Two-component coarse-grained molecular-dynamics model for the human erythrocyte membrane

Biophysical Journal

Volumn 102, Issue 1, 2012, Pages 75-84

  Li, He ^a   Lykotrafitis, George ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPECTRIN;

ARTICLE; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CYTOSKELETON; ERYTHROCYTE MEMBRANE; HUMAN; LIPID BILAYER; MEMBRANE FLUIDITY; SHEAR STRENGTH; ULTRASTRUCTURE; YOUNG MODULUS;

COMPUTER SIMULATION; CYTOSKELETON; ELASTIC MODULUS; ERYTHROCYTE MEMBRANE; HUMANS; LIPID BILAYERS; MEMBRANE FLUIDITY; MODELS, CARDIOVASCULAR; MODELS, CHEMICAL; MODELS, MOLECULAR; SHEAR STRENGTH; SPECTRIN;

EID: 84855471435     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.11.4012     Document Type: Article

References (74)

1. B. Alberts, and A. Johnson P. Walter Molecular Biology of the Cell 2002 Garland New York
2. W.T. Tse, and S.E. Lux Red blood cell membrane disorders Br. J. Haematol. 104 1999 2 13 (Pubitemid 29037011)
3. T.J. McIntosh, and S.A. Simon Roles of bilayer material properties in function and distribution of membrane proteins Annu. Rev. Biophys. Biomol. Struct. 35 2006 177 198 (Pubitemid 43877375)
4. P.B. Canham The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell J. Theor. Biol. 26 1970 61 81
5. E.A. Evans Bending resistance and chemically induced moments in membrane bilayers Biophys. J. 14 1974 923 931
6. W. Helfrich Elastic properties of lipid bilayers: theory and possible experiments Z. Naturforsch. C 28 1973 693 703
7. F. Feng, and W.S. Klug Finite element modeling of lipid bilayer membranes J. Comput. Phys. 220 2006 394 408 (Pubitemid 44742738)
8. H.W.G. Lim, M. Wortis, and R. Mukhopadhyay Stomatocyte-discocyte- echinocyte sequence of the human red blood cell: evidence for the bilayer- couple hypothesis from membrane mechanics Proc. Natl. Acad. Sci. USA 99 2002 16766 16769 (Pubitemid 36034047)
9. T.R. Powers, G. Huber, and R.E. Goldstein Fluid-membrane tethers: minimal surfaces and elastic boundary layers Phys. Rev. E 65 2002 041901
10. R. Lipowsky Vesicles and biomembranes G.L. Trigg, Encyclopedia of Applied Physics 1998 VCH Publishers Weinheim/New York 199 222
11. U. Seifert Configurations of fluid membranes and vesicles Adv. Phys. 46 1997 13 137 (Pubitemid 127535649)
12. A.M. Smondyrev, and M.L. Berkowitz Molecular dynamics simulation of fluorination effects on a phospholipid bilayer J. Chem. Phys. 111 1999 9864 9870 (Pubitemid 129579941)
13. S.E. Feller Molecular dynamics simulations of lipid bilayers Curr. Opin. Colloid Interface Sci. 5 2000 217 223
14. L. Saiz, S. Bandyopadhyay, and M.L. Klein Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations Biosci. Rep. 22 2002 151 173 (Pubitemid 35222730)
15. D.P. Tieleman, S.J. Marrink, and H.J.C. Berendsen A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems Biochim. Biophys. Acta 1331 1997 235 270 (Pubitemid 28015516)
16. K.C. Tu, M.L. Klein, and D.J. Tobias Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer Biophys. J. 75 1998 2147 2156 (Pubitemid 28492096)
17. H. Noguchi, and G. Gompper Shape transitions of fluid vesicles and red blood cells in capillary flows Proc. Natl. Acad. Sci. USA 102 2005 14159 14164 (Pubitemid 41430500)
18. S.K. Boey, D.H. Boal, and D.E. Discher Simulations of the erythrocyte cytoskeleton at large deformation. I. Microscopic models Biophys. J. 75 1998 1573 1583 (Pubitemid 28397626)
19. D.E. Discher, D.H. Boal, and S.K. Boey Simulations of the erythrocyte cytoskeleton at large deformation. II. Micropipette aspiration Biophys. J. 75 1998 1584 1597 (Pubitemid 28397627)
20. M. Venturoli, and M.M. Sperotto B. Smit Mesoscopic models of biological membranes Phys. Rev. Lett. 437 2006 1 54 (Pubitemid 44739752)
21. J.M. Drouffe, A.C. Maggs, and S. Leibler Computer simulations of self-assembled membranes Science 254 1991 1353 1356 (Pubitemid 21917465)
