Please wait a minute...
Chin. Phys. B, 2016, Vol. 25(12): 128704    DOI: 10.1088/1674-1056/25/12/128704

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

Li Deng(邓礼)1, Yurong Zhao(赵玉荣)1, Peng Zhou(周鹏)1, Hai Xu(徐海)1, Yanting Wang(王延颋)2,3
1. Center for Bioengineering and Biotechnology, China University of Petroleum(East China), Qingdao 266580, China;
2. CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences(CAS), Beijing 100190, China;
3. School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China

Besides our previous experimental discovery (Zhao Y R, et al. 2015 Langmuir, 31, 12975) that acetonitrile (ACN) can tune the morphological features of nanostructures self-assembled by short peptides KⅢIK (KI4K) in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding (H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations.

Keywords:  solvent effect      peptide self-assembly      molecular dynamics simulation  
Received:  14 September 2016      Revised:  18 October 2016      Accepted manuscript online: 
PACS:  87.10.Tf (Molecular dynamics simulation)  
  87.14.ef (Peptides)  
  87.15.bk (Structure of aggregates)  

Project supported by the National Basic Research Program of China (Grant No. 2013CB932804), the National Natural Science Foundation of China (Grant Nos. 91227115, 11421063, 11504431, and 21503275), the Fundamental Research Funds for Central Universities of China (Grant No. 15CX02025A), and the Application Research Foundation for Post-doctoral Scientists of Qingdao City, China (Grant No. T1404096).

Corresponding Authors:  Hai Xu, Yanting Wang     E-mail:;

Cite this article: 

Li Deng(邓礼), Yurong Zhao(赵玉荣), Peng Zhou(周鹏), Hai Xu(徐海), Yanting Wang(王延颋) Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution 2016 Chin. Phys. B 25 128704

