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脱氧核糖核酸柔性的分子动力学模拟:Amber bsc1和bsc0力场的对比研究

熊开欣 席昆 鲍磊 张忠良 谭志杰

脱氧核糖核酸柔性的分子动力学模拟:Amber bsc1和bsc0力场的对比研究

熊开欣, 席昆, 鲍磊, 张忠良, 谭志杰
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  • 脱氧核糖核酸(DNA)的结构柔性对DNA生物功能的实现具有重要作用,全原子分子动力学模拟是一种研究DNA结构柔性的重要方法.DNA的分子动力学力场在Amber bsc0基础上有了进一步的发展,即Amber bsc1.本文采用基于最新bsc1力场和先前bsc0力场的分子动力学模拟对DNA的宏观柔性和微观柔性进行对比研究,发现力场的改进对DNA宏观柔性参量的预测有一定改善,即所预测的拉伸模量和扭转-伸缩耦合比与实验值更为接近,而弯曲持久长度和扭转持久长度两种力场结果皆与实验值一致.微观分析发现,除了滑移量稍变大,bsc1力场得到的微观结构参量如扭转角和倾斜角与实验值更为接近,且新力场下DNA宏观柔性的改善与DNA的微观结构参量及其涨落紧密相关.
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    Peters J P, Maher L J 2010 Q. Rev. Biophys. 43 23

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    Bao L, Zhang X, Jin L, Tan Z J 2015 Chin. Phys. B 24 018703

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    Lionnet T, Joubaud S, Lavery R, Bensimon D, Croquette V 2006 Phys. Rev. Lett. 96 178102

    [4]

    Forth S, Sheinin M Y, Inman J, Wang M D 2013 Ann. Rev. Biophys. 42 583

    [5]

    Zhang Z L, Wu Y Y, Xi K, Sang J P, Tan Z J 2017 Biophys. J. 113 517

    [6]

    Richmond T J, Davey C A 2003 Nature 423 145

    [7]

    Noll M 1977 J. Mol. Biol. 116 49

    [8]

    Felsenfeld G, Boyes J, Chung J H, Clark D J, Studitsky V M 1996 Proc. Natl. Acad. Sci. USA 93 9384

    [9]

    Li W, Wang P Y, Yan J, Li M 2012 Phys. Rev. Lett. 109 218102

    [10]

    Xiao S Y, Zhu H, Wang L, Liang H J 2014 Soft Matter 10 1045

    [11]

    Xiao S Y, Liang H J 2012 J. Chem. Phys. 136 205102

    [12]

    Bryant Z, Stone M D, Gore J, Smith S B, Cozzarelli N R, Bustamante C 2003 Nature 424 338

    [13]

    Wu Y Y, Bao L, Zhang X, Tan Z J 2015 J. Chem. Phys. 142 125103

    [14]

    Wang F H, Wu Y Y, Tan Z J 2013 Biopolymers 99 370

    [15]

    Kratky O, Porod G 2010 Rel. Trav. Chim. Pays-Bas. 68 1106

    [16]

    Noy A, Golestanian R 2012 Phys. Rev. Lett. 109 228101

    [17]

    Zhang X H, Chen H, Fu H X, Doyle P S, Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103

    [18]

    Fu W B, Wang X L, Zhang X H, Ran S Y, Yan J, Li M 2006 J. Am. Chem. Soc. 128 15040

    [19]

    Zhang X, Bao L, Wu Y Y, Zhu X L, Tan Z J 2017 J. Chem. Phys. 147 054901

    [20]

    Travers A A 2004 Phil. Trans. R. Soc. Lond. A 362 1423

    [21]

    Tan Z J, Chen S J 2008 Biophys. J. 94 3137

    [22]

    Zhou H J, Zhang Y, Ouyang Z C 1998 Phys. Rev. Lett. 82 4560

    [23]

    Zhou H, Zhang Y, Ouyang Z C 2000 Phys. Rev. E 62 1045

    [24]

    Gore J, Bryant Z, Nöllmann M, Le M U, Cozzarelli N R, Bustamante C 2006 Nature 442 836

    [25]

    Moroz J D, Nelson P C 1997 Proc. Natl. Acad. Sci. USA 94 14418

    [26]

    Marko J F 1998 Phys. Rev. E 57 2134

    [27]

    Bao L, Zhang X, Shi Y Z, Wu Y Y, Tan Z J 2017 Biophys. J. 112 1094

    [28]

    Mazur A K, Maaloum M 2014 Phys. Rev. Lett. 112 068104

    [29]

    Abels J A, Moreno-Herrero F, van der Heiden T, Dekker C, Dekker N H 2005 Biophys. J. 88 2737

    [30]

    Yuan C, Chen H, Lou X W, Archer L A 2008 Phys. Rev. Lett. 100 018102

    [31]

    Mathew-Fenn R S, Das R, Harbury P A B 2008 Science 322 446

    [32]

    Mastroianni A J, Sivak D A, Geissler P L, Alivisatos A P 2009 Biophys. J. 97 1408

    [33]

    Smith S B, Cui Y, Bustamante C 1996 Science 271 795

    [34]

    Wang X L, Zhang X H, Cao M, Zheng H Z, Xiao B, Wang Y, Li M 2009 J. Phys. Chem. B 113 2328

    [35]

    Lipfert J, Skinner G M, Keegstra J M, Hensgens T, Jager T, Dulin D, Kober M, Yu Z, Donkers S P, Chou F C, Das R, Dekker N H 2014 Proc. Natl. Acad. Sci. USA 111 15408

    [36]

    Herrero-Galán E, Fuentes-Perez M E, Carrasco C, Valpuesta J M, Carrascosa J L, Moreno-Herrero F, Arias-Gonzalez J R 2013 J. Am. Chem. Soc. 135 122

