Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

doi:10.1088/1674-1056/27/3/038703

中国物理B ›› 2018, Vol. 27 ›› Issue (3): 38703-038703.doi: 10.1088/1674-1056/27/3/038703

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

Zhen-Lu Li(李振鲁)

1 Department of Physiology and Biophysics, Case Western Reserve University, Cleveland 44106, USA;
2 Department of Physics, Nanjing University, Nanjing 210093, China

收稿日期:2017-10-24 修回日期:2017-12-12 出版日期:2018-03-05 发布日期:2018-03-05
通讯作者: Zhen-Lu Li E-mail:zxl480@case.edu
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 91427302 and 11474155).

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

Zhen-Lu Li(李振鲁)^1,2

1 Department of Physiology and Biophysics, Case Western Reserve University, Cleveland 44106, USA;
2 Department of Physics, Nanjing University, Nanjing 210093, China

Received:2017-10-24 Revised:2017-12-12 Online:2018-03-05 Published:2018-03-05
Contact: Zhen-Lu Li E-mail:zxl480@case.edu
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 91427302 and 11474155).

摘要/Abstract

摘要：

The N-terminal amphiphilic helices of proteins Epsin,Sar1p,and Arf1 play a critical role in initiating membrane deformation.The interactions of these amphiphilic helices with the lipid membranes are investigated in this study by combining the all-atom and coarse-grained simulations.In the all-atom simulations,the amphiphilic helices of Epsin and Sar1p are found to have a shallower insertion depth into the membrane than the amphiphilic helix of Arf1,but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane.The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distributions of polar and non-polar residues along the helix.To directly compare their ability to deform the membrane,the coarse-grained simulations are performed to investigate the membrane deformation under the insertion of multiple helices.

关键词: cell membrane, amphiphilic helix, membrane deformation, molecular simulation

Abstract:

Key words: cell membrane, amphiphilic helix, membrane deformation, molecular simulation

中图分类号: (Protein-membrane interactions)

87.15.kt

87.14.ef (Peptides) 87.14.ep (Membrane proteins) 87.15.ap (Molecular dynamics simulation)

李振鲁. Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1[J]. 中国物理B, 2018, 27(3): 38703-038703.

Zhen-Lu Li(李振鲁). Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1[J]. Chin. Phys. B, 2018, 27(3): 38703-038703.

