Quantum mechanical/molecular mechanical studies of zinc hydrolases

International Reviews in Physical Chemistry

Volumn 33, Issue 1, 2014, Pages 1-41

  Xu, Dingguo ^a   Cui, Qiang ^b   Guo, Hua ^c  

^a China   (China)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

antibiotic resistance; catalytic mechanism; hydrolase; metallo lactamase; molecular dynamics; quantum mechanical molecular mechanical method; zinc enzyme

Indexed keywords

EID: 84897413333     PISSN: 0144235X     EISSN: 1366591X     Source Type: Journal    
DOI: 10.1080/0144235X.2014.889378     Document Type: Review

References (310)

1. D.W. Christianson, Adv. Protein Chem. 42, 281 (1991).
2. B.L. Vallee and D.S. Auld, Acc. Chem. Res. 26, 543 (1993).
3. W.M. Lipscomb and N. Sträter, Chem. Rev. 96, 2375 (1996).
4. A. Messerschmidt, W. Bode and M. Cygler, Handbook of Metalloproteins (Wiley, Chichester, 2004).
5. J. Weston, Chem. Rev. 105, 2151 (2005).
6. T. Dudev and C. Lim, Chem. Rev. 103, 773 (2003).
7. D.S. Auld, in Handbook of Metalloproteins, edited by A. Messerschmidt, W. Bode and M. Cygler (Wiley, Chichester, 2004), Vol. 3, pp. 416-431.
8. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976).
9. J. Aqvist and A. Warshel, Chem. Rev. 93, 2523 (1993).
10. J. Gao, in Reviews in Computational Chemistry, edited by K.B. Lipkowitz and D.B. Boyd (VCH, New York, 1996) Vol. 7, pp. 119-185.
11. A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003).
12. Y. Zhang, Theor. Chem. Acc. 116, 43 (2006).
13. D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. Konig, G. Li, D. Xu, H. Guo, M. Elstener and Q. Cui, J. Phys. Chem. B 110, 6458 (2006).
14. H. Lin and D. Truhlar, Theo. Chem. Acc. 117, 185 (2007).
15. H.M. Senn and W. Thiel, Angew. Chem. Int. Ed. 48, 1198 (2009).
16. K.E. Ranaghan and A.J. Mulholland, Int. Rev. Phys. Chem. 29, 65 (2010).
17. R. Lonsdale, K.E. Ranaghan and A.J. Mulholland, Chem. Commun. 46, 2354 (2010).
18. M.W. van der Kamp and A.J. Mulholland, Biochemistry 52, 2708 (2013).
19. G. Groenhof, in Biomolecular Simulations: Methods and Protocols, Methods in Molecular Biology, edited by L. Monticelli and E. Salonen (Springer Science + Business Media, New York, 2013), Vol. 924, pp. 43-65.
20. D.W. Christianson and W.N. Lipscomb, Acc. Chem. Res. 22, 62 (1989).
21. B.W. Matthews, Acc. Chem. Res. 21, 333 (1988).
22. Z. Wang, W. Fast, A.M. Valentine and S.J. Benkovic, Curr. Opin. Chem. Biol. 3, 614 (1999).
23. J.F. Fisher, S.O. Meroueh and S. Mobashery, Chem. Rev. 105, 395 (2005).
24. M.W. Crowder, J. Spencer and A.J. Vila, Acc. Chem. Res. 45, 13650 (2006).
25. D.S. Auld, Biometals 22, 141 (2009).
26. R.H. Stote and M. Karplus, Proteins: Struct. Funct. Genet. 23, 12 (1995).
27. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., 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 III, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin and M. Karplus, J. Phys. Chem. B 102, 3586 (1998).
28. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell and P.A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
29. Y.P. Pang, J. Mol. Model. 5, 196 (1999).
30. O.A. Donini and P.A. Kollman, J. Med. Chem. 43, 4080 (2000).
31. D.V. Sakarov and C. Lim, J. Am. Chem. Soc. 127, 4921 (2005).
32. S. Riahi, B. Roux and C.N. Rowley, Can. J. Chem. 91, 552 (2013).
33. Y.L. Li, Y. Mei, D.W. Zhang, D.Q. Xie and J.Z.H. Zhang, J. Phys. Chem. B 115, 10154 (2011).
34. A. Vedani and D.W. Huhta, J. Am. Chem. Soc. 112, 4759 (1990).
35. S.C. Hoops, K.W. Anderson and K.M. Merz Jr., J. Am. Chem. Soc. 113, 8262 (1991).
36. D. Lu and G.A. Voth, Proteins 33, 119 (1998).
37. R. Wu, P. Hu, S. Wang, Z. Cao and Y. Zhang, J. Chem. Theory Comput. 6, 337 (2010).
38. F. Lin and R. Wang, J. Chem. Theory Comput. 6, 1852 (2010).
39. M.B. Peters, Y. Yang, B. Wang, L. Fusti-Molnar, M.N. Weaver and K.M. Merz Jr., J. Chem. Theory Comput. 6, 2935 (2010).
