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A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases

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Abstract

We present the theoretical evaluation of new AMBER force field parameters for 12 copper-based nucleases with bis(2-pyridylmethyl) amine, 2,2′-dipyridylamine, imidazole, N,N-bis(2-benzimidazolylmethyl) amine and their derivative ligands based on first-principles electronic structure calculations at the B3LYP level of theory. A three-point approach was developed to accurately and efficiently evaluate the force field parameters for the copper-based nucleases with the ligands. The protocol of RESP atomic charges has been used to calculate the atomic charge distributions of the studied copper-based nucleases. The evaluated force field parameters and RESP atomic charges have been successfully applied in the testing molecular mechanics calculations and molecular dynamics simulations on the nucleases and the nuclease–DNA complexes, respectively. It has been demonstrated that the developed force field parameters and atomic charges can consistently reproduce molecular geometries and conformations in the available X-ray crystal structures and can reasonably predict the interaction properties of the nucleases with DNA. The developed force field parameters in this work provide an extension of the AMBER force field for its application to computational modeling and simulations of the copper-based artificial nucleases associated with DNA.

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References

  1. Thematic issue (no. 3) on RNA/DNA cleavage (1998) Chem Rev 98:937

  2. Erkkila KE, Odom DT, Barton JK (1999) Chem Rev 99:2777. doi:10.1021/cr9804341

    Article  CAS  Google Scholar 

  3. Pogozelski WK, Tullius TD (1998) Chem Rev 98:1089. doi:10.1021/cr960437i

    Article  CAS  Google Scholar 

  4. Sigman DS (1986) Acc Chem Res 19:180. doi:10.1021/ar00126a004

    Article  CAS  Google Scholar 

  5. Nasir MS, Karlin KD, McGowty D, Zubieta J (1991) J Am Chem Soc 113:698. doi:10.1021/ja00002a062

    Article  CAS  Google Scholar 

  6. Murthy NN, Mahroof-Tahir M, Karlin KD (1993) J Am Chem Soc 115:10404. doi:10.1021/ja00075a084

    Article  CAS  Google Scholar 

  7. Humphreys KJ, Karlin KD, Rokita SE (2002) J Am Chem Soc 124:6009. doi:10.1021/ja020039z

    Article  CAS  Google Scholar 

  8. Li L, Sarjeant AAN, Karlin KD (2006) Inorg Chem 45:7160. doi:10.1021/ic060598x

    Article  CAS  Google Scholar 

  9. Zhao Y, Zhu J, He W, Yang Z, Zhu Y, Li Y, Zhang J, Guo Z (2006) Chem Eur J 12:6621. doi:10.1002/chem.200600044

    Article  CAS  Google Scholar 

  10. Lu Z-L, Liu CT, Neverov AA, Brown RS (2007) J Am Chem Soc 129:11642. doi:10.1021/ja073780l

    Article  CAS  Google Scholar 

  11. An Y, Liu S-D, Deng S-Y, Ji L-N, Mao Z-W (2006) J Inorg Biochem 100:1586. doi:10.1016/j.jinorgbio.2006.05.002

    Article  CAS  Google Scholar 

  12. Mirica LM, Ottenwaelder X, Stack TDP (2004) Chem Rev 104:1013. doi:10.1021/cr020632z

    Article  CAS  Google Scholar 

  13. Thyagarajan S, Murthy NN, Sarjeant AAN, Karlin KD, Rokita SE (2006) J Am Chem Soc 128:7003. doi:10.1021/ja061014t

    Article  CAS  Google Scholar 

  14. Jiang Q, Xiao N, Shi P, Zhu Y, Guo Z (2007) Coord Chem Rev 251:1951. doi:10.1016/j.ccr.2007.02.013

    Article  CAS  Google Scholar 

  15. Niklas N, Heinemann FW, Hampel F, Clark T, Alsfasser R (2004) Inorg Chem 43:4663. doi:10.1021/ic0496774

    Article  CAS  Google Scholar 

  16. Liu C, Zhou J, Li Q, Wang L, Liao Z, Xu H (1999) J Inorg Biochem 75:233. doi:10.1016/S0162-0134(99)00037-9