参考文献 54

[1]	Kirchhausen T 2000 Nat. Rev. Mol. Cell Biol. 1 187
[2]	Bonifacino J S and Schwartz J L 2003 Nat. Rev. Mol. Cell Biol. 4 409
[3]	Faini M, Beck R, Wieland F T and Briggs J A G 2013 Trends Cell Biol. 23 279
[4]	Chen H, Fre S, Slepnev V I, Capua M R, Takei K, Butler M H, Fiore P P D and Camilli P D 1988 Nature 394 793
[5]	Fath S, Mancias J D, Bi X and Goldberg J 2007 Cell 129 1325
[6]	Schorey C D S and Chavrier P 2006 Nat. Rev. Mol. Cell Biol. 7 347
[7]	Ford M G J, Mills I G, Peter B. J, Vallis Y, Praefcke G J K, Evans P R and McMahon H T 2002 Nature 419 361
[8]	Lee M C, Orci L, Hamamoto S, Futai E, Ravazzola M and Schekman R 2005 Cell 122 605
[9]	Krauss M, Jia J Y, Roux A, Beck R, Wieland F T, Camilli P D and Haucke V 2008 J. Biol. Chem. 283 27717
[10]	Zimmerberg J and Kozlov M M 2006 Nat. Rev. Mol. Cell Biol. 7 9
[11]	McMahon H T and Gallop J L 2005 Nature 438 590
[12]	Drin G and Antonny B 2010 FEBS Lett. 584 1840
[13]	Campelo F, McMahon H T and Kozlov M 2008 Biophys. J. 95 2325
[14]	Li Z L, Ding H M and Ma, Y Q 2016 J. Phys.:Condens. Mat. 28 083001
[15]	Woo H J and Wallqvist A 2011 J. Phys. Chem. B 115 8122
[16]	Li Z L, Ding H M and Ma Y Q 2013 Soft Matter 9 1281
[17]	Yue T T, Zhang X R and Huang F 2014 Soft Matter 10 2024.
[18]	He X C, Lin M, Sha B Y, Feng S S, Shi X H, Qu Z G and Xu F 2015 Sci. Rep. 5 12808
[19]	Ding H M and Ma Y Q 2017 Nanoscale Horizons
[20]	Ma L, Li Y, Li M and Hu S 2017 Chin. Phys. B 26 128708
[21]	Zhang L, Hao C, Feng Y, Gao F, Lu X, Li J and Sun R 2016 Chin. Phys. B 25 9
[22]	Bond P J and Sansom M S P 2006 J. Am. Chem. Soc. 128 2697
[23]	Hu Y, Sinha S K and Patel S 2014 J. Phys. Chem. B 118 11973
[24]	Hu Y, Ou S and Patel S 2013 J. Phys. Chem. B 117 11641
[25]	He X C, Qu Z G, Xu F, Lin M, Wang J L, Shi X H and Lu T J 2014 Soft Matter 10 139
[26]	Peter B J, Kent H M, Mills I G, Vallis Y, Butler P J G, Evans P R and McMahon H T 2015 Science 303 495
[27]	Campelo F, Fabrikant G, McMahon H T and Kozlov M. 2010 FEBS Lett. 584 1830
[28]	Blood P D and Voth G A 2006 Proc. Natl. Acad. Sci. U. S. A. 103 15068
[29]	Cui H, Mim C, Vazquez F X, Lyman E, Unger V M and Voth G A 2013 Biophys. J. 104 404
[30]	Yin Y, Arkhipov A and Schulten K 2009 Structure 17 882
[31]	Chan C, Wen H, Lu L and Fan J 2015 Chin. Phys. B 25 1
[32]	Braun A R, Lacy M M, Ducas V C, Rhoades E and Sachs J N 2014 J. Am. Chem. Soc. 136 9962
[33]	Kandt C, Ash W L and Tieleman D P 2007 Methods 41 475
[34]	Schmidt T H and Kandt C 2012 J. Chem. Inf. Model. 52 2657
[35]	Klauda J B, Venable R M, Freites J A, O Connor J W, Mondragon-Ramirez C, Vorobyov I, Tobias D J, MacKerell A D and Pastor R W 2010 J. Phys. Chem. B 114 7830
[36]	Huang J and MacKerell A D 2010 J. Comput. Chem. 34 2135
[37]	Jorgensen W L and Madura J D 1983 J. Am. Chem. Soc. 105 1407
[38]	Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577
[39]	Hess B 2008 J. Chem. Theory Comput. 4 116
[40]	Spoel D V D, Lindahl E, Hess B, Groenhof G, Mark A E and Berendsen H J C 2005 J. Comput. Chem. 26 1701
[41]	Yesylevskyy S O, Schafer L V, Sengupta D and Marrink S J 2010 PLoS Comput. Biol. 6 e1000810
[42]	Marrink S J, Risselada H J, Yefimov S, Tieleman, D P and de Vires A H 2007 J. Phys. Chem. B 111 7812
[43]	de Jong D H, Singh G, Bennett W F D, Arnarez C, Wassenaar T A, Schafer L V, Periole X, Tieleman D P and Marrink S J 2013 J. Chem. Theory Comput. 9 687
[44]	Marrink S J, de Vries A H and Mark A E 2004 J. Phys. Chem. B 108 750
[45]	Zemel A, Ben-Shaul A, and May S 2008 J. Phys. Chem. B 112 6988
[46]	MacCallum J L, Bennett W F D and Tieleman D P 2008 Biophys. J. 94 3393
[47]	Eisenberg D, Weiss R M and Terwilliger T C 1982 Nature 299 371
[48]	Frolov V A and Zimmerberg, J 2010 FEBS Lett. 584 1824
[49]	Ding H M and Ma Y Q 2012 Biomaterials 33 5798
[50]	Nielsen S O, Bulo R E, Moore P B and Ensing B 2010 Phys. Chem. Chem. Phys. 12 12401
[51]	Yang K and Ma Y Q 2010 Nat. Nanotechnol. 5 579
[52]	Ding H M and Ma Y Q 2015 ACS Nano 6 1230
[53]	Ding H M and Ma Y Q 2015 Small 11 1055
[54]	Marrink S J and Tieleman D P 2013 Chem. Soc. Rev. 42 6801

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

RichHTML

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献 54

相关文章 4

Metrics

本文评价

推荐阅读 0

[1]	Xuanhao Fu(傅宣豪) and Xin Zhou(周昕). Different roles of surfaces' interaction on lattice mismatched/matched surfaces in facilitating ice nucleation[J]. 中国物理B, 2023, 32(2): 28202-028202.
[2]	Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜). Modeling hydrogen exchange of proteins by a multiscale method[J]. 中国物理B, 2021, 30(7): 78701-078701.
[3]	Weiwei Zhang(张伟伟) and Jian Zhang(张建). Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations[J]. 中国物理B, 2021, 30(10): 108703-108703.
[4]	顾斌, 张丰收, 黄余改, 方夏. Variations of water's local-structure induced by solvation of NaCl[J]. 中国物理B, 2010, 19(3): 36101-036101.