40. L. Hu and U. Ryde, J. Chem. Theory Comput. 7, 2452 (2011).
41. T. Zhu, X. Xiao, C. Ji and J.Z.H. Zhang, J. Chem. Theory Comput. 9, 1788 (2013).
42. S.K. Burger, M. Lacasse, T. Verstraelen, J. Drewry, P. Gunning and P.W. Ayers, J. Chem. Theory Comput. 8, 554 (2012).
43. N. Gresh and J. Šponer, J. Phys. Chem. B 103, 11415 (1999).
44. J. Antony, N. Gresh, L. Olsen, L. Hemmingsen, C.J. Schofield and R. Bauer, J. Comput. Chem. 23, 1281 (2002).
45. R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Chem. Theory Comput. 7, 433 (2011).
46. A. Warshel and R.M. Weiss, J. Am. Chem. Soc. 102, 6218 (1980).
47. J. Danielsson and M. Meuwly, J. Chem. Theory Comput. 4, 1083 (2008).
48. M. Head-Gordon, J. Phys. Chem. 100, 13213 (1996).
49. P.E.M. Siegbahn and M.R.A. Blomberg, Chem. Rev. 100, 421 (2000).
50. R.G. Parr and W. Yang, Density Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
51. W.J. Hehre, L. Radom, P.v.R. Schleyer and J.A. Pople, Ab initio Molecular Orbital Theory (Wiley, New York, 1986).
52. J. Tomasi and M. Persico, Chem. Rev. 94, 2027 (1994).
53. U.C. Singh and P.A. Kollman, J. Comput. Chem. 7, 718 (1986).
54. M.J. Field, P.A. Bash and M. Karplus, J. Comput. Chem. 11, 700 (1990).
55. J. Gao and X. Xia, Science 258, 631 (1992).
56. G. Monard and K.M. Merz Jr., Acc. Chem. Res. 32, 904 (1999).
57. M. Garcia-Viloca, J. Gao, M. Karplus and D.G. Truhlar, Science 303, 186 (2004).
58. R.A. Friesner and V. Guallar, Annu. Rev. Phys. Chem. 56, 389 (2005).
59. J. Gao, S. Ma, D.T. Major, K. Nam, J. Pu and D. Truhlar, Chem. Rev. 106, 3188 (2006).
60. A. Warshel, P.K. Sharma, M. Kato, Y. Xiang, H. Liu and M.H.M. Olsson, Chem. Rev. 106, 3210 (2006).
61. H. Hu and W. Yang, Annu. Rev. Phys. Chem. 59, 573 (2008).
62. A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley, New York, 1991).
63. D. Bakowies and W. Thiel, J. Phys. Chem. 100, 10580 (1996).
64. M. Svensson, S. Humbel, R.D.J. Froese, T. Matsubara, S. Sieber and K. Morokuma, J. Phys. Chem. 100, 19357 (1996).
65. V. Thery, D. Rinaldi, J.-L. Rivail, B. Maigret and G.G. Ferenczy, J. Comput. Chem. 15, 269 (1994).
66. J. Gao, P. Amara, C. Alhambra and M.J. Field, J. Phys. Chem. A102, 4714 (1998).
67. Y. Zhang, T. Lee and W. Yang, J. Chem. Phys. 110, 46 (1999).
68. Y. Zhang, J. Chem. Phys. 122, 24114 (2005).
69. C. Corminboeuf, P. Hu, M.E. Tuckerman and Y. Zhang, J. Am. Chem. Soc. 128, 4530 (2006).
70. C. Xiao and Y. Zhang, J. Phys. Chem. B 111, 6229 (2007).
71. J. Blumberger, G. Lamoureux and M.L. Klein, J. Chem. Theory Comput. 3, 1837 (2007).
72. R. Wu, S. Wang, N. Zhou, Z. Cao and Y. Zhang, J. Am. Chem. Soc. 132, 9471 (2010).
73. R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Am. Chem. Soc. 133, 6110 (2011).
74. M.J.S. Dewar, E.G. Zoebisch, E. Healy and J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).
75. J.J.P. Stewart, J. Comput. Chem. 10, 209 (1989).
76. N. Diaz, D. Suarez and K.M. Merz Jr., J. Am. Chem. Soc. 122, 4197 (2000).
77. E.N. Brothers, D. Suarez, D.W. Deerfield and K.M. Merz Jr., J. Comput. Chem. 25, 1677 (2004).
78. H. Kayi and T. Clark, J. Mol. Model. 13, 965 (2007).
79. H. Park, E.N. Brothers and K.M. Merz Jr., J. Am. Chem. Soc. 127, 4232 (2005).
80. A. Sokin, D. Truhlar and E.A. Amin, J. Chem. Theory Comput. 5, 1254 (2009).
81. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai and G. Seigert, Phys. Rev. B. 58, 7260 (1998).
