126/science.1615323
(16) Allison, S. D.; Chang, B.; Randolph, T.W.; Carpenter, J. F. Arch. Biochem. Biophys. 1999, 365, 289. doi: 10.1006/abbi.1999.1175
(17) Lins, R. D.; Hunenberger, P. H. J. Comput. Chem. 2005, 26, 1400. doi: 10.1002/jcc.20275
(18) Liu, F. F.; Dong, X. Y.; Sun, Y. J. Mol. Graph. Model. 2008, 27, 421. doi: 10.1016/j.jmgm.2008.07.002
(19) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. doi: 10.1021/ct700301q
(20) Berendsen, H. J. C.; Postma, J. P. M.; van gunsteren,W. F.; Hermans, J. In Intermolecular Forces; Pullman, B. Ed.; Reidel: Dordecht, Holland, 1981; pp 331.
(21) van gunsteren,W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Mark, A. E.; Scott,W. R. P.; Tironi, I. G. Biomolecular Simulation : The GROMOS96 Manual and User Guide; Zurich: Groninigen, 1996.
(22) Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463. doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
(23) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. doi: 10.1063/1.464397
(24) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren,W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. doi: 10.1063/1.448118
(25) Liu, F. F.; Dong, X. Y.;Wang, T.; Sun, Y. J. Chromatogr. A 2007, 1175, 249. doi: 10.1016/j.chroma.2007.10.074
(26) Stumpe, M. C.; Grubmuller, H. J. Am. Chem. Soc. 2007, 129, 16126. doi: 10.1021/ja076216j
(27) Sheu, S. Y.; Yang, D. Y.; Selzle, H. L.; Schlag, E.W. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 12683. doi: 10.1073/ pnas.2133366100
(28) Jenkins, S.; Morrison, I. Chem. Phys. Lett. 2000, 317, 97. doi: 10.1016/S0009-2614(99)01306-8
(29) Li,W.; Qin, M.; Tie, Z.;Wang,W. Phys. Rev. E 2011, 84, 041933. doi: 10.1103/PhysRevE.84.041933
(30) Li,W.; Zhang, J.;Wang, J.;Wang,W. J. Am. Chem. Soc. 2008, 130, 892. doi: 10.1021/ja075302g
(31) Lei, H.; Duan, Y. Curr. Opin. Struct. Biol. 2007, 17, 187. doi: 10.1016/j.sbi.2007.03.003

[1]	胡媛媛,王从洋. 双金属促进的均相碳氢键活化反应[J]. 物理化学学报, 2019, 35(9): 913 -922 .
[2]	朱月路,赵鑫阳,吴谦,陈颖,赵劲. 多功能氧酰胺导向基在碳氢键活化反应中的研究进展[J]. 物理化学学报, 2019, 35(9): 989 -1004 .
[3]	王庆兵,郭政伟,陈弓,何刚. 1, 1'-双(二苯基膦基)二茂铁介导的芳烃碳氢键芳基化反应制备联芳基骨架[J]. 物理化学学报, 2019, 35(9): 1021 -1026 .
[4]	张涛,仇运广,罗启超,程曦,赵丽芬,严昕,彭浡,蒋华良,阳怀宇. 钙离子和镁离子浓度变化对磷脂酰乙醇胺-磷脂酰甘油双分子层膜的影响[J]. 物理化学学报, 2019, 35(8): 840 -849 .
[5]	许谢君,肖兴庆,徐首红,刘洪来. 亮氨酸拉链型脂肽对脂质体温敏性调节的分子模拟[J]. 物理化学学报, 2019, 35(6): 598 -606 .
[6]	潘明光,赵永升,曾小勤,邹建新. 偶氮苯基型离子液体溶液对空气中湿度的变色响应[J]. 物理化学学报, 2019, 35(6): 624 -629 .
[7]	陈雯慧,陈胜利. 墨水溶剂对低铂含量质子交换膜燃料电池性能的影响[J]. 物理化学学报, 2019, 35(5): 517 -522 .
[8]	吕康杰,彭燕秋,肖丽,陆君涛,庄林. 醇/水混合溶剂中碱性聚合物电解质独特的溶解行为[J]. 物理化学学报, 2019, 35(4): 378 -384 .
[9]	杨化超,薄拯,帅骁睿,严建华,岑可法. 润湿特性对超级电容器储能动力学的影响机理[J]. 物理化学学报, 2019, 35(2): 200 -207 .
[10]	陈文君,薛智敏,王晋芳,蒋静云,赵新辉,牟天成. 低共熔溶剂的热稳定性研究[J]. 物理化学学报, 2018, 34(8): 904 -911 .
[11]	陈文琼,关永吉,张晓萍,邓友全. 分子动力学模拟研究外电场对咪唑类离子液体振动谱的影响[J]. 物理化学学报, 2018, 34(8): 912 -919 .
[12]	侯玉翠,么聪菲,吴卫泽. 低共熔溶剂：一种应用在混合物分离过程中的绿色溶剂[J]. 物理化学学报, 2018, 34(8): 873 -885 .
[13]	刘夫锋,范玉波,刘珍,白姝. Z_Aβ3和A_β16-40亲和作用的分子机理解析[J]. 物理化学学报, 2017, 33(9): 1905 -1914 .
[14]	王子民,郑默,谢勇冰,李晓霞,曾鸣,曹宏斌,郭力. 基于ReaxFF力场的对硝基苯酚臭氧氧化分子动力学模拟[J]. 物理化学学报, 2017, 33(7): 1399 -1410 .
[15]	曹了然,张春煜,张鼎林,楚慧郢,张跃斌,李国辉. 分子动力学模拟技术在生物分子研究中的进展[J]. 物理化学学报, 2017, 33(7): 1354 -1365 .

海藻糖和氨基酸之间相互作用的分子动力学模拟

Interactions between Trehalose and Amino Acids by Molecular Dynamics Simulations

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

本文评价

推荐阅读 10