22. R. Goetz, G. Gompper, and R. Lipowsky Mobility and elasticity of self-assembled membranes Phys. Rev. Lett. 82 1999 221 224 (Pubitemid 129661990)
23. P.B. Sunil Kumar, G. Gompper, and R. Lipowsky Budding dynamics of multicomponent membranes Phys. Rev. Lett. 86 2001 3911 3914 (Pubitemid 32425361)
24. H. Noguchi, and M. Takasu Adhesion of nanoparticles to vesicles: a Brownian dynamics simulation Biophys. J. 83 2002 299 308 (Pubitemid 34700193)
25. S. Yamamoto, Y. Maruyama, and S. Hyodo Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules J. Chem. Phys. 116 2002 5842 5849 (Pubitemid 34435888)
26. O. Farago "Water-free" computer model for fluid bilayer membranes J. Chem. Phys. 119 2003 596 605
27. C. Hofsäss, E. Lindahl, and O. Edholm Molecular dynamics simulations of phospholipid bilayers with cholesterol Biophys. J. 84 2003 2192 2206 (Pubitemid 36373542)
28. S.J. Marrink, and A.E. Mark Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles J. Am. Chem. Soc. 125 2003 15233 15242 (Pubitemid 37509686)
29. S.J. Marrink, and A.E. Mark The mechanism of vesicle fusion as revealed by molecular dynamics simulations J. Am. Chem. Soc. 125 2003 11144 11145 (Pubitemid 37108020)
30. G. Brannigan, P.F. Philips, and F.L.H. Brown Flexible lipid bilayers in implicit solvent Phys. Rev. E. 72 2005 011915
31. I.R. Cooke, K. Kremer, and M. Deserno Tunable generic model for fluid bilayer membranes Phys. Rev. E 72 2005 011506
32. M. Laradji, and P.B. Sunil Kumar Domain growth, budding, and fission in phase-separating self-assembled fluid bilayers J. Chem. Phys. 123 2005 224902
33. A.J. Markvoort, and K. Pieterse P.A. Hilbers The bilayer-vesicle transition is entropy driven J. Phys. Chem. B 109 2005 22649 22654 (Pubitemid 41796745)
34. Z.J. Wang, and D. Frenkel Modeling flexible amphiphilic bilayers: a solvent-free off-lattice Monte Carlo study J. Chem. Phys. 122 2005 234711
35. G. Brannigan, L.C.L. Lin, and F.L.H. Brown Implicit solvent simulation models for biomembranes Eur. Biophys. J. 35 2006 104 124 (Pubitemid 43042770)
36. A.J. Markvoort, R.A. van Santen, and P.A.J. Hilbers Vesicle shapes from molecular dynamics simulations J. Phys. Chem. B 110 2006 22780 22785 (Pubitemid 44787607)
37. H. Noguchi, and G. Gompper Meshless membrane model based on the moving least-squares method Phys. Rev. E 73 2006 021903
38. S.J. Marrink, and H.J. Risselada A.H. de Vries The MARTINI force field: coarse grained model for biomolecular simulations J. Phys. Chem. B 111 2007 7812 7824 (Pubitemid 47169693)
39. M. Muller, K. Katsov, and M. Schick Biological and synthetic membranes: what can be learned from a coarse-grained description? Phys. Rep. 434 2006 113 176 (Pubitemid 44615578)
40. T. Kohyama Simulations of flexible membranes using a coarse-grained particle-based model with spontaneous curvature variables Physica A 388 2009 3334 3344
41. P. Espanol, and P. Warren Statistical-mechanics of dissipative particle dynamics Europhys. Lett. 30 1995 191 196
42. P.J. Hoogerbrugge, and J. Koelman Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics Europhys. Lett. 19 1992 155 160
43. A. Grafmuller, J. Shillcock, and R. Lipowsky Dissipative particle dynamics of tension-induced membrane fusion Mol. Simul. 35 2009 554 560
44. J.C. Shillcock, and R. Lipowsky Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations J. Chem. Phys. 117 2002 5048 5061
45. R.D. Groot, and P.B. Warren Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation J. Chem. Phys. 107 1997 4423 4435 (Pubitemid 127611597)
46. G. Brannigan, and F.L.H. Brown Solvent-free simulations of fluid membrane bilayers J. Chem. Phys. 120 2004 1059 1071
47. H. Yuan, and C. Huang S. Zhang One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes Phys. Rev. E 82 2010 011905
48. T.J. Byers, and D. Branton Visualization of the protein associations in the erythrocyte membrane skeleton Proc. Natl. Acad. Sci. USA 82 1985 6153 6157 (Pubitemid 16223916)