82. M. Elstner, Q. Cui, P. Munih, E. Kaxiras, T. Frauenheim and M. Karplus, J. Comput. Chem. 24, 565 (2003).
83. M. Elstner, P. Hobza, T. Frauenheim and S. Suhai, J. Chem. Phys. 114, 5149 (2001).
84. M. Elstner, Theo. Chem. Acc. 116, 316 (2006).
85. Y. Yang, H. Yu, D. York, Q. Cui and M. Elstner, J. Phys. Chem. A 111, 10861 (2007).
86. M. Gaus, Q. Cui and M. Elstner, J. Chem. Theory Comput. 7, 931 (2011).
87. S. Kaminski, T.J. Giese, M. Gaus, D.M. York and M. Elstner, J. Phys. Chem. A 116, 9131 (2012).
88. G. Hou, X. Zhu, M. Elstner and Q. Cui, J. Chem. Theory Comput. 8, 4293 (2012).
89. J.A. Kalinowski, B. Lesyng, J.D. Thompson, C.J. Cramer and D.G. Truhlar, J. Phys. Chem. A108, 2545 (2004).
90. M. Gaus, Q. Cui and M. Elstner, WIREs Comput. Mol. Sci. 4, 49-61 (2014).
91. M. Elstner, T. Frauenheim, E. Kaxiras, G. Seifert and S. Suhai, Phys. Status Solidi B217, 357 (2000).
92. M. Elstner, K.J. Jalkanen, M. Knapp-Mohammady, T. Frauenheim and S. Suhai, Chem. Phys. 256, 15 (2000).
93. M. Elstner, K.J. Jalkanen, M. Knapp-Mohammady, T. Frauenheim and S. Suhai, Chem. Phys. 263, 203 (2001).
94. D. Reha, M. Kabelac, F. Ryjacek, J. Sponer, J.E. Sponer, M. Elstner, S. Suhai and P. Hobza, J. Am. Chem. Soc. 124, 3366 (2002).
95. H.A. Witek and K. Morokuma, J. Comput. Chem. 25, 1858 (2004).
96. T. Kruger, M. Elstner, P. Schiffels and T. Frauenheim, J. Chem. Phys. 122, 114110 (2005).
97. K.W. Sattelmeyer, J. Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. A 110, 13551 (2006).
98. T. Kubar, P. Jurecka, J. Cerny, J. Rezac, M. Otyepka, H. Valdes and P. Hobza, J. Phys. Chem. A 111, 56642 (2007).
99. N. Otte, M. Scholten and W. Thiel, J. Phys. Chem. A 111, 5751 (2007).
100. E.A. Amin and D.G. Truhlar, J. Chem. Theory Comput. 4, 75 (2008).
101. I. Polyak, T. Benighaus, E. Boulanger and W. Thiel, J. Chem. Phys. 139, (2013).
102. D. Xu, H. Guo and Q. Cui, J. Am. Chem. Soc. 129, 10814 (2007).
103. Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim and M. Karplus, J. Phys. Chem. B 105, 569 (2001).
104. H. Liu, M. Elstner, E. Kaxiras, T. Frauenheim, J. Hermans and W. Yang, Proteins: Struct. Funct. Bioinf. 44, 484 (2001).
105. J. Pu, J. Gao and D.G. Truhlar, J. Phys. Chem. A 108, 5454 (2004).
106. G.d.M. Seabra, R.C. Walker, M. Elstner, D.A. Case and A.E. Roitberg, J. Phys. Chem. A 111, 5655 (2007).
107. P.H. Konig, M. Hoffmann, T. Frauenheim and Q. Cui, J. Phys. Chem. B 109, 9082 (2005).
108. J.P. Ryckaert, G. Ciccotti and H.J. Berendsen, J. Comput. Phys. 23, 327 (1977).
109. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola and J.R. Haak, J. Chem. Phys. 81, 3684 (1984).
110. J.A. McCammon and M. Karplus, Acc. Chem. Res. 16, 187 (1983).
111. M.E. Tuckerman and G.J. Martyna, J. Phys. Chem. B 104, 159 (2000).
112. T. Cheatham and P.A. Kollman, Annu. Rev. Phys. Chem. 51, 435 (2000).
113. A.R. Leach, Molecular Modeling (Prentice Hall, Harlow, 2001).
114. S.A. Adcock and J.A. McCammon, Chem. Rev. 106, 1589 (2006).
115. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan and M. Karplus, J. Comput. Chem. 4, 187 (1983).
116. D.A. Case, T.E. Cheatham I, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods, J. Comput. Chem. 26, 1668 (2005).
117. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey and M.L. Klein, J. Chem. Phys. 79, 926 (1983).
118. M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 1986).
119. T. Darden, D. York and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
120. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee and L. Pedersen, J. Chem. Phys. 103, 8577 (1995).