[1] Ulijn R V and Smith A M 2008 Chem. Soc. Rev. 37 664
[2] Chiti F and Dobson C M 2009 Nat. Chem. Biol. 5 15
[3] Caughey B and Lansbury P T 2003 Ann. Rev. Neurosci. 26 267
[4] Dobson C M 2003 Nature 426 884
[5] Nyrkova I, Semenov A N, Aggeli A, Bell M, Boden N and McLeish T C 2000 Eur. Phys. J. B 17 499
[6] Nelson R, Sawaya M R, Balbirnie M, Madsen A O, Riekel C, Grothe R and Eisenberg D 2005 Nature 435 773
[7] Sawaya M R, Sambashivan S, Nelson R, Ivanova M I, Sievers S A, Apostol M I, Thompson M J, Balbirnie M, Wiltzius J J W, McFarlane H T, Madsen A O, Riekel C and Eisenberg D 2007 Nature 447 453
[8] Ghadiri M R, Granja J R, Milligan R A, McRee D E and Khazanovich N 1993 Nature 366 324
[9] Deechongkit S, Powers E T, You S L and Kelly J W 2005 J. Am. Chem. Soc. 127 8562
[10] Scanlon S and Aggeli A 2008 Nano Today 3 22
[11] Adamcik J, Castelletto V, Bolisetty S, Hamley I W and Mezzenga R 2011 Angew. Chem. Int. Ed. 50 5495
[12] Baldwin R L and Rose G D 1999 Trends Biochem. Sci. 24 26
[13] Baldwin R L and Rose G D 1999 Trends Biochem. Sci. 24 77
[14] Nyrkova I, Semenov A N, Aggeli A and Boden N 2000 Eur. Phys. J. B 17 481
[15] Aggeli A, Nyrkova I A, Bell M, Harding R, Carrick L, McLeish T C B, Semenov A N and Boden N 2001 Proc. Natl. Acad. Sci. USA 98 11857
[16] Lu K, Jacob J, Thiyagarajan P, Conticello V P and Lynn D G 2003 J. Am. Chem. Soc. 125 6391
[17] Lamm M S, Rajagopal K, Schneider J P and Pochan D J 2005 J. Am. Chem. Soc. 127 16692
[18] Pashuck E T and Stupp S I 2010 J. Am. Chem. Soc. 132 8819
[19] Ziserman L, Lee H Y, Raghavan S R, Mor A and Danino D 2011 J. Am. Chem. Soc. 133 2511
[20] Childers W S, Anthony N R, Mehta A K, Berland K M and Lynn D G 2012 Langmuir 28 6386
[21] Whitesides G M and Grzybowski B 2002 Science 295 2418
[22] Knowles T P, Fitzpatrick A W, Meehan S, Mott H R, Vendruscolo M, Dobson C M and Welland M E 2007 Science 318 1900
[23] Bowerman C J, Ryan D M, Nissan D A and Nilsson B L 2009 Mol. Biosyst. 5 1058
[24] Xu H, Wang J, Han S Y, Wang J Q, Yu D Y, Zhang H Y, Xia D H, Zhao X B, Waigh T A and Lu J R 2009 Langmuir 25 4115
[25] Lee N R, Bowerman C J and Nilsson B L 2013 Biomacromolecules 14 3267
[26] Mehta A K, Lu K, Childers W S, Liang Y, Dublin S N, Dong J J, Snyder J P, Pingali S V, Thiyagarajan P and Lynn D G 2008 J. Am. Chem. Soc. 130 9829
[27] Adamcik J and Mezzenga R 2011 Soft Matter 7 5437
[28] Jordens S, Adamcik J, Amar-Yuli I and Mezzenga R 2011 Biomacromolecules 12 187
[29] Castelletto V, Hamley I W, Harris P J F, Olsson U and Spencer N 2009 J. Phys. Chem. B 113 9978
[30] Hua L, Zhou R H, Thirumalai D and Berne B J 2008 Proc. Natl. Acad. Sci. USA 105 16928
[31] Hwang S, Shao Q, Williams H, Hilty C and Gao Y Q 2011 J. Phys. Chem. B 115 6653
[32] Shao Q, Fan Y B, Yang L J and Gao Y Q 2012 J. Chem. Phys. 136 115101
[33] Candotti M, Esteban-Martin S, Salvatella X and Orozco M 2013 Proc. Natl. Acad. Sci. USA 110 5933
[34] Xu W X, Ping J, Li W F and Mu Y G 2009 J. Chem. Phys. 130
[35] Emamyari S and Fazli H 2014 Eur. Biophys. J. Biophy 43 143
[36] Wei G H and Shea J E 2006 Biophys. J. 91 1638
[37] Yang C, Li J Y, Li Y and Zhu X L 2009 J. Mol. Structure-theochem 895 1
[38] Li W F, Qin M, Tie Z X and Wang W 2011 Phys. Rev. E 84 041933
[39] Klimov D K, Straub J E and Thirumalai D 2004 Proc. Natl. Acad. Sci. U.S.A. 101 14760
[40] Rissanou A N, Georgilis E, Kasotaids E, Mitraki A and Harmandaris V 2013 J. Phys. Chem. B 117 3962
[41] Zhao Y R, Deng L, Wang J Q, Xu H and Lu J R 2015 Langmuir 31 12975
[42] Buchanan L E, Dunkelberger E B, Tran H Q, Cheng P N, Chiu C C, Cao P, Raleigh D P, de Pablo J J, Nowick J S and Zanni M T 2013 Proc. Natl. Acad. Sci. USA 110 19285
[43] Krone M G, Hua L, Soto P, Zhou R H, Berne B J and Shea J E 2008 J. Am. Chem. Soc. 130 11066
[44] Jose J C, Khatua P, Bansal N, Sengupta N and Bandyopadhyay S 2014 J. Phys. Chem. B 118 11591
[45] Fitzpatrick A W P, Debelouchina G T, Bayro M J, Clare D K, Caporini M A, Bajaj V S, Jaroniec C P, Wang L C, Ladizhansky V, Muller S A, MacPhee C E, Waudby C A, Mott H R, De Simone A, Knowles T P J, Saibil H R, Vendruscolo M, Orlova E V, Griffin R G and Dobson C M 2013 Proc. Natl. Acad. Sci. USA 110 5468