    Article  CAS  Google Scholar 

  17. Chen J, Wang X, Shao Y, Zhu J, Zhu Y, Li Y, Xu Q, Guo Z (2007) Inorg Chem 46:3306. doi:10.1021/ic0614162

    Article  CAS  Google Scholar 

  18. Sreedhara A, Freed JD, Cowan JA (2000) J Am Chem Soc 122:8814. doi:10.1021/ja994411v

    Article  CAS  Google Scholar 

  19. Pitié M, Burrows CJ, Meunier B (2000) Nucleic Acids Res 28:4856. doi:10.1093/nar/28.24.4856

    Article  Google Scholar 

  20. Bales BC, Pitié M, Meunier B, Greenberg MM (2002) J Am Chem Soc 124:9062. doi:10.1021/ja026970z

    Article  CAS  Google Scholar 

  21. Li L, Karlin KD, Rokita SE (2005) J Am Chem Soc 127:520. doi:10.1021/ja044209e

    Article  CAS  Google Scholar 

  22. Tu C, Shao Y, Gan N, Xu Q, Guo Z (2004) Inorg Chem 43:4761. doi:10.1021/ic049731g

    Article  CAS  Google Scholar 

  23. Hegg EL, Burstyn JN (1998) Coord Chem Rev 173:133. doi:10.1016/S0010-8545(98)00157-X

    Article  CAS  Google Scholar 

  24. Oyoshi T, Sugiyama H (2000) J Am Chem Soc 122:6313. doi:10.1021/ja9919130

    Article  CAS  Google Scholar 

  25. Lu L-P, Zhu M-L, Yang P (2003) J Inorg Biochem 95:31. doi:10.1016/S0162-0134(03)00049-7

    Article  CAS  Google Scholar 

  26. Comba P, Remenyi R (2003) Coord Chem Rev 238–239:9. doi:10.1016/S0010-8545(02)00286-2

    Article  Google Scholar 

  27. Oda A, Yamaotsu N, Hirono S (2005) J Comput Chem 26:818. doi:10.1002/jcc.20221

    Article  CAS  Google Scholar 

  28. Cornell WD, Cieplak P, Bayly CI, Gould IR, Kenneth M, Merz J, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179. doi:10.1021/ja00124a002

    Article  CAS  Google Scholar 

  29. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25:1157. doi:10.1002/jcc.20035

    Article  CAS  Google Scholar 

  30. Yang L, Tan C-h, Hsieh M-J, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R (2006) J Phys Chem B 110:13166. doi:10.1021/jp060163v

    Article  CAS  Google Scholar 

  31. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187. doi:10.1002/jcc.540040211

    Article  CAS  Google Scholar 

  32. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586

    Google Scholar 

  33. Rappé AK, Casewit CJ, Colwell KS, Goddard WA III, Skiff WM (1992) J Am Chem Soc 114:10024 doi:10.1021/ja00051a040

    Google Scholar 

  34. Scott WRP, Hünenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Krüger P, Gunsteren WFv (1999) J Phys Chem A 103:3596. doi:10.1021/jp984217f

    Article  CAS  Google Scholar 

  35. Rigby D, Sun H, Eichinger BE (1997) Polym Int 44:311. doi:10.1002/(SICI)1097-0126(199711)44:3<311::AID-PI880>3.0.CO;2-H

    Article  CAS  Google Scholar 

  36. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Salvatore Profeta J, Weinerl P (1984) J Am Chem Soc 106:765. doi:10.1021/ja00315a051

    Article  CAS  Google Scholar 

  37. Aduri R, Psciuk BT, Saro P, Taniga H, Schlegel HB, John SantaLucia J (2007) J Chem Theory Comput 3:1464. doi:10.1021/ct600329w

    Article  CAS  Google Scholar 

  38. Comba P, Remenyi R (2002) J Comput Chem 23:697. doi:10.1002/jcc.10084

    Article  CAS  Google Scholar 

  39. Autenrieth F, Tajkhorshid E, Baudry J, Luthey-Schulten Z (2004) J Comput Chem 25:1613. doi:10.1002/jcc.20079

    Article  CAS  Google Scholar 

  40. Comba P, Daubinet A, Martin B, Pietzsch H-J, Stephan H (2006) J Organomet Chem 691:2495. doi:10.1016/j.jorganchem.2006.01.068

    Article  CAS  Google Scholar 

  41. Shuku T, Sugimori K, Sugiyama A, Nagao H, Sakurai T, Nishikawa K (2005) Polyhedron 24:2665. doi:10.1016/j.poly.2005.03.141