121. C.L. Brooks III and M. Karplus, J. Chem. Phys. 79, 6312 (1983).
122. C.L. Brooks III and M. Karplus, J. Mol. Biol. 208, 159 (1989).
123. W. Im, S. Berneche and B. Roux, J. Chem. Phys. 114, 2924 (2001).
124. P. Schaefer, D. Riccardi and Q. Cui, J. Chem. Phys. 123, 014905 (2005).
125. X.Y. Lu and Q. Cui, J. Phys. Chem. B 117, 2005 (2013).
126. P.G. Bolhuis, D. Chandler, C. Dellago and P.L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002).
127. Y. Zhang, H. Liu and W. Yang, J. Chem. Phys. 112, 3483 (2000).
128. G.M. Torrie and J.P. Valleau, J. Comput. Phys. 23, 187 (1977).
129. A. Laio and M. Parrinello, Proc. Nat. Acad. Sci. USA 99, 12562 (2002).
130. B. Ensing, M. De Vivo, Z. Liu, P. Moore and M.L. Klein, Acc. Chem. Res. 39, 73 (2006).
131. L. Zheng, M. Chen and W. Yang, Proc. Nat. Acad. Sci. USA 105, 20227 (2008).
132. D. Min, L. Zheng, W. Harris, M. Chen, C. Lv and W. Yang, J. Chem. Theory Comput. 6, 2253 (2010).
133. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman and J.M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
134. D.G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M.L. Sanchez and J. Villa, Acc. Chem. Res. 35, 341 (2002).
135. B.L. Vallee, A. Galdes, D.S. Auld and J.F. Riordan, in Zinc Enzymes, edited by T.G. Spiro (John Wiley & Sons, New York, 1983), Vol. 5, pp. 26-75.
136. W.W. Cleland, Adv. Enzymol. Relat. Areas Mol. Biol. 45, 273 (1977).
137. W.N. Lipscomb, Proc. Nat. Acad. Sci. 77, 3875 (1980).
138. M.A. Ondetti and D.W. Cushman, Annu. Rev. Biochem. 51, 283 (1982).
139. D.W. Christianson and W.N. Lipscomb, Proc. Nat. Acad. Sci. USA. 83, 7568 (1986).
140. D.W. Christianson and W.N. Lipscomb, J. Am. Chem. Soc. 110, 5560 (1988).
141. M.A. Phillips, R. Fletterick and W.J. Rutter, J. Biol. Chem. 265, 20692 (1990).
142. M.A. Phillips and W.J. Rutter, Protein Sci. 1, 517 (1992).
143. W.L. Mock and J.Z. Zhang, J. Biol. Chem. 266, 6393 (1991).
144. R. Breslow and D.L. Wernick, J. Am. Chem. Soc. 98, 259 (1976).
145. R. Breslow and D.L. Wernick, Proc. Nat. Acad. Sci. 74, 1303 (1977).
146. D.S. Auld, A. Galdes, K.F. Geoghegan, B. Holmquit, R.A. Martinelli and B.L. Vallee, Proc. Nat. Acad. Sci. 81, 5041 (1984).