49. B.W. Shen, R. Josephs, and T.L. Steck Ultrastructure of the intact skeleton of the human erythrocyte membrane J. Cell Biol. 102 1986 997 1006 (Pubitemid 16013157)
50. C. Bustamante, Z. Bryant, and S.B. Smith Ten years of tension: single-molecule DNA mechanics Nature 421 2003 423 427 (Pubitemid 36157948)
51. J.F. Marko, and E.D. Siggia Stretching DNA Micromolecules 28 1995 8759 8770
52. D. Boal Mechanics of the Cell 2002 Cambridge University Press Cambridge, UK
53. H. Strey, M. Peterson, and E. Sackmann Measurement of erythrocyte membrane elasticity by flicker eigenmode decomposition Biophys. J. 69 1995 478 488
54. N. Gov, A.G. Zilman, and S. Safran Cytoskeleton confinement and tension of red blood cell membranes Phys. Rev. Lett. 90 2003 228101
55. U. Seifert, and R. Lipowsky Morphology of vesicles A.J. Hoff, Structure and Dynamics of Membranes: From Cells to Vesicles Vol. 1 1995 Elsevier, Amsterdam 403 463
56. M. Allen, and D. Tildesley Computer Simulations of Liquids 1987 Clarendon Press New York
57. D. Frenkel, and B. Smit Understanding Molecular Simulation: From Algorithms to Applications 2002 Academic Press San Diego
58. A. Imparato, J.C. Shillcock, and R. Lipowsky Shape fluctuations and elastic properties of two-component bilayer membranes Europhys. Lett. 69 2005 650 656 (Pubitemid 40306250)
59. R. Goetz, and R. Lipowsky Computer simulations of bilayer membranes: self-assembly and interfacial tension J. Chem. Phys. 108 1998 7397 7410
60. P.F. Fahey, and W.W. Webb Lateral diffusion in phospholipid bilayer membranes and multilamellar liquid crystals Biochemistry 17 1978 3046 3053 (Pubitemid 8392637)
61. D. Nelson, T. Piran, and S. Weinberg Statistical Mechanics of Membranes and Surfaces 2004 World Scientific Hackensack, NJ
62. A. Tsuji, and S. Ohnishi Restriction of the lateral motion of band 3 in the erythrocyte membrane by the cytoskeletal network: dependence on spectrin association state Biochemistry 25 1986 6133 6139 (Pubitemid 17204050)
63. G.C. Kodippili, and J. Spector P.S. Low Imaging of the diffusion of single band 3 molecules on normal and mutant erythrocytes Blood 113 2009 6237 6245
64. I.R. Cooke, and M. Deserno Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials J. Chem. Phys. 123 2005 224710
65. J.P. Mills, and L. Qie S. Suresh Nonlinear elastic and viscoelastic deformation of the human red blood cell with optical tweezers Mech. Chem. Biosyst. 1 2004 169 180
66. J. Li, and G. Lykotrafitis S. Suresh Cytoskeletal dynamics of human erythrocyte Proc. Natl. Acad. Sci. USA 104 2007 4937 4942 (Pubitemid 47186155)
67. S.C. Liu, L.H. Derick, and J. Palek Visualization of the hexagonal lattice in the erythrocyte membrane skeleton J. Cell Biol. 104 1987 527 536 (Pubitemid 17024707)
68. S.C. Liu, and L.H. Derick J. Palek Alteration of the erythrocyte membrane skeletal ultrastructure in hereditary spherocytosis, hereditary elliptocytosis, and pyropoikilocytosis Blood 76 1990 198 205 (Pubitemid 20220811)
69. F.J. Liu, and J. Burgess A. Ostafin Sample preparation and imaging of erythrocyte cytoskeleton with the atomic force microscopy Cell Biochem. Biophys. 38 2003 251 270 (Pubitemid 41282440)
70. Y.K. Park, and A.B. Catherine M.S. Feld Metabolic remodeling of the human red blood cell membrane Proc. Natl. Acad. Sci. USA 107 2010 1289 1294
71. M. Dao, J. Li, and S. Suresh Molecularly based analysis of deformation of spectrin network and human erythrocyte Mater. Sci. Eng. C 26 2006 1232 1244 (Pubitemid 44163188)
72. J. Li, and M. Dao S. Suresh Spectrin-level modeling of the cytoskeleton and optical tweezers stretching of the erythrocyte Biophys. J. 88 2005 3707 3719 (Pubitemid 40586618)
73. A.H. Swihart, and J.M. Mikrut R.C. Macdonald Atomic force microscopy of the erythrocyte membrane skeleton J. Microsc. 204 2001 212 225 (Pubitemid 34075119)
74. M. Takeuchi, and H. Miyamoto A. Kusumi Structure of the erythrocyte membrane skeleton as observed by atomic force microscopy Biophys. J. 74 1998 2171 2183 (Pubitemid 28225214)