2002 60 12, 2129 2134 ACTA CHIMICA SINICA Vol 60, 2002 No 12, 2129 2134 ( 0022 ) Ξ Ξ (MD) 600 ps, R6 MD,,, ;,, Study on the Stability of Insulin Hexamer in Solution by Molecular Dynamics Simulations WANG, Wei2Yan LU, Ben2Zhuo CHEN, Wei2Zu WANG, Cun2Xin Ξ (Center of Biomedical Engineering, Beijing Polytechnic University, Beijing 0022) Abstract In order to study the stability of insulin hexamer in solution and the role of Zn 2 + and phenol, two 600 ps MD simulations of the R62state human insulin hexamer system were carried out respectively The MD simulation data were analyzed by comparison Through the comparison, we found that the electrostatic interaction is the key point for the stability of the insulin hexamer, the hydrogen bonds also play an important role in the stability of the hexamer When the system includes Zn 2 + ions and phenol, the stability of insulin hexamer is enhanced In the absence of Zn 2 + and phenol, the stability of insulin hexamer is decreased and the insulin hexamer tends to dissociate These simulation results agree well with the experimental data Keywords insulin hexamer, molecular dynamics simulation, structural stability [5, T, T3R3 R6 ] R6,, ph,, [1 3,, ], 2 Zn 2 +, [1,4], 6, 12 306, B N,, Ξ E2mail : cxwang @bjpu edu cn Received June 25, 2002 ; accepted September 13, 2002 (Nos 2999259022, 30170230)
2130 Vol 60, 2002 1 MD Table 1 The box dimensions, the number of water molecule and the total number of atoms, - [6,7 ] Shi [8 ] Mark [9 ] x/ nm y/ nm z/ nm MD, MDALL 7 498 7 498 7 498 5493 19712,, MDNO 7 498 7 498 7 498 5518 19692 MD, Gaussian 98,MD [7,] T = 300 K Maxwell MD MD, R6, 300 K,, = 0 1 ps [12] MD Zn 2 +,MD 2 fs SHAKE [13], 0 8 nm, 1 1 4 nm [11] 0 ps MD, 500 ps MD, 50, Zn 2 +, Cl - 0 1 ps MDALL, Zn 2 +,,Cl - GROMOS96, MDNO,, GROMOS96, 600 ps MD, GROMOS96 Brookhaven PDB GROMOS X, 0 2 nm, InsightII, PDB 1ZNJ, GROMOS96, InsightII (SASA) NACCESS [14 ], MD [7, 2 GROMOS96 43A1,11], 50, 1 MD 1, 0 ps,, 0 90 nm, SPC 2, 2, Zn 2 + (MDALL, ) 1 82 nm, Zn 2 +, 0 (MDNO ) 1 84 nm, 3 1 (RMSD) MDALL 4 e, MDNO, 3, MDALL, 6 e Zn 2 +, Zn 2 + RMSD 0 21 nm, MDNO, Zn 2 + B, F, J, RMSD 0 23 nm 2 Cl -, MDNO, Zn 2 + D, H, L 2 Cl - (1 3 %), RMSD,, MDALL Zn 2 + Zn 2 +,
No 12 : 2131,,, (SASA) 4 5, MDNO, SASA 79 6 nm 2, SASA 71 9 nm 2 MDALL, SASA 72 3 nm 2, SASA 78 2 nm 2 Zn 2 +, SASA 1 %, SASA 8 1 % 1 Figure 1 The total potential energy of the insulin hexamer as a function of time 4 SASA Figure 4 The SASA of non2polar residues as a function of time 2 Figure 2 The Radius of gyration of the insulin hexamer as a function of time 5 SASA Figure 5 The SASA of polar residues as a function of time 3 RMSD Figure 3 The positional RMSD of all atoms for the two simulations as a function of time 6, 6, B, D, F, H, J, L N, B N B12Phe, B142Ala, B172 Leu, B182Val [15,16] 5, MDALL,B12Phe, B142Ala, B172Leu, B182Val 0 962 nm 2, MDNO, 1 205 nm 2 MDNO, B 1,