147. K.F. Geoghegan, A. Galdes, G. Hanson, B. Holmquit, D.S. Auld and B.L. Vallee, Biochemistry 25, 4669 (1986).
148. M.W. Makinen, L.C. Kuo, J.J. Dymowski and S. Jaffer, J. Biol. Chem. 254, 356 (1979).
149. L.C. Kuo and M.W. Makinen, J. Biol. Chem. 257, 24 (1982).
150. J. Suh, W. Cho and S. Chung, J. Am. Chem. Soc. 107, 4530 (1985).
151. M.E. Sander and H. Witzel, Biochem. Biophys. Res. Commun. 132, 681 (1985).
152. B.M. Britt and W.L. Peticolas, J. Am. Chem. Soc. 114, 5295 (1992).
153. S.J. Hoffman, S.S.-T. Chu, H.-H. Lee, E.T. Kaiser and P.R. Carey, J. Am. Chem. Soc. 105, 6971 (1983).
154. L. Banci, I. Bertini and G. La Penna, Proteins 18, 186 (1994).
155. A. Alex and T. Clark, J. Comput. Chem. 13, 704 (1992).
156. S. Alvarez-Santos, A. Gonzalez-Lafont and J.M. Lluch, Can. J. Chem. 72, 2077 (1994).
157. S. Alvarez-Santos, A. Gonzalez-Lafont, J.M. Lluch, B. Oliva and F.X. Aviles, New J. Chem. 319, (1998).
158. A. Kilshtain-Vardi, G. Shoham and A. Goldblum, Int. J. Quantum Chem. 88, 87 (2002).
159. A. Vardi-Kilshtain, G. Shoham and A. Goldblum, Mol. Phys. 101, 2715 (2003).
160. L. Phoon and N.A. Burton, J. Mol. Graphics Modell. 24, 94 (2005).
161. J.B. Cross, T. Vreven, S.O. Meroueh, S. Mobashery and H.B. Schlegel, J. Phys. Chem. B 109, 4761 (2005).
162. M.W.Y. Szeto, J.I. Mujika, J. Zurek, A.J. Mulholland and J.N. Harvey, J. Mol. Struct. (Theochem). 898, 106 (2009).
163. A. Vardi-Kilshtain and A. Warshel, Proteins 77, 536 (2009).
164. D. Xu and H. Guo, J. Am. Chem. Soc. 131, 9780 (2009).
165. S. Wu, C. Zhang, D. Xu and H. Guo, J. Phys. Chem. B 114, 9259 (2010).
166. S. Wu, C. Zhang, R. Cao, D. Xu and H. Guo, J. Phys. Chem. B 115, 10360 (2011).
167. S.J. Gardell, C.S. Craik, D. Hilvert, M.S. Urdea and W.J. Rutter, Nature 317, 551 (1985).
168. D. Hilvert, S.J. Gardell, W.J. Rutter and E.T. Kaiser, J. Am. Chem. Soc. 108, 5298 (1986).
169. H.C. Lee, Y.H. Ko, S.B. Baek and D.H. Kim, Bioorg. Med. Chem. Lett. 8, 3379 (1998).
170. N. Izumiya and H. Uchio, J. Biochem. 46, 235 (1959).
171. S. Yanari and M.A. Mitz, J. Am. Chem. Soc. 79, 1150 (1956).
172. S. Yanari and M.A. Mitz, J. Am. Chem. Soc. 79, 1154 (1956).
173. K.J. Lee and D.H. Kim, Bioorg. Med. Chem. 6, 1613 (1998).
174. W.R. Kester and B.W. Matthews, J. Biol. Chem. 252, 7704 (1977).
175. B.W. Matthews, J.N. Jansonius, P.M. Colman, B.P. Schoenborn and D. Dupourque, Nature New Biol. 238, 37 (1972).
176. A. Patchett, E. Harris, E. Tristram, M. Wyvratt, M. Wu, D. Taub, E. Peterson, T. Ikeler, J. Ten Broeke, L. Payne, D. Ondeyka, E. Thorsett, W. Greenlee, N. Lohr, R. Hoffsommer, H. Joshua, W. Ruyle, J. Rothrock, S. Aster, A. Maycock, F. Robinson, R. Hirschmann, C. Sweet, E. Ulm, D. Gross, T. Vassil and C. Stone, Nature 288, 280 (1980).
177. M.A. Holmes and B.W. Matthews, Biochemistry 20, 6912 (1981).
178. S. Toma, S. Campagnoli, E. De Gregoriis, R. Gianna, I. Margarit, M. Zamai and G. Grandi, Protein Eng. 2, 359 (1989).
179. M. Kubo, Y. Mitsuda, M. Takagi and T. Imanaka, Appl. Environ. Microbiol. 58, 3779 (1992).
180. W.L. Mock and M. Aksamavati, Biochem. J. 302, 57 (1994).
181. W.L. Mock and D.J. Stanford, Biochemistry 35, 7369 (1996).
182. A. Beaumont, M.J. O'Donohue, N. Paredes, N. Rousselet, M. Assicot, C. Bohuon, M.-C. Fournie-Zaluski and B.P. Roques, J. Biol. Chem. 270, 16803 (1995).
183. S. Antonczak, G. Monard, M.F. Fuiz-Lopez and J.-L. Rivail, J. Am. Chem. Soc. 120, 8825 (1998).
184. S. Antonczak, G. Monard, M.F. Fuiz-Lopez and J.-L. Rivail, J. Mol. Model. 6, 527 (2000).
185. V. Pelmenschikov, M.R.A. Blomberg and P.E.M. Siegbahn, J. Biol. Inorg. Chem. 7, 284 (2002).
186. H.M. Holden, D.E. Tronrud, A.F. Monzingo, L.H. Weaver and B.W. Matthews, Biochemistry 26, 8542 (1987).
187. M.A. Zaman, S. Oparil and D.A. Calhoun, Nat. Rev. Drug Discovery 1, 621 (2002).
188. M.A. Ondetti, B. Rubin and D.W. Cushman, Science 196, 441 (1977).
189. R. Natesh, S.L.U. Schwager, E.D. Sturrock and K.R. Acharya, Nature 421, 551 (2003).
190. K.R. Acharya, E.D. Sturrock, J.F. Riordan and M.R. Ehlers, Nat. Rev. Drug Discovery 2, 891 (2003).
191. M. Sramko, V. Garaj and M. Remko, J. Mol. Struct. Theochem 869, 19 (2008).
192. L.S.N. dos Santos, M.T. Sonoda, R.A. da Silva Gomes and O. Abrahao Jr., Int. J. Quantum Chem. 112, 3414 (2012).
193. R. Norris, F. Casey, R.J. FitzGeral, D. Shields and C. Mooney, Food Chem. 133, 1349 (2012).
194. A. Papakyriakou, G.A. Spyroulias, E.D. Sturrock, E. Manessi-Zoupa and P. Cordopatis, Biochemistry 46, 8753 (2007).
195. E.D. Sturrock, R. Natesh, J.M. van Rooyen and K.R. Acharya, Cell. Mol. Life Sci. 61, 2677 (2004).
196. X. Wang, S. Wu, D. Xu, D. Xie and H. Guo, J. Chem. Inf. Comput. Sci. 51, 1074 (2011).
197. R. Natesh, S.L.U. Schwager, H.R. Evans, E.D. Sturrock and K.R. Acharya, Biochemistry 43, 8718 (2004).
198. C. Zhang, S. Wu and D. Xu, J. Phys. Chem. B 117, 6635 (2013).
199. P. Bunning and J.F. Riordan, Biochemistry 22, 110 (1983).
200. S. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992).
201. B.E. Turk, Biochem. J. 402, 405 (2007).
202. B.E. Turk, T.Y. Wong, R. Schwarzenbacher, E.T. Jarrell, S.H. Leppla, R.J. Collier, R.C. Liddington and L.C. Cantley, Nat. Struct. Mol. Biol. 11, 60 (2004).
