Replica Exchange Molecular Dynamics Simulations on the Folding of Trpzip4 β-Hairpin

doi:10.6023/A13010015

Acta Chimica Sinica ›› 2013, Vol. 71 ›› Issue (04): 593-601.DOI: 10.6023/A13010015 Previous Articles Next Articles

Article

β发卡多肽Trpzip4折叠的副本交换分子动力学模拟

廖晨伊, 周健

华南理工大学化学与化工学院广东省绿色化学产品技术重点实验室广州 510640

投稿日期:2013-01-04 发布日期:2013-03-01
通讯作者: 周健 E-mail:jianzhou@scut.edu.cn
基金资助:
项目受教育部新世纪优秀人才支持计划(No. NCET-07-0313)、国家自然科学基金(No. 20876052)及广东省自然科学基金(No. S2011010002078)资助.

Replica Exchange Molecular Dynamics Simulations on the Folding of Trpzip4 β-Hairpin

Liao Chenyi, Zhou Jian

School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640

Received:2013-01-04 Published:2013-03-01
Supported by:
Project supported by the Program for New Century Excellent Talents in Universities, Ministry of Education, China (No. NCET-07-0313), the National Natural Science Foundation of China (No. 20876052) and the Natural Science Foundation of Guangdong Province(No. S2011010002078).

β-Hairpin is an essential secondary structure unit of protein. Understanding the formation mechanism of the β hairpin and kinetic stability helps to gain insight into the formation of protein secondary structure as well as the mechanism of protein folding. Replica exchange molecular dynamics (REMD) approach is applied to investigate the folding mechanism of Trpzip4 β-hairpin. The REMD method is more efficient than conventional MD in searching for a representative set of the low energy minima in the existence of a large energy gap between the native state and any of the other possible state. The potential energy, backbone RMSD and solvent-accessible surface area (SASA) present descending trends in the process of REMD at 288 K. Methyl groups (most in threonines) show hydrophobic interactions with SASA decrements. The hydrophobic interactions and intra hydrogen bond forming drive the folding and maintain the low energy structure. Two low energy structures, β-hairpin and helix-coil conformation, are sampled by REMD. In β-hairpin structure, the hydroxyl group (OH) of Thr49 at β turn is accessible to form hydrogen bonds with carboxyl group (COO^-) or C＝O group of Asp46; while the hydroxyl group (OH) of Thr51 is inclined to interact with water molecule with methyl orienting inwards. As a result, the strong interactions between Asp46 and Thr49 cause a bend at β turn. In helix-coil conformation, hydrophobic interactions play between indole ring and methyl group. One of the zip-in paths of Trpzip4 indicates that, the forming of hydrogen bonds at β turn affects the whole folding process of β hairpin. The forming of hydrogen bonds at β turn takes place first, since it has advantages of distance and strong interactions in both side chains and backbone. Total solvent-accessible surface area decreases significantly as it folds to the β hairpin structure. REMD method could sample large phase space for the low energy minima, and present scenarios of potential energy distribution on phase space with related variables as hydrophobic SASA, backbone RMSD, and hydrogen bonds for specific conformation. This work sheds some lights on the understanding of β hairpin folding.

Key words: β-hairpin, folding, replica exchange molecular dynamics, hydrogen bond, hydrophobic interaction

Cite this article

Liao Chenyi, Zhou Jian. Replica Exchange Molecular Dynamics Simulations on the Folding of Trpzip4 β-Hairpin[J]. Acta Chimica Sinica, 2013, 71(04): 593-601.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

References

[1] Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins 1995, 21, 167.

[2] Karplus, M.; Šali, A. Curr. Opin. Struct. Biol. 1995, 5, 58.

[3] Bian, L.; Yang, X.; Liu, L. Acta Chim. Sinica 2005, 63, 1081. (边六交, 杨晓燕, 刘莉, 化学学报, 2005, 63, 1081.)

[4] Yang, F.; Liang, Y.; Yang, F. J. Acta Chim. Sinica 2003, 61, 803 (杨芳, 梁毅, 杨芳(小), 化学学报, 2003, 61, 803.)

[5] Zhou, J.; Thorpe, I. F.; Izvekov, S.; Voth, G. A. Biophys. J. 2007, 92, 4289.

[6] Thorpe, I. F.; Zhou, J.; Voth, G. A. J. Phys. Chem. B 2008, 112, 13079.

[7] Dobson, C. M. Nature 2003, 426, 884.

[8] Hansmann, U. H. E. Chem. Phys. Lett. 1997, 281, 140.

[9] Kinnear, B. S.; Jarrold, M. F.; Hansmann, U. H. E. J. Mol. Graphics Modell. 2004, 22, 397.

[10] Hansmann, U. H. E. J. Chem. Phys. 2004, 120, 417.

