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Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments: The Influence of Force Field Polarisation and Capping |
| Zhi-Li Zuo1, Ling Guo2, Ricardo L. Mancera3 |
1. State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
2. College of Animal Husbandry & Veterinary, Liaoning Medical University, Jinzhou 121001, China;
3. School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia |
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Abstract Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1(AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics(MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.
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| Keywords
Free energy of binding
c-Fos
c-Jun
Leucine zipper
Molecular dynamics
MM/GBSA
Coiled-coil
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| Fund:This work was supported by the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences(P2013-ZZ05). We also thank National Supercomputing Center of Jinan to provid the computational resource. |
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Issue Date: 11 February 2018
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1. J. Aqvist, C. Medina, J.E. Samuelsson, Protein Eng. 7(3), 385-391 (1994)
2. A. Perdih, U. Bren, T. Solmajer, J. Mol. Model. 15(8), 983-996 (2009)
3. F.S. Lee, Z.T. Chu, M.B. Bolger, A. Warshel, Protein Eng. 5(3), 215-228 (1992)
4. U. Bren, J. Lah, M. Bren, V. Martinek, J. Florian, J. Phys. Chem. B 114(8), 2876-2885 (2010)
5. J. Florian, M.F. Goodman, J. Phys. Chem. B 106(22), 5739-5753 (2002)
6. A. Weis, K. Katebzadeh, P. Soderhjelm, I. Nilsson, U. Ryde, J. Med. Chem. 49(22), 6596-6606 (2006)
7. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman, J. Am. Chem. Soc. 117(19), 5179-5197 (1995)
8. W.L. Jorgensen, D.S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 118(45), 11225-11236 (1996)
9. A.D. MacKerell, D. Bashford, M.L.D.R. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J. Chem. Phys. B 102(18), 3586-3616 (1998)
10. C. Oostenbrink, A. Villa, A.E. Mark, W.F. Van Gunsteren, J. Comput. Chem. 25(13), 1656-1676 (2004)
11. O. Guvench, A.D. MacKerell Jr., Methods Mol. Biol. 443, 63-88 (2008)
12. B. Ma, J.H. Lii, N.L. Allinger, J. Comput. Chem. 21(10), 813-825 (2000)
13. A.T. Amos, Int. J. Quantum Chem. 60(1), 67-74 (1996)
14. S. Patel, C.L. Brooks, J. Comput. Chem. 25(1), 1-16 (2004)
15. S.W. Rick, S.J. Stuart, B.J. Berne, J. Chem. Phys. 101(7), 6141-6156 (1994)
16. P. Lopes, B. Roux, A. MacKerell, Theoret. Chim. Acta 124(1), 11-28 (2009)
17. Z.X. Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, Y. Duan, J. Comput. Chem. 27(6), 781-790 (2006)
18. T. Ogawa, N. Kurita, H. Sekino, O. Kitao, S. Tanaka, Chem. Phys. Lett. 397(4-6), 382-387 (2004)
19. I. Vorobyov, L. Li, T.W. Allen, J. Chem. Phys. B 112(32), 9588-9602 (2008)
20. V.M. Anisimov, G. Lamoureux, I.V. Vorobyov, N. Huang, B. Roux, A.D. MacKerell, J. Chem. Theory Comput. 1(1), 153-168 (2004)
21. E. Shaulian, M. Karin, Nat. Cell Biol. 4(5), E131-E136 (2002)
22. P. Selvakumar, R.K. Sharma, Int. J. Mol. Med. 19(5), 823-827 (2007)
23. J.W. Lee, J. Harrigan, P.L. Opresko, V.A. Bohr, Mech. Ageing Dev. 126(1), 79-86 (2005)
24. C. Lu, Q. Shen, E. DuPre, H. Kim, S. Hilsenbeck, P.H. Brown, Oncogene 24(43), 6516-6524 (2005)