203. A.D. Pannifer, T.Y. Wong, R. Schwarzenbacher, M. Renatus, C. Petosa, J. Bienkowska, D.B. Lacy, R.J. Collier, S. Park, S.H. Leppla, P. Hanna and R.C. Liddington, Nature 414, 229 (2001).
204. R. Hong, A. Magistrato and P. Carloni, J. Chem. Theory Comput. 4, 1745 (2008).
205. G.A. Dalkas, A. Papakyriakou, A. Vlamis-Gardikas and G.A. Spyroulias, Protein Sci. 18, 1774 (2009).
206. C.R. Smith, G.K. Smith, Z. Yang, D. Xu and H. Guo, Theo. Chem. Acc. 128, 83 (2011).
207. F. Tonello, L. Naletto, V. Romanello, F. Dal Molin and C. Montecucco, Biochem. Biophys. Res. Commun. 313, 496 (2004).
208. M. Hernick and C.A. Fierke, Arch. Biochem. Biophys. 433, 71 (2005).
209. A.G. Kazantsev and L.M. Thompson, Nat. Rev. Drug Discovery. 7, 854 (2008).
210. M. Haberland, R.L. Montgomery and E.N. Olson, Nat. Rev. Genet. 10, 32 (2009).
211. I.V. Gregoretti, Y.M. Lee and H.V. Goodson, J. Mol. Biol. 338, 17 (2004).
212. M.S. Finnin, J.R. Donigian, A. Cohen, V.M. Richon, R.A. Rifkind, P.A. Marks, R. Breslow and N.P. Pavletich, Nature 401, 188 (1999).
213. S.M. Sternson, J.C. Wong, C.M. Grozinger and S.L. Schreiber, Org. Lett. 3, 4239 (2001).
214. S. Xiang, S.A. Short, R. Wolfenden and C.W. Carter Jr., Biochemistry 34, 4516 (1995).
215. D.C. Carlow, A.A. Smith, C.C. Yang, S.A. Short and R. Wolfenden, Biochemistry 34, 4220 (1994).
216. L. Frick, C. Yang, V.E. Marquez and R. Wolfenden, Biochemistry 28, 9423 (1989).
217. Q. Xu and H. Guo, J. Phys. Chem. B 108, 2477 (2004).
218. H. Guo, N. Rao, Q. Xu and H. Guo, J. Am. Chem. Soc. 127, 3191 (2005).
219. Q. Xu, H. Guo, A. Corin and H. Guo, J. Phys. Chem. B 111, 6501 (2007).
220. K. Bush and J.F. Fisher, Annu. Rev. Microbiol. 65, 455 (2011).
221. K. Bush, Clin. Infect. Dis. 27, S48 (1998).
222. C. Walsh, Nature 406, 775 (2000).
223. T.R. Walsh, M.A. Toleman, L. Poirel and P. Nordmann, Clin. Microbiol. Rev. 18, 306 (2005).
224. D. Yong, M.A. Toleman, C.G. Giske, H.S. Cho, K. Sundman, K. Lee and T.R. Walsh, Antimicrob. Agents Chemother. 53, 5046 (2009).
225. M. Galleni, J. Lamotte-Brasseur, G.M. Rossolini, J. Spencer, O. Dideberg and J.-M. Frere, Antimicrob. Agents Chemother. 45, 660 (2001).
226. C. Bebrone, Biochem. Pharmacol. 74, 1686 (2007).
227. G. Estiu, D. Suarez and K.M. Merz Jr., J. Comput. Chem. 27, 1240 (2006).
228. A. Cavalli, P. Carloni and M. Recanatini, Chem. Rev. 106, 3497 (2006).
229. D. Suarez and K.M. Merz Jr., J. Am. Chem. Soc. 123, 3759 (2001).
230. N. Diaz, D. Suarez and K.M. Merz Jr., J. Am. Chem. Soc. 123, 9867 (2001).
231. J.F.R. Salsbury, M.F. Crowley and C.L. Brooks III, Proteins 44, 448 (2001).
232. D. Suarez, N. Diaz and K.M. Merz Jr., J. Comput. Chem. 23, 1587 (2002).
233. D. Suarez, E.N. Brothers and K.M. Merz Jr., Biochemistry 41, 6615 (2002).
234. P. Oelschlaeger, R.D. Schmid and J. Pleiss, Protein Eng. Des. Sel. 16, 341 (2003).
235. P. Oelschlaeger, R.D. Schmid and J. Pleiss, Biochemistry 42, 8945 (2003).
236. M. Krauss, N. Gresh and J. Antony, J. Phys. Chem. B 107, 1215 (2003).
237. M. Dal Peraro, A.J. Vila and P. Carloni, Proteins: Struct. Funct. Bioinf. 54, 412 (2004).
238. H. Park and K.M. Merz Jr., J. Med. Chem. 48, 1630 (2005).
239. D. Xu, Y. Zhou, D. Xie and H. Guo, J. Med. Chem. 48, 6679 (2005).
240. C. Wang and H. Guo, J. Phys. Chem. B 111, 9986 (2007).
241. D. Xu, H. Guo and Q. Cui, J. Phys. Chem. A 111, 5630 (2007).
242. F. Simona, A. Magistrato, D.M.A. Vera, G. Garau, A.J. Vila and P. Carloni, Proteins: Struct. Funct. Bioinf. 69, 595 (2007).