    Article  CAS  Google Scholar 

  42. Sugiyama A, Takamatsu Y, Nishikawa K, Nagao H, Nishikawa K (2006) Int J Quantum Chem 106:3071. doi:10.1002/qua.21148

    Article  CAS  Google Scholar 

  43. Zhu YY, Su YW, Li XC, Wang Y, Chen GJ (2008) Chem Phys Lett 455:354. doi:10.1016/j.cplett.2008.03.004

    Article  CAS  Google Scholar 

  44. Humphreys KJ, Karlin KD, Rokita SE (2002) J Am Chem Soc 124:8055. doi:10.1021/ja012539i

    Article  CAS  Google Scholar 

  45. Scarpellini M, Neves A, Hörner R, Bortoluzzi AJ, Szpoganics B, Zucco C, Silva RAN, Drago V, Mangrich AS, Ortiz WA, Passos WAC, Oliveira MCBd, Terenzi H (2003) Inorg Chem 42:8353. doi:10.1021/ic026277c

    Article  CAS  Google Scholar 

  46. Scarpellini M, Neves A, Castellano EE, Franco DW (2004) J Mol Struct 694:193. doi:10.1016/j.molstruc.2004.03.028

    Article  CAS  Google Scholar 

  47. Vaidyanathan VG, Nair BU (2003) J Inorg Biochem 93:271. doi:10.1016/S0162-0134(02)00593-7

    Article  CAS  Google Scholar 

  48. Young MJ, Wahnon D, Hynes RC, Chin J (1995) J Am Chem Soc 117:9441. doi:10.1021/ja00142a010

    Article  CAS  Google Scholar 

  49. Becke AD (1992) J Chem Phys 98:5648. doi:10.1063/1.464913

    Article  Google Scholar 

  50. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T Jr, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) GAUSSIAN 03, Gaussian, Inc, Wallingford, CT

  51. Schäfer A, Horn H, Ahlrichs R (1992) J Chem Phys 97:2571. doi:10.1063/1.463096

    Article  Google Scholar 

  52. Olsson MHM, Ryde U (2001) J Am Chem Soc 123:7866. doi:10.1021/ja010315u

    Article  CAS  Google Scholar 

  53. Ditchfield R, Hehre WJ, Pople JA (1971) J Chem Phys 54:724. doi:10.1063/1.1674902

    Article  CAS  Google Scholar 

  54. Schultz NE, Zhao Y, Truhlar DG (2008) J Comput Chem 29:185. doi:10.1002/jcc.20717

    Article  CAS  Google Scholar 

  55. Zhao Y, Truhlar DG (2006) J Chem Phys 125:194101. doi:10.1063/1.2370993

    Article  Google Scholar 

  56. Schultz NE, Zhao Y, Truhlar DG (2005) J Phys Chem A 109:11127. doi:10.1021/jp0539223

    Article  CAS  Google Scholar 

  57. Schultz NE, Zhao Y, Truhlar DG (2005) J Phys Chem A 109:4388. doi:10.1021/jp0504468

    Article  CAS  Google Scholar 

  58. Zhao Y, Truhlar DG (2008) J Phys Chem A 112:6794. doi:10.1021/jp804583d

    Article  CAS  Google Scholar 

  59. Zhao Y, Truhlar DG (2008) J Phys Chem A 112:1095. doi:10.1021/jp7109127

    Article  CAS  Google Scholar 

  60. Schultz NE, Gherman BF, Crammer CJ, Truhlar DG (2006) J Phys Chem B 110:24030. doi:10.1021/jp064467t

    Article  CAS  Google Scholar 

  61. Zhao Y, Schultz NE, Truhlar DG (2005) J Chem Phys 123:161103. doi:10.1063/1.2126975

    Article  Google Scholar 

  62. Zhao Y, Schultz NE, Truhlar DG (2006) J Chem Theory Comput 2:364. doi:10.1021/ct0502763

    Article  Google Scholar 

  63. Raghavachari K, Trucks GW (1989) J Chem Phys 91:1062. doi:10.1063/1.457230

    Article  Google Scholar 

  64. Bol JE, Buning C, Comba P, Reedijk J, Ströhle M (1998) J Comput Chem 19:512. doi:10.1002/(SICI)1096-987X(19980415)19:5<512::AID-JCC4>3.0.CO;2-P

    Article  CAS  Google Scholar 

  65. Qiu D, Dasgupta S, Kozlowski PM, III WAG, Spiro TG (1998) J Am Chem Soc 120:12791. doi:10.1021/ja964472i

    Google Scholar 

  66. Reichert DE, Norrby P-O, Welch MJ (2001) Inorg Chem 40:5223. doi:10.1021/ic0012118

    Article  CAS  Google Scholar 

  67. Hzffnera F, Brinck T, Haeberlein M, Moberg C (1997) J Mol Struct Theochem 397:39. doi:10.1016/S0166-1280(96)04978-0

    Article  Google Scholar 

  68. Branco RJF, Fernandes PA, Ramos MJ (2006) J Phys Chem B 110:16754. doi:10.1021/jp056855l

    Article  CAS  Google Scholar 

  69. Bayly CI, Cieplak P, Cornell W, Kollman PA (1993) J Phys Chem 97:10269. doi:10.1021/j100142a004

    Article  CAS  Google Scholar 

  70. Singh UC, Kollman PA (1984) J Comput Chem 5:129. doi:10.1002/jcc.540050204

    Article  CAS  Google Scholar 

  71. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) J Comput Chem 19:1639. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B

