Molecular dynamics simulation of hydrated phospholipid bilayers

Indian Journal of Biochemistry and Biophysics

Volumn 33, Issue 6, 1996, Pages 431-447

  Kothekar, V ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PHOSPHOLIPID; WATER;

CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DIFFUSION; LIPID BILAYER; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; REVIEW;

COMPUTER SIMULATION; DIFFUSION; LIGANDS; LIPID BILAYERS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PHOSPHOLIPIDS; WATER;

EID: 0030325611     PISSN: 03011208     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (124)

1. Sundaralingarn M(1972) Ann N Y Acad Sci USA 195, 324-355.
2. Hauser H, Pascher I, Pearson R H & Sundell S (1981) Biochim et Biophys Acta 650, 21-51.
3. Pearson R H & Pascher I (1979) Nature (London) 281, 499-501.
4. Hosur R V & Govil G (1979) Proc Indian Nat Sci Acad 45A, 513.
5. Akutsu H & Kyogoku Y (1977) Chem Phys Lipids 18, 285 .
6. Seelig J (1978) Biochim et Biophys Acta 515,105-140.
7. Hauser H, Pascher I & Sundell S (1988) Biochemistry, 27, 9166-9174.
8. Strenk L M, Westerman P W & Doane J W (1985) Biophys J 48, 765-773.
9. Akutsu H (1981 ) Biochemistry 20,7359-7366 .
10. Seelig J, Gaily H U & Wohlgemuth R (1977) Biochim et Biophysics Acta 467,109-119.
11. Skarjune R & Oldfield E (1979) Biochemistry 26,5903-5909.
12. Gupta S P & Govil G (1972) FEBS Lett 27,68.
13. Gupta S P, Govil G & Mishra R K (1975) J Theoret Biol 51,13.
14. Pullman B & Berthod H (1974) FEBS Lett 44, 266-272.
15. Pullman B & Saran A (1975) Int J Quant Chem Quant Biol symp 2, 71.
16. Pullman B & Couriere Ph (1976) Int J Quantum Chem Quantum Biol Symp 3, 29.
17. Hosur R V, Saran A & Govil G (1979) Indian J Biochem & Biophys 16, 165.
18. Govil G, Hosur R & Saran A (1978) Chem Phys Lipids 21, 77.
19. Seelig A & Seelig J ( 1974) Biochemistry 13, 4839-4845.
20. Oldfield E, Meadows M, Rice D & Jacobs R (1978) Biochemistry 17, 2727-2740
21. Luzzati V & Hussan F (1962) J Cell Biol 12,207-211 .
22. Reiss-Husson F (1967) J Mol Biol 25, 363-369.
23. Chapman D, Williams R M, Ladbrooke B D (1967) Chem Phys Lipids 1,445-468.
24. Janiak M J, Small D M & Shipley G G (1979) J Biol Chem 254(3) 6068-6078.
25. Tardieu A, Luzzati V & Reman F C (1973) J Mol Biol 75, 711-716.
26. Hauser H C (1975) in Water a Comprehensive Treatise (Franks,F ed )pp 209-303 Plenum Press, New York .
27. Elworthy P H (1961) J Chem Soc 5585-5589.
28. Finer E G & Drake A (1974) Chem Phys Lipids 12, 1-16.
29. Salsbury N J, Darke A & Chapman D ( 1972) Lipids 8,142-156.
30. McIntosch T J & Simon S A (1986) Biochemistry 25, 4058-4066.
31. Buildt G, Gaily H U, Seelig A, Seelig J & Zaccai G (1978) Nature (London) 271, 182-184 ; (1979) J Mol Biol Biol 134, 673-691 .
32. Buildt G, Gaily H U, Seelig A, Seelig J & Zaccai G (1978) Nature (London) 271, 182-184 ; (1979) J Mol Biol Biol 134, 673-691 .
33. Janiak M J, Small D M & Shipley G G (1976) Biochemistry 15, 4575-4580.
34. Levine Y K & Wilkins M H F (1971) Nature, New Biol 230, 89-92.
35. Phillips M C, Williams R M & Chapman D (1968) Phys Lipids 3, 234-240.
36. Trauble H & Haynes D H (1974) Chem Phys Lipids, 7, 324-335.
37. Lewis B A & Engelman D M (1983) J Mol Biol 166,211-217.
38. Lis L J, McAlister M, Fuller N, Rand R P & Perssegian V A (1982) Biophys J 37, 657-666 .