243. P. Oelschlaeger and J. Pleiss, J. Mol. Biol. 366, 316 (2007).
244. F.R. Salsbury, M.W. Crowder, S.F. Kingsmore and J.J.A. Huntley, J. Mol. Model. 15, 133 (2009).
245. D. Suarez, E. Suarez and N. Diaz, J. Mol. Struct. Theochem. 912, 105 (2009).
246. H.S.R. Gilson and M. Krauss, J. Am. Chem. Soc. 121, 6984 (1999).
247. M. Krauss, M. Gilson and N. Gresh, J. Phys. Chem. B 105, 8040 (2001).
248. L. Olsen, J. Antony, L. Hemmingsen and K.V. Mikkelsen, J. Phys. Chem. A 106, 1046 (2002).
249. M. Dal Peraro, A.J. Vila and P. Carloni, J. Biol. Inorg. Chem. 7, 704 (2002).
250. W. Gu, J. Zhu and H. Liu, J. Theor. Comput. Chem. 1, 62 (2002).
251. L. Olsen, T. Rasmussen, L. Hemmingsen and U. Ryde, J. Phys. Chem. B 108, 17639 (2004).
252. X. Li, S.A. Hayik and K.M. Merz Jr., J. Inorg. Biochem. 104, 512 (2010).
253. P.W. Thomas, M. Zheng, S. Wu, H. Guo, D. Liu, D. Xu and W. Fast, Biochemistry 50, 10102 (2011).
254. M. Zheng and D. Xu, J. Phys. Chem. B 117, 11596 (2013).
255. L. Olsen, J. Antony, U. Ryde, H.-W. Adolph and L. Hemmingsen, J. Phys. Chem. B 107, 2366 (2003).
256. M. Dal Peraro, L.I. Llarrull, U. Rothlisberger, A.J. Vila and P. Carloni, J. Am. Chem. Soc. 126, 12661 (2004).
257. D. Xu, D. Xie and H. Guo, J. Biol. Chem. 281, 8740 (2006).
258. M. Dal Peraro, A.J. Vila, P. Carloni and M.L. Klein, J. Am. Chem. Soc. 129, 2808 (2007).
259. F. Simona, A. Magistrato, M. Dal Peraro, A. Cavalli, A.J. Vila and P. Carloni, J. Biol. Chem. 284, 28164 (2009).
260. S. Wu, D. Xu and H. Guo, J. Am. Chem. Soc. 132, 17986 (2010).
261. U. Heinz and H.W. Adolph, Cell. Mol. Life Sci. 61, 2827 (2004).
262. J. Sgrignani, A. Magistrato, M. Dal Peraro, A.J. Vila, P. Carloni and R. Pierattelli, J. Comput. Aided Mol. Des. 26, 425 (2012).
263. L.I. Llarrull, M.F. Tioni and A.J. Vila, J. Am. Chem. Soc. 130, 15842 (2008).
264. M.F. Tioni, L.I. Llarrull, A.A. Poeylaut-Palena, M.A. Marti, M. Saggu, G.R. Periyannan, E.G. Mata, B. Bennett, D.H. Murgida and A.J. Vila, J. Am. Chem. Soc. 130, 15852 (2008).
265. D.L. Gatti, Plos Biol. 7, e30079 (2012).
266. S.H. Ackerman and D.L. Gatti, Plos One 8, e55136 (2013).
267. G. Garau, C. Bebrone, C. Anne, M. Galleni, J.-M. Frere and O. Dideberg, J. Mol. Biol. 345, 785 (2005).
268. J. Spencer, J. Read, R.B. Sessions, S. Howell, G.M. Blackburn and S.J. Gamblin, J. Am. Chem. Soc. 127, 14439 (2005).
269. J.H. Toney, G.G. Hammond, P.M. Fitzgerald, N. Sharma, J.M. Balkovec, G.P. Rouen, S.H. Olson, M.L. Hammond, M.L. Greenlee and Y.-D. Gao, J. Biol. Chem. 276, 31913 (2001).
270. D.J. Payne, J.A. Hueso-Rodriguez, H. Boyd, N.O. Concha, C.A. Janson, M. Gilpin, J.H. Bateson, C.A. Cheever, N.L. Niconovich, S. Pearson, S. Rittenhouse, D. Tew, E. Diez, P. Perez, J. De la Fuente, M. Rees and A. Rivera-Sagredo, Antimicrob. Agents Chemother. 46, 1880 (2002).