[46] Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A E and Berendsen H J C 2005 J. Comput. Chem. 26 1701
[47] Jorgensen W L, Maxwell D S and Titado-Rives J 1996 J. Am. Chem. Soc. 118 11225
[48] Jorgensen W L and Tirado-Rives J 2005 Proc. Natl. Acad. Sci. USA 102 6665
[49] Caleman C, van Maaren P J, Hong M Y, Hub J S, Costa L T and van der Spoel D 2012 J. Chem. Theory Comput. 8 61
[50] Jorgensen W L, William L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 J. Chem. Phys. 79 926
[51] Deng L, Zhou P, Zhao Y R, Wang Y T and Xu H 2014 J. Phys. Chem. B 118 12501
[52] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
[53] Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577
[54] Ravikumar K M and Hwang W 2011 J. Am. Chem. Soc. 133 11766
[55] Patel A J, Varilly P, Jamadagni S N, Acharya H, Garde S and Chandler D 2011 Proc. Natl. Acad. Sci. USA 108 17678
[56] Patel A J, Varilly P, Jamadagni S N, Hagan M F, Chandler D and Garde S 2012 J. Phys. Chem. B 116 2498
[57] Shao Q 2014 J. Phys. Chem. B 118 6175
[1] Molecular dynamics study of interactions between edge dislocation and irradiation-induced defects in Fe–10Ni–20Cr alloy
Tao-Wen Xiong(熊涛文), Xiao-Ping Chen(陈小平), Ye-Ping Lin(林也平), Xin-Fu He(贺新福), Wen Yang(杨文), Wang-Yu Hu(胡望宇), Fei Gao(高飞), and Hui-Qiu Deng(邓辉球). Chin. Phys. B, 2023, 32(2): 020206.
[2] Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions
Mengjiao Wu(吴梦娇), Huishu Ma(马慧姝), Haiping Fang(方海平), Li Yang(阳丽), and Xiaoling Lei(雷晓玲). Chin. Phys. B, 2023, 32(1): 018701.
[3] Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass
Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Chin. Phys. B, 2022, 31(9): 096401.
[4] Strengthening and softening in gradient nanotwinned FCC metallic multilayers
Yuanyuan Tian(田圆圆), Gangjie Luo(罗港杰), Qihong Fang(方棋洪), Jia Li(李甲), and Jing Peng(彭静). Chin. Phys. B, 2022, 31(6): 066204.
[5] Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations
Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Chin. Phys. B, 2022, 31(5): 058702.
[6] Evolution of defects and deformation mechanisms in different tensile directions of solidified lamellar Ti-Al alloy
Yutao Liu(刘玉涛), Tinghong Gao(高廷红), Yue Gao(高越), Lianxin Li(李连欣), Min Tan(谭敏), Quan Xie(谢泉), Qian Chen(陈茜), Zean Tian(田泽安), Yongchao Liang(梁永超), and Bei Wang(王蓓). Chin. Phys. B, 2022, 31(4): 046105.
[7] Evaluation on performance of MM/PBSA in nucleic acid-protein systems
Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Chin. Phys. B, 2022, 31(4): 048701.
[8] Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution
Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Chin. Phys. B, 2022, 31(4): 048702.
[9] Molecular dynamics simulations on the wet/dry self-latching and electric fields triggered wet/dry transitions between nanosheets: A non-volatile memory nanostructure
Jianzhuo Zhu(朱键卓), Xinyu Zhang(张鑫宇), Xingyuan Li(李兴元), and Qiuming Peng(彭秋明). Chin. Phys. B, 2022, 31(2): 024703.
[10] Comparison of formation and evolution of radiation-induced defects in pure Ni and Ni-Co-Fe medium-entropy alloy
Lin Lang(稂林), Huiqiu Deng(邓辉球), Jiayou Tao(陶家友), Tengfei Yang(杨腾飞), Yeping Lin(林也平), and Wangyu Hu(胡望宇). Chin. Phys. B, 2022, 31(12): 126102.
[11] Learning physical states of bulk crystalline materials from atomic trajectories in molecular dynamics simulation
Tian-Shou Liang(梁添寿), Peng-Peng Shi(时朋朋), San-Qing Su(苏三庆), and Zhi Zeng(曾志). Chin. Phys. B, 2022, 31(12): 126402.
[12] Mechanism of microweld formation and breakage during Cu-Cu wire bonding investigated by molecular dynamics simulation
Beikang Gu(顾倍康), Shengnan Shen(申胜男), and Hui Li(李辉). Chin. Phys. B, 2022, 31(1): 016101.
[13] Non-monotonic temperature evolution of nonlocal structure-dynamics correlation in CuZr glass-forming liquids
W J Jiang(江文杰) and M Z Li(李茂枝). Chin. Phys. B, 2021, 30(7): 076102.
[14] Simulation and experiment of the cooling effect of trapped ion by pulsed laser
Chang-Da-Ren Fang(方长达人), Yao Huang(黄垚), Hua Guan(管桦), Yuan Qian(钱源), and Ke-Lin Gao(高克林). Chin. Phys. B, 2021, 30(7): 073701.
[15] Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex
Yun-Qiang Bian(边运强), Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华). Chin. Phys. B, 2021, 30(7): 078702.
No Suggested Reading articles found!