2132 Vol 60, 2002 B14, B17, B18 MDALL 0 243 nm 2 MDNO Zn 2 +, (4), 6 SASA Figure 6 The average SASA of every residue 324-967 9-348 6-1442 0-419 5, MDNO, 425 42 8-0 8 8 1-1 2, 526-749 3 621 38 2, - 423 2-0 9-912 8-27 1-408 2-0 9 [17 ] 2, 2 : 3 (1) (RMSF) 3,, (2) MDALL MDNO Zn 2 +,,, 2 ( kj/ mol) a Table 2 Comparison of the non2bonded interaction energies between monomer and monomer of the insulin hexamer in the two simulations (kj/ mol) ES MDNO LJ MDNO ES MDALL LJ MDALL 122-1238 3-398 2-1453 9-401 3 223 32 4-0 2 0 1-0 5 a 122, 324, 526, 1 2, 3 4, 5 6 ; 223, 425, 621 ES,LJ,, ( 3) MDALL, : 0 25 3 Zn 2 + Table 3 The average distance and the RMSF of the distance between the Zn 2 + ions and the atoms coordinating with the Zn 2 + ions Zn 2 + Zn 2 + / nm / nm B 0 212 0 007 Zn(1) 2 + Zn(2) 2 + Cl (1) - Cl (2) - F J D H L 0 212 0 211 0 276 0 219 0 222 0 222 0 270 0 007 0 006 0 018 0 012 0 009 0 008 0 014
No 12 : 2133 4 Table 4 Percentage of hydrogen bonds between phenol and insulin hexamer / % A11 Cys N IPH1 Phenol OE 80 2 C11 Cys N IPH2 Phenol OE 72 3 E11 Cys N IPH3 Phenol OE 68 2 G11 Cys N IPH4 Phenol OE 78 2 I11 Cys N IPH5 Phenol OE 89 2 K11 Cys N IPH6 Phenol OE 88 0 IPH1 Phenol OE A6 Cys O 72 3 IPH2 Phenol OE C6 Cys O 66 7 IPH3 Phenol OE E6 Cys O 85 0 IPH4 Phenol OE G6 Cys O 83 3 IPH5 Phenol OE I6 Cys O 93 5 IPH6 Phenol OE K6 Cys O 98 2 nm, - - 135,, [11 ] MDALL, 156 70 %, MDNO,, 66 70 %, ;, Zn 2 +,,, MDALL, 12 60 %, 4 OE A van Gunsteren, W 6 Cys, GROMOS96 OE A 11 Cys References [18 20 ] - 14 3 kj/ mol, 1 Adams, M ; Blundell, T ; Dodson, E ; Dodson, G ; - 80 3 kj/ mol Vijayan, M ; Baker, E ; Harding, M ; Rimmer, B ; 2 Liu, X2Q ; Jin, L ; Zhang, Y ; Jan, M ; Wang, D2C Chin Sci Bull 1999, 44 (4), 403 (in Chinese),, 4 (Cys), 6, 591 (in Chinese) (,, 1974, 6, 591 ) 4 Blundell, T L ; Cutfield, J F ; Cutfield, S M ; 3 5 Kaarsholm, N C ; Ko, H C ; Dunn, M F Biochemistry,,,, Mol Biol 1999, 286, 1567 Zn 2 +, Sheat, S Nature 1969, 224, 491 F (,,, Jan, M,,, 1999, 44 (4), 403 ) 3 The Group on Insulin Structure in Beijing, Sci China 1974, Dodsonm, E J ; Dodson, G G ; Hodgkin, D C ; Mercola, D A ; Vijayan, M Nature 1971, 231, 506 1989, 28, 4427 6 Karplus, M ; Petsko, G A Nature 1990, 347, 631 7 Smith, L J ; Dobson, C M ; van Gunsteren, W F J
2134 Vol 60, 2002 8 Shi, Y2Y ; Yun, R2H ; van Gunsteren, W F J Mol Biol 1988, 200, 571 9 Mark, A E ; Berendsen, H J C ; van Gunsteren, W F Biochemistry 1991, 30, 866 de Bakker, P I W ; H nenberger, P H ; McCammon, J A J Mol Biol 1999, 285, 1811 11 van Gunsteren, W F ; Billeter, S R ; Eising, A A ; H nenberger, P H ; Kr ger, P ; Mark, A E ; Scott, W R P ; Tironi, I G Biomolecular Simulation : The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Z rich, Z rich, Switzerland, 1996 12 Berendsen, H J C ; Postma, J P M ; van Gunsteren, W F ; DiNola, A ; Haak, J R J Chem Phys 1984, 81 (8), 3684 13 Rychaert, J P ; Ciccotti, G ; Berendsen, H J C J Comput Phys 1977, 23, 327 14 Hubbard, S J ; Thornton, J M NACCESS Computer Program, Department of Biochemistry and Molecular Biology, University College London, London, 1993 15 Liang, D2C ; Chang, W2R ; Zhang, J 2P ; Wan, Z2L Sci China, Ser B 1991, 7, 715 (,,,, (B ), 1991, 7, 715 ) 16 Zhang, X 2T ; Xu, M2H Acta Biochimica et Biophysica Sinica 1994, 26 (3), 277 (in Chinese) (,,, 1994, 26 (3), 277 ) 17 Kadima, W Biochemistry 1999, 38, 13443 18 Derewenda, U ; Dorewenda, Z ; Dodson, E J ; Dodson, G G ; Reynolds, C D ; Smith, G D ; Sparks, C ; Swenson, D Nature 1989, 338, 594 19 Smith, G D ; Dodson, G G Biopolymers 1992, 32, 441 20 Liang, D2C ; Song, L2Z ; Wan, Z2L ; Chang, W2R Sci China, Ser B 1993, 23 (9), 931 (in Chinese) (,,,, (B ), 1993, 23 (9), 931 ) (A0206251 CHENG, B )