[11] Hansmann, U. H. E.; Wille, L. T. Phys. Rev. Lett. 2002, 88, 68105.

[12] Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141.

[13] Zhang, J.; Qin, M.; Wang, W. Proteins: Struct., Funct., Bioinf. 2006, 62, 672.

[14] Munoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196.

[15] Chen, C.; Xiao, Y. Bioinformatics 2008, 24, 659.

[16] Zhou, R. Methods Mol. Biol. 2006, 350, 205.

[17] Xie, Y.; Zhou, J.; Jiang, S. Y. J. Chem. Phys. 2010, 132, 065101.

[18] Earl, D. J.; Deem, M. W. Phys. Chem. Chem. Phys. 2005, 7, 3910.

[19] Zhou, R.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 14931.

[20] Zhou, R. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 13280.

[21] Zhou, R. J. Mol. Graphics Modell. 2004, 22, 451.

[22] Haliloglu, T.; Kolinski, A.; Skolnick, J. Biopolymers 2003, 70, 548.

[23] Chen, J.; Won, H. S.; Im, W.; Dyson, H. J.; Brooks, C. L. J. Biomol. NMR. 2005, 31, 59.

[24] La Penna, G.; Mitsutake, A.; Masuya, M.; Okamoto, Y. Chem. Phys. Lett. 2003, 380, 609.

[25] Vreede, J.; Crielaard, W.; Hellingwerf, K. J.; Bolhuis, P. G. Biophys. J. 2005, 88, 3525.

[26] Jas, G. S.; Kuczera, K. Biophys. J. 2004, 87, 3786.

[27] Gnanakaran, S.; Hochstrasser, R. M.; García, A. E. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 9229.

[28] Antoine, R.; Compagnon, I.; Rayane, D.; Broyer, M.; Dugourd, P.; Breaux, G.; Hagemeister, F. C.; Pippen, D.; Hudgins, R. R.; Jarrold, M. F. J. Am. Chem. Soc. 2002, 124, 6737.

[29] Chebaro, Y.; Mousseau, N.; Derreumaux, P. J. Phys. Chem. B 2009, 113, 7668.

[30] Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A. J. Chem. Phys. 2004, 121, 10748.

[31] Lu, Y.; Wei, G.; Derreumaux, P. J. Phys. Chem. B 2011, 115, 1282.

[32] Cochran, A. G.; Skelton, N. J.; Starovasnik, M. A. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 5578.

[33] Du, D.; Zhu, Y.; Huang, C. Y.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15915.

[34] Juraszek, J. Ph.D. Dissertation, University of Amsterdam, Amsterdam, 2008.

[35] Olsen, K. A.; Fesinmeyer, R. M.; Stewart, J. M.; Andersen, N. H. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15483.

[36] Wei, H.; Shao, Q.; Gao, Y. Q. Phys. Chem. Chem. Phys. 2010, 12, 9292.

[37] Rathore, N.; Chopra, M.; De Pablo, J. J. J. Chem. Phys. 2005, 122, 024111.

[38] Rao, F.; Caflisch, A. J. Chem. Phys. 2003, 119, 4035.

[39] Zhang, W.; Wu, C.; Duan, Y. J. Chem. Phys. 2005, 123, 154105.

[40] Sindhikara, D.; Meng, Y.; Roitberg, A. E. J. Chem. Phys. 2008, 128, 024103.

[41] Sindhikara, D. J.; Emerson, D. J.; Roitberg, A. E. J. Chem. Theory Comput. 2010, 6, 2804.

[42] Katzgraber, H. G.; Trebst, S.; Huse, D. A.; Troyer, M. J. Stat. Mech.: Theory Exp. 2006, 2006, P03018.

[43] van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual, version 4.5, 2010, www.gromacs.org.

[44] Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.

[45] Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.

[46] Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. J. Chem. Phys. 1984, 81, 3684.

[47] Shaytan, A. K.; Shaitan, K. V.; Khokhlov, A. R. Biomacromolecules 2009, 10, 1224.

[48] Marsh, J. A.; Teichmann, S. A. Structure 2011, 19, 859.

[49] Lins, L.; Thomas, A.; Brasseur, R. Protein Sci. 2003, 12, 1406.

[50] Periole, X.; Mark, A. E. J. Chem. Phys. 2007, 126, 014903.

[51] Jang, S.; Kim, E.; Pak, Y. Proteins 2007, 66, 53.

[52] Blanco, F. J.; Rivas, G.; Serrano, L. Nat. Struct. Mol. Biol. 1994, 1, 584. Zagrovic, B.; Sorin, E. J.; Pande, V. J. Mol. Biol. 2001, 313, 151.

