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Chin. Phys. B, 2021, Vol. 30(6): 068701    DOI: 10.1088/1674-1056/abf129
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers

Xuegui Lin(林雪桂)1, Xiaojie Chen(陈晓洁)2, and Qing Liang(梁清)1,†
1 Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, China;
2 Department of Industrial Automation, Guangdong Polytechnic College, Zhaoqing 526100, China
Abstract  Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine (PE) lipids rather than with phosphatidylcholine (PC) lipids, and tend to contact with the liquid-disordered (Ld) domains enriched in unsaturated PE. Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases.
Keywords:  protein      lipid bilayer      interaction      molecular dynamics simulation  
Received:  17 February 2021      Revised:  14 March 2021      Accepted manuscript online:  24 March 2021
PACS:  87.16.D- (Membranes, bilayers, and vesicles)  
  87.15.kt (Protein-membrane interactions)  
  87.15.ap (Molecular dynamics simulation)  
  87.14.ep (Membrane proteins)  
Fund: Project supported by the National Natural Science Foundation of China (Grant No. 11674287) and Zhejiang Provincial Natural Science Foundation of China (Grant No. LY19A040009).
Corresponding Authors:  Qing Liang     E-mail:  qliang@zjnu.edu.cn

Cite this article: 

Xuegui Lin(林雪桂), Xiaojie Chen(陈晓洁), and Qing Liang(梁清) Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers 2021 Chin. Phys. B 30 068701

