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1.
1.P. O. Brown, Retroviruses (Cold Spring Harbor, New York, 1998), pp. 161203.
2.
2.T. K. Chiu and D. R. Davies, Curr. Med. Chem. 4, 965 (2004).
http://dx.doi.org/10.2174/1568026043388547
3.
3.K. Zhu, C. Dobard, and S. A. Chow, J. Virol. 78, 5045 (2004).
http://dx.doi.org/10.1128/JVI.78.10.5045-5055.2004
4.
4.Y. Pommier, A. A. Johnson, and C. Marchand, Nat. Rev. Drug Discovery 4, 236 (2005).
http://dx.doi.org/10.1038/nrd1660
5.
5.P. A. Sherman and J. A. Fyfe, Proc. Natl. Acad. Sci. U.S.A. 87, 5119 (1990).
http://dx.doi.org/10.1073/pnas.87.13.5119
6.
6.W. Yang and T. A. Steitz, Structure (London) 3, 131 (1995).
http://dx.doi.org/10.1016/S0969-2126(01)00142-3
7.
7.J. R. Schames, R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. H. Ni, and J. A. McCammon, J. Med. Chem. 47, 1879 (2004).
http://dx.doi.org/10.1021/jm0341913
8.
8.Y. Goldgur, F. Dyda, A. B. Hickman, T. M. Jenkins, R. Craigie, and D. R. Davies, Proc. Natl. Acad. Sci. U.S.A. 95, 9150 (1998).
http://dx.doi.org/10.1073/pnas.95.16.9150
9.
9.S. Maignan, J. P. Guilloteau, Q. Zhou-Liu, C. Clement-Mella, and V. J. Mikol, Mol. Biol. 282, 359 (1998).
http://dx.doi.org/10.1006/jmbi.1998.2002
10.
10.R. D. Lins, J. M. Briggs, T. P. Straatsma, H. A. Carlson, J. Greenwald, S. Choe, and J. A. McCammon, Biophys. J. 76, 2999 (1999).
http://dx.doi.org/10.1016/S0006-3495(99)77453-9
11.
11.R. D. Lins, T. P. Straatsma, and J. M. Briggs, Biopolymers 53, 308 (2000).
http://dx.doi.org/10.1002/(SICI)1097-0282(20000405)53:4<308::AID-BIP3>3.0.CO;2-H
12.
12.C. Laboulais, E. Deprez, H. Leh, J. F. Mouscadet, J. C. Brochon, and M. Le Bret, Biophys. J. 81, 473 (2001).
http://dx.doi.org/10.1016/S0006-3495(01)75715-3
13.
13.H. H. Ni, C. A. Sotriffer, and J. A. McCammon, J. Med. Chem. 44, 3043 (2001).
http://dx.doi.org/10.1021/jm010205y
14.
14.M. L. Barreca, K. W. Lee, A. Chimirri, and J. M. Briggs, Biophys. J. 84, 1450 (2003).
http://dx.doi.org/10.1016/S0006-3495(03)74958-3
15.
15.M. C. Lee, J. X. Deng, J. M. Briggs, and Y. Duan, Biophys. J. 88, 3133 (2005).
http://dx.doi.org/10.1529/biophysj.104.058446
16.
16.A. Brigo, K. W. Lee, G. I. Mustata, and J. M. Briggs, Biophys. J. 88, 3072 (2005).
http://dx.doi.org/10.1529/biophysj.104.050286
17.
17.C. N. Alves, S. Marti, R. Castillo, J. Andres, V. Moliner, I. Tunon, and E. Silla, Chem.-Eur. J. 13, 7715 (2007).
http://dx.doi.org/10.1002/chem.200700040
18.
18.J. P. Hu, X. Q. Gong, J. G. Su, W. Z. Chen, and C. X. Wang, Biophys. Chem. 132, 69 (2008).
http://dx.doi.org/10.1016/j.bpc.2007.09.008
19.
19.C. N. Alves, S. Marti, R. Castillo, J. Andres, V. Moliner, I. Tunon, and E. Silla, Biophys. J. 94, 2443 (2008).
http://dx.doi.org/10.1529/biophysj.107.107623
20.
20.W. Weber, H. Demirdjian, R. D. Lins, J. M. Briggs, R. Ferreira, and J. A. McCammon, J. Biomol. Struct. Dyn. 16, 733 (1998).
21.
21.P. Oelschlaeger, M. Klahn, W. A. Beard, S. H. Wilson, and A. Warshel, J. Mol. Biol. 366, 687 (2007).
http://dx.doi.org/10.1016/j.jmb.2006.10.095
22.
22.T. A. Halgren, Curr. Opin. Struct. Biol. 11, 236 (2001).
http://dx.doi.org/10.1016/S0959-440X(00)00196-2
23.