25. N.S. Gandhi, R.L. Mancera, Curr. Bioinform. 3(3), 149-161 (2008)
26. Z. Zuo, N.S. Gandhi, R.L. Mancera, J. Chem. Inf. Model. 50(12), 2201-2212 (2010)
27. Z. Zuo, N.S. Gandhi, K.M. Arndt, R.L. Mancera, Biopolymers 97(11), 899-909 (2012)
28. D. Jiao, P.A. Golubkov, T.A. Darden, P. Ren, Proc. Natl. Acad. Sci. USA 105(17), 6290-6295 (2008)
29. H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68(1), 16-34 (2003)
30. Q. Cui, T. Sulea, J.D. Schrag, C. Munger, M.N. Hung, M. Naim, M. Cygler, E.O. Purisima, J. Mol. Biol. 379(4), 787-802 (2008)
31. T. Hou, J. Wang, Y. Li, W. Wang, J. Chem. Inf. Model. 51(1), 69-82 (2010)
32. J.M. Mason, M.A. Schmitz, K.M. Muller, K.M. Arndt, Proc. Natl. Acad. Sci. USA 103(24), 8989-8994 (2006)
33. U.B. Hagemann, J.M. Mason, K.M. Muller, K.M. Arndt, J. Mol. Biol. 381(1), 73-88 (2008)
34. J. Higo, N. Ito, M. Kuroda, S. Ono, N. Nakajima, H. Nakamura, Protein Sci. 10(6), 1160-1171 (2001)
35. D.A. Case, T.E. Cheatham Iii, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr, A. Onufriev, C. Simmerling, B. Wang, R.J. Woods, J. Comput. Chem. 26(16), 1668-1688 (2005)
36. D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, Comput. Phys. Commun. 91, 1-41 (1995)
37. P. Cieplak, J. Caldwell, P. Kollman, J. Comput. Chem. 22(10), 1048-1057 (2001)
38. R. Jain, M. Hammel, R.E. Johnson, L. Prakash, S. Prakash, A.K. Aggarwal, J. Mol. Biol. 394(3), 377-382 (2009)
39. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, J. Chem. Phys. 79, 926-936 (1983)
40. R. Schirmbeck, P. Riedl, N. Fissolo, F.A. Lemonnier, A. Bertoletti, J. Reimann, J. Immunol. 174(8), 4647-4656 (2005)
41. D. Tom, Y. Darrin, P. Lee, J. Chem. Phys. 98(12), 10089-10092 (1993)
42. J.P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, J. Comput. Phys. 23(3), 327-341 (1977)
43. H.J.C. Berendsen, J.P.M. Postma, WFv Gunsteren, A. DiNola, J.R. Haak, J. Chem. Phys. 81(8), 3684-3690 (1984)
44. C.M. Stith, J. Sterling, M.A. Resnick, D.A. Gordenin, P.M. Burgers, J. Biol. Chem. 283(49), 34129-34140 (2008)
45. J. Srinivasan, T.E. Cheatham, P. Cieplak, P.A. Kollman, D.A. Case, J. Am. Chem. Soc. 120(37), 9401-9409 (1998)
46. P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham 3rd, Acc. Chem. Res. 33(12), 889-897 (2000)
47. T.L. Hill (ed.), An introduction to statistical thermodynamics (Dover Publications, Inc., New York, 1960)
48. B.J. Carrington, R.L. Mancera, J. Mol. Graph. Model. 23(2), 167-174 (2004)
49. W.C. Still, A. Tempczyk, R.C. Hawley, T. Hendrickson, J. Am. Chem. Soc. 112(16), 6127-6129 (1990)
50. D. Sitkoff, K.A. Sharp, B. Honig, J. Phys. Chem. 98(7), 1978-1988 (1994)
51. M.F. Sanner, A.J. Olson, J.C. Spehner, Biopolymers 38(3), 305-320 (1996)
52. B. Meher, M. Satish Kumar, P. Bandyopadhyay, Indian J. Phys. 83(1), 81-90 (2009)
53. C.G. Ji, J.Z.H. Zhang, J. Phys. Chem. B 113(49), 16059-16064 (2009)
54. Y. Tong, C.G. Ji, Y. Mei, J.Z.H. Zhang, J. Am. Chem. Soc. 131(24), 8636-8641 (2009)
55. K.R. Shoemaker, P.S. Kim, E.J. York, J.M. Stewart, R.L. Baldwin, Nature 326(6113), 563-567 (1987)
56. K. Patrice, Curr. Opin. Struct. Biol. 16(2), 142-151 (2006)
57. D.R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling, J. Phys. Chem. B 111(7), 1846-1857 (2007) |
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