[1] Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K and Walter P 2014 Molecular Biology of the Cell, 6th edn. (New York, NY: Garland Science) pp. 1244-1245
[2] Nigra A D, Casale C H and Santander V S 2020 Cell. Mol. Life Sci. 77 1681
[3] Lux S E 2016 Blood 127 187
[4] Pan L, Yan R, Li W and Xu K 2018 Cell Rep. 22 1151
[5] Dupire J, Socol M and Viallat A 2012 Proc. Natl. Acad. Sci. USA 109 20808
[6] Manno S, Takakuwa Y and Mohandas N 2002 Proc. Natl. Acad. Sci. USA 99 1943
[7] Czogalla A, Grzymajlo K, Jezierski A and Sikorski A F 2008 Biochim. Biophys. Acta, Biomembr. 1778 2612
[8] Machnicka B, Czogalla A, Hryniewicz-Jankowska A, Boguslawska D M, Grochowalska R, Heger E and Sikorski A F 2014 Biochim. Biophys. Acta, Biomembr. 1838 620
[9] Li J, Lykotrafitis G, Dao M and Suresh S 2007 Proc. Natl. Acad. Sci. USA 104 4937
[10] Hoore M, Yaya F, Podgorski T, Wagner C, Gompper G and Fedosov D A 2018 Soft Matter 14 6278
[11] Mohandas N and Gallagher P G 2008 Blood 112 3939
[12] Ipsaro J J, Harper S L, Messick T E, Marmorstein R, Mondragón A and Speicher D W 2010 Blood 115 4843
[13] Bignone P A and Baines A J 2003 Biochem. J. 374 613
[14] Salomao M, An X, Guo X, Gratzer W B, Mohandas N and Baines A J 2006 Proc. Natl. Acad. Sci. USA 103 643
[15] Harper S L, Sriswasdi S, Tang H Y, Gaetani M, Gallagher P G and Speicher D W 2013 Blood 122 3045
[16] Da Costa L, Galimand J, Fenneteau O and Mohandas N 2013 Blood Rev. 27 167
[17] Delaunay J 2007 Blood Rev. 21 1
[18] Li H and Lykotrafitis G 2015 Phys. Rev. E 92 012715
[19] Li H, Papageorgiou D P, Chang H Y, Lu L, Yang J and Deng Y 2018 Biosensors 8 76
[20] Li H, Lu L, Li X, Buffet P A, Dao M, Karniadakis G E and Suresh S 2018 Proc. Natl. Acad. Sci. USA 115 9574
[21] Zhang R, Zhang C, Zhao Q and Li D 2013 Sci. China: Life Sci. 56 1076
[22] Nicolas G, Pedroni S, Fournier C, Gautero H, Craescu C, Dhermy D and Lecomte M C 1998 Biochem. J. 332 81
[23] De Vecchis D, Reithmeier R A and Kalli A C 2019 Biophys. J. 117 1364
[24] Yawata Y 2003 Cell Membrane: the Red Blood Cell as a Model (Weinheim, Germany: Wiley-VCH) pp. 27-32
[25] Dumitru A C, Poncin M A, Conrard L, Dufrêne Y F, Tyteca D and Alsteens D 2018 Nanoscale Horiz 3 293
[26] Corradi V, Sejdiu B I, Mesa-Galloso H, Abdizadeh H, Noskov S Y, Marrink S J and Tieleman D P 2019 Chem. Rev. 119 5775
[27] Bennett V and Healy J 2009 Cold Spring Harbor Perspect. Biol. 1 a003012
[28] Civenni G, Test S T, Brodbeck U and Bütikofer P 1998 Blood 91 1784
[29] Lorenzo D N 2020 Cytoskeleton 77 129
[30] Kalli A C and Reithmeier R A 2018 PLoS Comput. Biol. 14 e1006284
[31] An X, Debnath G, Guo X, Liu S, Lux S E, Baines A, Gratzer W and Mohandas N 2005 Biochemistry 44 10681
[32] Smith A S, Nowak R B, Zhou S, Giannetto M, Gokhin D S, Papoin J, Ghiran I C, Blanc L, Wan J and Fowler V M 2018 Proc. Natl. Acad. Sci. USA 115 E4377
[33] Li H, Zhang Y, Ha V and Lykotrafitis G 2016 Soft Matter 12 3643
[34] Campanella M E, Chu H and Low P S 2005 Proc. Natl. Acad. Sci. USA 102 2402
[35] Jin Y, Liang Q and Tieleman D P 2020 J. Phys. Chem. B 124 3054
[36] Kapus A and Janmey P 2013 Compr. Physiol. 3 1231
[37] Peng Z, Li X, Pivkin I V, Dao M, Karniadakis G E and Suresh S 2013 Proc. Natl. Acad. Sci. USA 110 13356
[38] Grzybek M, Chorzalska A, Bok E, Hryniewicz-Jankowska A, Czogalla A, Diakowski W and Sikorski A F 2006 Chem. Phys. Lipids 141 133
[39] Smith J E 1987 Vet. Pathol. 24 471
[40] Boguslawska D M, Machnicka B, Hryniewicz-Jankowska A and Czogalla A 2014 Cell. Mol. Biol. Lett. 19 158
[41] Wolny M, Grzybek M, Bok E, Chorzalska A, Lenoir M, Czogalla A, Adamczyk K, Kolondra A, Diakowski W, Overduin M and Sikorski A F 2011 PLoS One 6 e21538
[42] Hryniewicz-Jankowska A, Bok E, Dubielecka P, Chorzalska A, Diakowski W, Jezierski A, Lisowski M and Sikorski A F 2004 Biochem. J. 382 677
[43] Diakowski W, Prychidny A, ŚWistak M, Nietubyć M, BialKowska K, Szopa J and Sikorski A F 1999 Biochem. J. 338 83
[44] Diakowski W, Ozimek L, Bielska E, Bem S, Langner M and Sikorski A F 2006 Biochim. Biophys. Acta, Biomembr. 1758 4
[45] Shukla S, Jin R, Robustelli J, Zimmerman Z E and Baumgart T 2019 Biophys. J. 117 962
[46] Li Z, Venable R M, Rogers L A, Murray D and Pastor R W 2009 Biophys. J. 97 155
[47] Mitra M, Patra M and Chakrabarti A 2015 Eur. Biophys. J. 44 635
[48] Rodgers W and Glaser M 1991 Proc. Natl. Acad. Sci. USA 88 1364
[49] Head B P, Patel H H and Insel P A 2014 Biochim. Biophys. Acta, Biomembr. 1838 532
[50] Ciana A, Achilli C, Balduini C and Minetti G 2011 Biochim. Biophys. Acta, Biomembr. 1808 183
[51] Kamata K, Manno S, Ozaki M and Takakuwa Y 2008 Am. J. Hematol. 83 371
[52] Ciana A, Achilli C and Minetti G 2014 Mol. Membr. Biol. 31 47
[53] Sikder M K U, Stone K A, Kumar P B S and Laradji M 2014 J. Chem. Phys. 141 054902
[54] Li H and Lykotrafitis G 2014 Biophys. J. 107 642
[55] Marrink S J, Risselada H J, Yefimov S, Tieleman D P and De Vries A H 2007 J. Phys. Chem. B 111 7812
[56] Marrink S J and Tieleman D P 2013 Chem. Soc. Rev. 42 6801
[57] Marrink S J, De Vries A H and Mark A E 2004 J. Phys. Chem. B 108 750
[58] Lupyan D, Mezei M, Logothetis D E and Osman R 2010 Biophys. J. 98 240
[59] Schmidt M R, Stansfeld P J, Tucker S J and Sansom M S P 2013 Biochemistry 52 279
[60] Chen X J and Liang Q 2017 Chin. Phys. B 26 048701
[61] Wassenaar T A, Ingólfsson H I, Böckmann R A, Tieleman D P and Marrink S J 2015 J. Chem. Theory Comput. 11 2144
[62] Marrink S J, Corradi V, Souza P C T, Ingólfsson H I, Tieleman D P and Sansom M S P 2019 Chem. Rev. 119 6184
[63] Li W, Lin Z, Yuan B and Yang K 2020 Chin. Phys. B 29 128701
[64] Liang Y R and Liang Q 2019 Acta Phys. Sin. 68 028701 (in Chinese)
[65] Ding H M, Yin Y W, Sheng Y J and Ma Y Q 2021 Chin. Phys. Lett. 38 018701
[66] Corradi V, Sejdiu B I, Mesa-Galloso H, Abdizadeh H, Noskov S Y, Marrink S J and Tieleman D P 2019 Chem. Rev. 119 5775
[67] Bussi G, Donadio D and Parrinello M 2007 J. Chem. Phys. 126 014101
[68] Parrinello M and Rahman A 1981 J. Appl. Phys. 52 7182
[69] Martyna G J, Tobias D J and Klein M L 1994 J. Chem. Phys. 101 4177
[70] Humphrey W, Dalke A and Schulten K 1996 J. Mol. Graphics 14 33
[71] Wu Q Y and Liang Q 2014 Langmuir 30 1116
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