β发卡多肽Trpzip4折叠的副本交换分子动力学模拟

Replica Exchange Molecular Dynamics Simulations on the Folding of Trpzip4 β-Hairpin

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Xiaomao Tian, Yuequn Lin, Han Zhu, Chao Huang, Bixue Zhu. Enantiomers Identification of Penicillamine by Chiral Mono-Schiff Base Macrocycles [J]. Acta Chimica Sinica, 2023, 81(1): 20-28.
[2]	Hao Yin, Xitong Chen, Xingyan Fu, Yannan Ma, Yimei Xu, Te Zhang, Shuai Liang, Shanshan Du, Yunkun Qi, Kewei Wang. Efficient Chemical Synthesis and Oxidative Folding Studies of Scorpion Toxin Peptide WaTx [J]. Acta Chimica Sinica, 2022, 80(4): 444-452.
[3]	Chuanzhi Liu, Fen Li, Jingjing Wang, Xiaolu Zhao, Tingmei Zhang, Xin Huang, Mengli Wu, Zhiyuan Hu, Xinming Liu, Zhanting Li. Self-assembly of Supramolecular Planar Macrocycle Driven by Intermolecular Halogen Bonding [J]. Acta Chimica Sinica, 2022, 80(10): 1365-1368.
[4]	Lin Zu-Jin, Cao Rong. Porous Hydrogen-bonded Organic Frameworks (HOFs): Status and Challenges [J]. Acta Chimica Sinica, 2020, 78(12): 1309-1335.
[5]	Qin Xiaozhuan, Wang Xinchao, Feng Dandan, He Jiabei, Zheng Liping, Wang Yong, Xie Guanghui, Li Jingjing, Ding Ge. Study on Properties of Excited-state Intermolecular Proton Transfer (ESPT) Reaction Dendrite Containing Benzidine Fragments of Organic Chromophore [J]. Acta Chim. Sinica, 2019, 77(8): 751-757.
[6]	Zhu Xuewei, Cui Xiaoyu, Cai Wensheng, Shao Xueguang. Temperature Dependent Near Infrared Spectroscopy for Understanding the Hydrogen Bonding of Amines [J]. Acta Chim. Sinica, 2018, 76(4): 298-302.
[7]	Zhang Yu-Jian, Xie Bin, Jiang Tao. Preparation and Properties of Crown Ethers Containing Amphiphilic Copolymer Nano-aggregates [J]. Acta Chim. Sinica, 2016, 74(9): 752-757.
[8]	Zhao Qing, Qi Boyu, Wang Baojin, Chen Feiwu. Theoretical Investigation on Weak Interactions of HXeBr with Benzene and Its Derivatives [J]. Acta Chim. Sinica, 2016, 74(3): 285-292.
[9]	Zong Qianying, Geng Huimin, Wang Lu, Ye Lin, Zhang Aiying, Shao Ziqiang, Feng Zengguo. A Study on Synthesis and Gelation Capability of Fmoc and Boc Disubstituted Cyclo(L-Lys-L-Lys)s [J]. Acta Chim. Sinica, 2015, 73(5): 423-430.
[10]	Zhang Qi, Fang Hongxia, Zhang Huili, Qin Dan, Hong Zhi, Du Yong. Co-crystal between Nitrofurantion and Urea Investigated by Terahertz Spectroscopy and Density Functional Theory [J]. Acta Chim. Sinica, 2015, 73(10): 1069-1073.
[11]	Zhang Qianhui, Wang Yang, Liu Cui, Yang Zhongzhi. Investigation of Base Pairs Containing 7,8-Dihydro-8-oxoguanine by Quantum Chemistry [J]. Acta Chimica Sinica, 2014, 72(8): 956-962.
[12]	Wang Xinhua, Feng Li, Cao Zexing. Structure, Energetics and Vibrational Frequency Shifts of Water Molecules Confined Inside Single-walled Carbon Nanotubes：A DFT Study [J]. Acta Chimica Sinica, 2014, 72(4): 487-494.
[13]	Du Le, Cao Peng, Liao Jian. Bifunctional Ligand Promoted Pd-Catalyzed Asymmetric Allylic Etherification/Amination [J]. Acta Chimica Sinica, 2013, 71(9): 1239-1242.
[14]	Zhang Chao, Wang Xing, Song Xiliang, Song Kaihui, Qian Ping, Yin Hongzong. Quantum Chemical Study of Intercalation of Hydrazine Hydrate in Kaolinite [J]. Acta Chimica Sinica, 2013, 71(11): 1553-1562.
[15]	Wang Xinhua, Feng Li, Cao Zexing, Liu Xiangchun, Tang Haiyan, Zhang Man. Theoretical Study of Substituent Effects on Bond Dissociation Enthalpies in Lignite Model Compounds [J]. Acta Chimica Sinica, 2013, 71(07): 1047-1052.