23.G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, Y. X. X. Cao, R. B. Murphy, R. H. Zhou, and T. A. Halgren, J. Comput. Chem. 23, 1515 (2002).
http://dx.doi.org/10.1002/jcc.10125
24.
24.M. Kato and A. Warshel, J. Phys. Chem. B 110, 11566 (2006).
http://dx.doi.org/10.1021/jp061190o
25.
25.C. G. Ji, Y. Mei, and J. Z. H. Zhang, Biophys. J. 95, 1080 (2008).
http://dx.doi.org/10.1529/biophysj.108.131110
26.
26.D. W. Zhang, X. H. Chen, and J. Z. H. Zhang, J. Comput. Chem. 24, 1846 (2003).
http://dx.doi.org/10.1002/jcc.10346
27.
27.D. W. Zhang and J. Z. H. Zhang, J. Chem. Phys. 119, 3599 (2003).
http://dx.doi.org/10.1063/1.1591727
28.
28.Y. Mei, D. W. Zhang, and J. Z. H. Zhang, J. Phys. Chem. A 109, 2 (2005).
http://dx.doi.org/10.1021/jp045109y
29.
29.C. G. Ji and J. Z. H. Zhang, J. Am. Chem. Soc. 130, 17129 (2008).
http://dx.doi.org/10.1021/ja807374x
30.
30.L. L. Duan, Y. Mei, Q. G. Zhang, and J. Z. H. Zhang, J. Chem. Phys. 130, 115102 (2009).
http://dx.doi.org/10.1063/1.3089723
31.
31.Y. Tong, C. G. Ji, Y. Mei, and J. Z. H. Zhang, J. Am. Chem. Soc. 131, 8636 (2009).
http://dx.doi.org/10.1021/ja901650r
32.
32.Y. Goldgur, R. Craigie, G. H. Cohen, T. Fujiwara, T. Yoshinaga, T. Fujishita, H. Sugimoto, T. Endo, H. Murai, and D. R. Davies, Proc. Natl. Acad. Sci. U.S.A. 96, 13040 (1999).
http://dx.doi.org/10.1073/pnas.96.23.13040
33.
33.M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN03, Revision E.01, Gaussian, Inc., Wallingford, CT, 2004.
34.
34.D. A. Case, T. A. Darden, T. E. Cheatham III et al., AMBER9, University of California, San Francisco, 2006.
35.
35.W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983).
http://dx.doi.org/10.1002/bip.360221211
36.
36.See supplementary material at http://www.aip.org/pubservs/epaps.html for secondary structure evolution during MD simulation and hydrogen bond analysis from MD simulation using AMBER03 and PPC, respectively. A video summarizing this work is also included.[Supplementary Material]
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/content/aip/journal/jcp/132/13/10.1063/1.3360769
2010-04-01
2016-09-25

Abstract

In this paper, we present a detailed dynamics study of the catalytic core domain (CCD) of HIV-1 integrase using both polarized and nonpolarized force fields. The numerical results reveal the critical role of proteinpolarization in stabilizing coordination complex in CCD. Specifically, when nonpolarized force field is used, a remarkable drift of the complex away from its equilibrium position is observed, which causes the binding site blocked by the complex. In contrast, when polarized force field is employed in MD simulation, HIV-1 integrase CCD structure is stabilized and both the position of the complex and the binding site are well preserved. The detailed analysis shows the transition of -helix to -helix adjacent to the catalytic loop (residues 139–147), which correlates with the dislocation of the complex. The current study demonstrates the importance of electronic polarization of protein in stabilizing the metal complex in the catalytic core domain of HIV-1 integrase.

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