    Article  CAS  Google Scholar 

  72. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9, University of California, San Francisco

  73. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14.1:33

    Article  Google Scholar 

  74. Burton VJ, Deeth RJ, Kemp CM, Gilbert PJ (1995) J Am Chem Soc 117:8407. doi:10.1021/ja00137a014

    Article  CAS  Google Scholar 

  75. Deeth RJ (2001) Coord Chem Rev 212:11. doi:10.1016/S0010-8545(00)00354-4

    Article  CAS  Google Scholar 

  76. Deeth RJ (2006) Chem Commun (Camb) 2551. doi:10.1039/b604290b

  77. Deeth RJ (2007) Inorg Chem 46:4492. doi:10.1021/ic062399j

    Article  CAS  Google Scholar 

  78. Diedrich C, Deeth RJ (2008) Inorg Chem 47:2494. doi:10.1021/ic701803g

    Article  CAS  Google Scholar 

  79. Deeth RJ, Hearnshaw LJA (2006) Dalton Trans 1092. doi:10.1039/b509274d

  80. Deeth RJ, Anastasi A, Diedrich C, Randell K (2008) Coord Chem Rev. doi:10.1016/j.ccr.2008.06.018

  81. Deeth RJ, Hearnshaw LJA (2005) Dalton Trans 3638. doi:10.1039/b507295f

  82. Mcmillen DF, Golden DM (1982) Annu Rev Phys Chem 33:493. doi:10.1146/annurev.pc.33.100182.002425

    Article  CAS  Google Scholar 

  83. Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) J Comput Chem 16:1357. doi:10.1002/jcc.540161106

    Article  CAS  Google Scholar 

  84. Breneman CM, Wiberg KB (1990) J Comput Chem 11:361. doi:10.1002/jcc.540110311

    Article  CAS  Google Scholar 

  85. Shi S, Liu J, Li J, Zheng KC, Tan CP, Chen LM, Ji LN (2005) Dalton Trans 2038. doi:10.1039/b501112d

  86. Detmer CAI, Pamatong FV, Bocarsly JR (1996) Inorg Chem 35:6292. doi:10.1021/ic960519p

    Article  CAS  Google Scholar 

  87. Pamatong FV, Charles A, Detmer I, Bocarsly JR (1996) J Am Chem Soc 118:5339. doi:10.1021/ja953282p

    Article  CAS  Google Scholar 

  88. Jin Y, Cowan JA (2005) J Am Chem Soc 127:8408. doi:10.1021/ja0503985

    Article  CAS  Google Scholar 

  89. Decker A, Chow MS, Kemsley JN, Lehnert N, Solomon EI (2006) J Am Chem Soc 128:4719. doi:10.1021/ja057378n

    Article  CAS  Google Scholar 

  90. Oikawa S, Kawanishi S (1996) Biochemistry 35:4584. doi:10.1021/bi9527000

    Article  CAS  Google Scholar 

  91. Leaver SA, Palaniandavar M, Kilner CA, Halcrow MA (2003) Dalton Trans 4224. doi:10.1039/b310144d

  92. Nielsen A, Veltzé S, Bond AD, McKenzie CJ (2007) Polyhedron 26:1649. doi:10.1016/j.poly.2006.12.005

    Article  CAS  Google Scholar 

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Acknowledgments

Financial support from the National Natural Science Foundation of China (Nos. 20673011, 20631020 and 20771017) and the Major State Basic Research Development Programs (Grant No. G2004CB719900) is gratefully acknowledged. We also thank computing resources provided by the HPSC of Beijing Normal University.

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  1. College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Haidian District, 100875, Beijing, People’s Republic of China

    Yanyan Zhu, Yan Wang & Guangju Chen

  2. Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA

    Chang-Guo Zhan

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  1. Yanyan Zhu
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Correspondence to Yan Wang or Guangju Chen.

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Zhu, Y., Wang, Y., Chen, G. et al. A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases. Theor Chem Account 122, 167–178 (2009). https://doi.org/10.1007/s00214-008-0496-6

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