271. N.P. Sharma, C. Hajdin, S. Chandrasekar, B. Bennett, K.-W. Yang and M.W. Crowder, Biochemistry 45, 10729 (2006).
272. Z. Wang, W. Fast and S.J. Benkovic, Biochemistry 38, 10013 (1999).
273. M.-N. Lisa, L. Hemmingsen and A.J. Vila, J. Biol. Chem. 285, 4570 (2010).
274. M. Dal Peraro, A.J. Vila and P. Carloni, Inorg. Chem. 42, 4245 (2003).
275. C.E. Valdez and A.N. Alexandrova, J. Phys. Chem. B 116, 10649 (2012).
276. C.E. Valdez, M. Sparta and A.N. Alexandrova, J. Chem. Theory Comput. 9, 730 (2013).
277. Z. Wang, W. Fast and S.J. Benkovic, J. Am. Chem. Soc. 120, 10788 (1998).
278. R. Bicknell, A. Schaffer, S.G. Waley and D.S. Auld, Biochemistry 25, 7208 (1986).
279. J.D. Garrity, B. Bennett and M.W. Crowder, Biochemistry 44, 1078 (2005).
280. A. Costello, G. Periyannan, K.-W. Yang, M.W. Crowder and D.L. Tierney, J. Biol. Inorg. Chem. 11, 351 (2006).
281. J.D. Garrity, A.L. Carenbauer, L.R. Herron and M.W. Crowder, J. Biol. Chem. 279, 920 (2004).
282. Z. Hu, G. Periyannan, B. Bennett and M.W. Crowder, J. Am. Chem. Soc. 130, 14207 (2008).
283. J. Moran-Barrio, J.M. Gonzalez, M.-N. Lisa, A.L. Costello, M. Dal Peraro, P. Carloni, B. Bennett, D.L. Tierney, A.S. Limansky, A.M. Viale and A.J. Vila, J. Biol. Chem. 282, 18286 (2007).
284. M.W. Crowder, T.R. Walsh, L. Banovic, M. Pettit and J. Spencer, Antimicrob. Agents Chemother. 42, 921 (1998).
285. H. Zhang and Q. Hao, FASEB J. 25, 2574 (2011).
286. Y. Kim, M.A. Cunningham, J. Mire, C. Tesar, J. Sacchettini and A. Joachimiak, FASEB J. 27, 1917 (2013).
287. K. Zhu, Z. Liang, X. Kong, F. Ye, L. Jin, H. Geng, Y. Chen, M. Zheng, H. Jiang, J.Q. Li and C. Luo, J. Comput. Aided Mol. Des. 27, 247 (2013).
288. M.B. Miller and B.L. Bassler, Annu. Rev. Microbiol. 55, 165 (2001).
289. H. Suga and K.M. Smith, Curr. Opin. Chem. Biol. 7, 586 (2003).
290. W. Fast and P.A. Tipton, Trends Biochem. Sci. 37, 7 (2011).
291. H. Daiyasu, K. Osaka, Y. Ishino and H. Toh, FEBS Lett. 503, 1 (2001).
292. D. Liu, B.W. Lepore, G.A. Petsko, P.W. Thomas, E.M. Stone, W. Fast and D. Ringe, Proc. Nat. Acad. Sci. 102, 11882 (2005).
293. M.H. Kim, W.-C. Choi, H.O. Kang, J.S. Lee, B.S. Kang, K.-J. Kim, Z.S. Derewenda, T.-K. Oh, C.H. Lee and J.-K. Lee, Proc. Nat. Acad. Sci. 102, 17606 (2005).
294. P.W. Thomas, E.M. Stone, A.L. Costello, D.L. Tierney and W. Fast, Biochemistry 44, 7559 (2005).
295. J. Momb, C. Wang, D. Liu, P.W. Thomas, G.A. Petsko, H. Guo, D. Ringe and W. Fast, Biochemistry 47, 7715 (2008).
296. D. Liu, J. Momb, P.W. Thomas, A. Moulin, G.A. Petsko, W. Fast and D. Ringe, Biochemistry 47, 7706 (2008).
297. R.-Z. Liao, J.-G. Yu and F. Himo, Inorg. Chem. 48, 1442 (2009).
298. M.N. Charendoff, H.P. Shah and J.M. Briggs, Plos One 8, e75395 (2013).
299. W.T. Lowther and B.W. Matthews, Chem. Rev. 102, 4581 (2002).
300. S.-L. Chen, T. Marino, W.-H. Fang, N. Russo and F. Himo, J. Phys. Chem. B 112, 2494 (2008).
301. W. Desmarais, D.L. Bienvenue, K.P. Bzymek, G.A. Petsko, D. Ringe and R.C. Holz, J. Biol. Inorg. Chem. 11, 398 (2006).
302. R.-Z. Liao, F. Himo, J.-G. Yu and R.-Z. Liu, J. Inorg. Biochem. 104, 37 (2010).
303. G. Schurer, H. Lanig and T. Clark, Biochemistry 43, 5414 (2004).
304. G. Schurer, A.H.C. Horn, P. Gedeck and T. Clark, J. Phys. Chem. B 106, 8815 (2002).
305. C.-G. Zhan and F. Zheng, J. Am. Chem. Soc. 123, 2835 (2001).
306. E.A. Salter and A. Wierzbicki, J. Phys. Chem. B 111, 45477 (2007).
307. V. Lopez-Canut, M. Roca, J. Bertran, V. Moliner and I. Tunon, J. Am. Chem. Soc. 132, 6955 (2010).
308. K.-Y. Wong and J. Gao, FEBS J. 278, 2579 (2011).
309. G. Hou and Q. Cui, J. Am. Chem. Soc. 134, 229 (2012).
310. G. Hou and Q. Cui, J. Am. Chem. Soc. 135, 10457 (2013).