39. Hui S W & He N B (1983) Biochemistry 22,1159-1164.
40. De Young L R & Dill K A (1988) Biochemistry 27, 5281-5289.
41. Rand R P & Parsegian V A (1992) in The structure of Biological membrane, CRC Press BOCA Raton FL pp 251-306 .
42. Pastor R W, Venable R M & Karplus M (1988) J Chem Phys 89,1112-1127.
43. Dill K A, Naghizadeh J & Marqusee J A (1988) Annu Rev Phys Chem 39, 425-461.
44. Marcelja S (1974) Biochim et Biophys Acta 367,165-176.
45. Ferrarini A, Nordio P L, Moro G J, Crepeau R H & Freed J H (1989) J Chem Phys 91,5707-5721 .
46. Pastor R W (1990) in Molecular description of biological membrane components by computer aided conformational analysis ed Brasseur R (CRC press. Boca Raton FL) pp171-201 .
47. Pastor R W , Venable R M & Karplus M (1991) Proc Natl Acad Sci (USA) 88,892-896.
48. Scott H L & Kalaskar S (1989) Biochemistry 28, 3687-3692.
49. Scott H L (1991) Biophys J 59, 445-455 .
50. Sperotto M M & Mouritsen O G (1991) Biophys J 59, 261-270.
51. Van der Ploeg P & Berendsen H J C (1982) J Chem Phys 76, 3271-3276.
52. Van der Ploeg P & Berendsen H J C (1983) Mol Phys 49, 233-248.
53. Jonsson B, Edholm O & Teleman O (1986) J Chem Phys 85, 2259-2271.
54. Watanabe K, Ferrario M & Klein M L (1988) J Phys Chem 92, 818-821 .
55. Watanabe K & Klein M L (1989) J Phys Chem 93, 6897-6901 .
56. Watanabe K & Klein M L (1991) J Phys Chem 95, 4158-4166.
57. Wendoloski J J, Kimatian S J, Schutt C E & Salemme F R (1989) Science Wash, 243, 636-638 .
58. Shelley J C , Sprik M & Klein M L (1993) Langmuir 9, 916-926.
59. Edholm O, Berendsen H J C & Van der Ploeg P (1983) Mol Phys 49, 379-388.
60. Edholm O & Nyberg A M (1992) Biophys J 63, 1081-1089.
61. Charifson P S, Hiskey R G & Pederson L G (1990) J Comput Chem 11, 1181-1186.
62. Alper H E, Bassolino D & Stouch T R (1993) J Chem Phys 98 9798-9807.
63. Alper H E, Bassolino D & Stouch T R (1993) J Chem Phys 99, 5547-5559.
64. Egberts E & Berendsen H J C (1988) J Chem Phys 89, 3718-3732.
65. Egberts E (1988) Molecular dynamics simulation of multilayer membranes Ph D thesis, University of Groningen, The Netherlands.
66. Berkowitz M L & Raghavan K (1991) Langmuir 7, 1042-1044.
67. Damodaran K V, Merz K M & Gaber P B ( 1992) Biochemistry 31, 7656-7664 .
68. Damodaran K V & Merz K M (1993) Langmuir 9, 1179-1183.
69. Raghavan K, Reddy M R & Berkowitz M L (1992) Langmuir 8, 233-240.
70. De Loof H, Harvey S C, Segrest J P & Pastor R W (1991) Biochemistry 30, 2099-2113 .
71. Karaborni S, van Os N M, Esselink E & Hilbers P A J (1993) Langmuir 9, 1175-1178 .
72. Heller H, Schaefer M & Schulten K (1993) J Phys Chem 97, 8343-8360.
73. Venable R M, Zhang Y, Hardy B J & Pastor R W (1993) Science, 262, 223-226.
74. Milik M & Skolnick J (1993) Proteins 15, 10-25 .
75. Milik M, Skolnick J & Kolinski A (1992) J Phys Chem 96, 4015-4022.
76. Biswas A & Schurmann B L (1991) J Chem Phys 95, 5377-5386.
77. Fukuda T, Okozoki S & Okada I (1993) Biophys J 64, 1344-1353.
78. Stouch T R (1993) Mol Simul 10, 317-345 .
79. Xiang T (1993) Biophys J 65,1108-1120 .
80. Damodaran K V & Merz K M (1994) Biophys J 66,1076-1087.
81. Essex J W, Hann M M & Richards W G (1994) Phil Trans R Soc Lond B 344, 239-260 .
82. Huang P, Perez J J & Loew G H (1994) J Biomole Struc Dyn 11, 927-956.
83. Robinson A J, Richards W G, Thomas P J & Hann M M (1994) Biophys J 67, 2345-2354.
