Effect of channel–protein interaction on translocation of a protein-like chain through a finite channel

doi:10.1088/1674-1056/21/3/038702

中国物理B ›› 2012, Vol. 21 ›› Issue (3): 38702-038702.doi: 10.1088/1674-1056/21/3/038702

孙婷婷¹,马海珠¹,姜舟婷²

收稿日期:2011-03-02 修回日期:2011-10-10 出版日期:2012-02-15 发布日期:2012-02-15
通讯作者: 孙婷婷,Tingtingsun@mail.zjgsu.edu.cn E-mail:Tingtingsun@mail.zjgsu.edu.cn

Effect of channel–protein interaction on translocation of a protein-like chain through a finite channel

Sun Ting-Ting(孙婷婷)^a)†, Ma Hai-Zhu(马海珠)^a), and Jiang Zhou-Ting(姜舟婷)^b)

a. School of Information and Electronic Engineering, Zhejiang Gongshang University, Hangzhou 310018, China;
b. Department of Physics, China Jiliang University, Hangzhou 310018, China

Received:2011-03-02 Revised:2011-10-10 Online:2012-02-15 Published:2012-02-15
Contact: Sun Ting-Ting,Tingtingsun@mail.zjgsu.edu.cn E-mail:Tingtingsun@mail.zjgsu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 20904047), the Science and Technology Planning Project of Zhejiang Province, China (Grant No. 20100022), and the Natural Science Foundation of Zhejiang Province, China (Grant No. Y6110304).

摘要/Abstract

Abstract: We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method (PERM) and the modified orientation-dependent monomer-monomer interaction (ODI) model. Attractive channels (ε_cp=-2.0, -1.0, -0.5), repulsive channels (ε_cp=0.5, 1.0, 2.0), and a neutral channel (ε_cp =0) are discussed. The results of the chain dimension and the energy show that Z₀=1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.

Key words: pruned-enriched Rosenbluth method, translocation, protein-like chain

中图分类号: (Transport, including channels, pores, and lateral diffusion)

87.16.dp

孙婷婷, 马海珠, 姜舟婷. [J]. 中国物理B, 2012, 21(3): 38702-038702.

Sun Ting-Ting(孙婷婷), Ma Hai-Zhu(马海珠), and Jiang Zhou-Ting(姜舟婷) . Effect of channel–protein interaction on translocation of a protein-like chain through a finite channel[J]. Chin. Phys. B, 2012, 21(3): 38702-038702.

参考文献

[1] Alberts B and Bray D 1994 Molecular Biology of the Cell (New York: Garland)
[2] Darnell J, Lodish H and Baltimore D 1995 Molecular Cell Biology (New York: Scientific American Books)
[3] Lingappa V R, Chaidez J, Yost C S and Hedgepetch J 1984 Proc. Natl. Acad. Sci. USA 81 456
[4] Choi K M and Brimacombe R 1998 Nucleic. Acids. Res. 26 887
[5] Gabashvili I S, Gregory S T, Valle M, Grassucci R, Worbs M, Wahl M C, Dahlberg A E and Frank J 2001 Mol. Cell. 8 181
[6] Hardesty B and Kramer G 2001 Prog. Nucleic. Acid. Res. Mol. Biol. 65 41
[7] Han J, Turner S W and Craighead H G 1999 Phys. Rev. Lett. 83 1688
[8] Turner S W P, Calodi M and Craighead H G 2002 Phys. Rev. Lett. 88 128103
[9] Chang D C 1992 Guide to Electroporation and Electrofusion (New York: Academic)
[10] Sung W and Park P J 1996 Phys. Rev. Lett. 77 783
[11] Muthkumar M 2001 Phys. Rev. Lett. 86 3188
[12] Muthkumar M 2003 J. Chem. Phys. 118 5174
[13] Chern S S, C醨denas A E and Coalson R D 2001 J. Chem. Phys. 115 7772
[14] Tian P and Smith G D 2003 J. Chem. Phys. 119 11475
[15] Lansac Y, Maiti P K and Glaser M A 2004 Polymer 45 3099
[16] Randel R, Loebl H C and Matthai C C 2004 Macromol. Theory. Simul. 13 387
[17] Luo K F, Huopaniemi I, Ala-Nissila T and Ying S C 2006 J. Chem. Phys. 124 114704
[18] Muthukumar M and Kong C Y 2006 Proc. Natl. Acad. Sci. USA 103 5273
[19] Kantor Y and Kardar M 2004 Phys. Rev. E 69 021806
[20] Huopaniemi I, Luo K, Tapio A N and Ying S C 2006 J. Chem. Phys. 125 124901
[21] Tian P and Smith G D2003 J. Chem. Phys. 119 11475
[22] Cacciuto A and Luijten E 2006 Phys. Rev. Lett. 96 238104
[23] Milchev A, Binder K and Bhattacharya A 2004 J. Chem. Phys. 121 6042
[24] Ali I and Yeomans J M 2005 J. Chem. Phys. 123 234903
[25] Luo K F, Ala-Nissila T and Ying S C 2006 J. Chem. Phys. 124 034714
[26] Xie Y J, Yang H Y, Yu H T, Shi Q W, Wang X P and Chen J 2006 J. Chem. Phys. 124 174906
[27] Chuang J, Kantor Y and Kardar M 2002 Phys. Rev. E 65 011802
[28] Zhang L X and Chen J 2006 Polymer 47 1732
[29] Jiang S C, Zhang L X, Xia A G and Chen H P 2010 Acta Phys. Sin. 59 4337 (in Chinese)
[30] Wen X H and Zhang L X 2010 Acta Phys. Sin. 59 7404 (in Chinese)
[31] Wang Y and Zhang L X 2008 Acta Phys. Sin. 17 1480 (in Chinese)
[32] Su J Y and Zhang L X 2008 Chin. Phys. B 17 3115
[33] Shen Y and Zhang L X 2008 Chin. Phys. B 17 1480
[34] Guo H X, Yang X Z and Li T 2000 Phys. Rev. E 61 4185
[35] Jiang S C, Zhang L X, Xia A G, Chen H P and Chen J 2010 Chin. Phys. B 19 018106
[36] Xie Y J, Shi Q W, Wang X P, Zhu P P, Yang H Y and Zhang X Y 2004 Acta Phys. Sin. 53 2796 (in Chinese)
[37] Sun T T, Zhang L X and Su J Y 2006 J. Chem. Phys. 125 034702
[38] Henrickson S E, Misakian M, Robertson B and Kasianowicz J J 2000 Phys. Rev. Lett. 85 3057
[39] Chang H, Venkatesan B M, Iqbal S M, Andreadakis G, Kosari F and Vasmatzis G 2006 Biomed. Microdevices 8 263
[40] Sun T T and Zhang L X 2004 Polymer 45 7759
[41] Sun T T and Zhang L X 2005 Polymer 46 5714
[42] Jagodzinski O, Eisenriegler E and Kremer K 1992 J. Phys. I 2 2243

Effect of channel–protein interaction on translocation of a protein-like chain through a finite channel

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