84. Stouch T R, Alper H E & Bassolino D (1994) Int J Super Compu Appl 8,6-23.
85. Kothekar V (1996) J Biosciences (in press).
86. Edholm O & Johansson J (1987) Eur Biophys J 14,203-209.
87. Bassolino-Klimas D, Alper H E & Stouch T R(1993) Biochemistry 32, 12624-12637; (1995)J Am Chem Soc 117,4118-4129.
88. Bassolino-Klimas D, Alper H E & Stouch T R(1993) Biochemistry 32, 12624-12637; (1995)J Am Chem Soc 117,4118-4129.
89. Huang P, Bertaccini E D & Loew G H (1995) J Biomole Struct Dyn. 12, 725-754.
90. Huang P & Loew G H (1995)J Biomole Struct Dyn 12,937-955.
91. Woolf T B & Roux B (1994) Proc Natl Acad Sci USA 91, 11631-11635.
92. Alper H E & Stouch T R (1995) J Phys Chem 99, 5724-5731.
93. Robinson A J, Richards WG, Thomas PJ & Hann M M (1995) Biophys J 68, 164-170.
94. Damodaran KV & Merz K M (1995)J Am Chem Soc. 117,6561-6571.
95. Gupta D & Kothekar V (communicated to Biosciences).
96. Kothekar V(1996) J.Biomolec. StrucDyn13,601-613.
97. Kothekar V, Mahajan K, Kaushik R & Gupta, D J Biomolec Struct Dyna (in Press).
98. Jorgenson W L , Chandrasekhar J, Medura J D , Impey R W & Klein M L (1983) J Chem Phys 79,926-935 .
99. Mrigank, Royyuru A K & Kothekar V (1986) FEBS Lett 195,203-207.
100. Teleman O & Von Der Lieth C W (1990) Biopolymers, 30, 13-23 .
101. Muller-Plathe F , Rogers B C & Van Gunsteren W F (1992) Chem Phys Lett 199, 237-243 .
102. Williams D E (1967) J Chem Phys 47, 4680-4686.
103. Ryckaert J P & Klein M L (1986) J Chem Phys 85, 1613-1620.
104. Ryckaert J P , McDonald I R & Klein M L (1989) Mol Phys 67, 957-979.
105. Jorgenson W L (1991) Boss Version 3 1 Yale University New Haven, Connecticut U S A.
106. Jorgenson W L & Tirado-Rives J (1988) J Am Chem Soc 110, 1657-1666.
107. Weiner S J, Kollman P A, Case D A , Singh U C , Ghio C, Alagona G , Profeta S & Weiner P (1984) J Am Chem Soc 106,765-784.
108. Pearlman D A , Case D A , Caldwell J C , Seibel G L , Singh U C , Weiner P & Kollman P A (1991) AMBER 4 0 UCSF version .
109. Ryckaert J P & Bellemans A (1975) Chem Phys Lett 30, 123-126.
110. Ryckaert J P & Belleman A (1978) Far Disc Chem Soc 66, 95-99.
111. Merz K M Jr (1992) J Comput Chem 13,749-767 .
112. Stewart J J P(1990), MOPAC 6 0 QCPE 455 Bloomington Indiana.
113. Pople J A , Santry D P & Segal G A (1965) J Chem Phys 43, 129-135.
114. Ryckaert J P G, Ciccotti G & Berendsen H J C (1977) J Compu Phys 23, 327-341 .
115. Jorgensen W L (1989) Acc Chem Res 22,184-189.
116. Alper H E & Levy R M (1989) J Chem Phys 91, 1242-1251 .
117. Allen M P & Tildesley D J (1987) Computer simulation of liquids 385 pp.Oxford Univ Press
118. Berendsen H J C, Postma, J P M, DiNola A , Van Gunsteren W F & Haak, J R (1984) J Chem Phys 81,3684-3690.
119. McIntosh T J (1990) In Molecular description of biological membrane by computer aided conformational analysis, BOCA Raton FL Ed pp 247-265, CRC press.
120. Gruner S M, Tate M W, Kirk G L So P T C, Turner D C, Keane D T, Tilcock C P S & Cullis P R (1988) Biochemistry 27, 2853-2866.
121. Meier P, Ohmes E, Kothe G, Blume A, Weldner J & Elbl H J (1986) J Phys Chem 87, 4904-4912.
122. Mendelsohn R, Davies M A, Schuster H F, Xu ZZ & Bittman R (1991) Biochemistry 30, 8558-8563.
123. Mendelson R, Davies M A, Brauner J W, Schuster H F & Dluhy R A (1989) Biochemistry 28, 8934-8939.
124. Ketchem R R, Hu W & Cross TA (1993) Science 261, 1457-1460.