    [37]

    Lipfert J, Kerssemakers J W, Jager T, Dekker N H 2010 Nat. Methods 7 977

    [38]

    Baumann C G, Smith S B, Bloomfield V A, Bustamante C 1997 Proc. Natl. Acad. Sci. USA 94 6185

    [39]

    Zhang X H, Qu Y Y, Chen H, Rouzina I, Zhang S L, Doyle P S, Yan J 2014 J. Am. Chem. Soc. 136 16073

    [40]

    Orozco M, Noy A, Pérez A 2008 Curr. Opin. Struct. Biol. 18 185

    [41]

    Wang Y, Gong S, Wang Z, Zhang W 2016 J. Chem. Phys. 144 115101

    [42]

    Qi W P, Lei X L, Fang H P 2010 ChemPhysChem 11 2146

    [43]

    Qi W P, Song B, Lei X L, Wang C L, Fang H P 2011 Biochemistry 50 9628

    [44]

    Yin Y D, Yang L J, Zheng G Q, Gu C, Yi C Q, He C, Gao Y Q, Zhao X S 2014 Proc. Natl. Acad. Sci. USA 111 8043

    [45]

    Gu C, Zhang J, Yang Y I, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S, Gao Y Q 2015 J. Phys. Chem. B 119 13980

    [46]

    Lankaš F,Šponer J, Langowski J, Iii T E C 2003 Biophys. J. 85 2872

    [47]

    Perez A, Lankas F, Luque F J, Orozco M 2008 Nucleic Acids Res. 36 2379

    [48]

    Zuo G, Li W, Zhang J, Wang J, Wang W 2010 J. Phys. Chem. B 114 5835

    [49]

    Zhang Y J, Zhang J, Wang W 2011 J. Am. Chem. Soc. 133 6882

    [50]

    Bian Y, Tan C, Wang J, Sheng Y, Zhang J, Wang W 2014 PLoS Comput. Biol. 10 25

    [51]

    Wang J, Zhao Y, Wang J, Xiao Y 2015 Phys. Rev. E 92 062705

    [52]

    Wang J, Xiao Y 2016 Phys. Rev. E 94 040401

    [53]

    Wu Y Y, Zhang Z L, Zhang J S, Zhu X L, Tan Z J 2015 Nucleic Acids Res. 43 6156

    [54]

    Galindomurillo R, Robertson J, Zgarbová M,Šponer J, Otyepka M, Jurečka P, Iii T E C 2016 J. Chem. Theory Comput. 12 4114

    [55]

    Cheatham T E, Young M A 2000 Biopolymers 56 232

    [56]

    Fujii S, Kono H, Takenaka S, Go N, Sarai A 2007 Nucleic Acids. Res. 35 6063

    [57]

    Zhang Y, Zhou H J, Ouyang Z C 2001 Biophys. J. 81 1133

    [58]

    Wang J, Wolf R M, Caldwell J W, Kollman P A, Case D A 2004 J. Comput. Chem. 25 1157

    [59]

    Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W, Kollman P A 2015 J. Am. Chem. Soc. 117 5179

    [60]

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    Case D A, Cheatham T E, Darden T, Gohlke H, Luo R, Merz K M, Onufriev A, Simmerling C, Wang B, Woods R J 2010 J. Comput. Chem. 26 1668

    [62]

    Joung I S 2008 J. Phys. Chem. B 112 9020

    [63]

    Tan Z J, Chen S J 2006 Biophys. J. 90 1175

    [64]

    Tan Z J, Chen S J 2007 Biophys. J. 92 3615

    [65]

    Shi Y Z, Wang F H, Wu Y Y, Tan Z J 2014 J. Chem. Phys. 141 2654

    [66]

    Shi Y Z, Jin L, Wang F H, Zhu X L, Tan Z J 2015 Biophys. J. 109 2654

    [67]

    Hess B, Kutzner C, van der Spoel D, Lindahl E 2008 J. Chem. Theory Comput. 4 435

    [68]

    Pérez A, Marchán I, Svozil D, Sponer J, Rd C T, Laughton C A, Orozco M 2007 Biophys. J. 92 3817

    [69]

    Parrinello M, Rahman A 1981 J. Appl. Phys. 52 7182

    [70]

    Martonák R, Laio A, Parrinello M 2003 Phys. Rev. Lett. 90 075503

    [71]

    Gunsteren W F V, Berendsen H J C 1988 Mol. Simulat. 1 173

    [72]

    Lavery R, Moakher M, Maddocks J H, Petkeviciute D, Zakrzewska K 2009 Nucleic Acids. Res. 37 5917

    [73]

    Mazur A K 2006 Biophys. J. 91 4507

    [74]

    Faustino I, Pérez A, Orozco M 2010 Biophys. J. 99 1876

    [75]

    Lavery R, Sklenar H 1989 J. Biomol. Struct. Dyn. 6 655

    [76]

    Forth S, Deufel C, Sheinin M Y, Daniels B, Sethna J P, Wang M D 2008 Phys. Rev. Lett. 100 148301

    [77]

    Manning G S 2006 Biophys. J. 91 3607

    [78]

    Wenner J R, Williams M C, Rouzina I, Bloomfield V A 2002 Biophys. J. 82 3160

    [79]

    Moroz J D, Nelson P 1997 Macromolecules 31 6333

    [80]

    Drew H R, Wing R M, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R E 1981 Proc. Natl. Acad. Sci. USA 78 2179

    [81]

    Wu Z R, Delaglio F, Tjandra N, Zhurkin V B, Bax A 2003 J. Biomol. NMR 26 297

    [82]

    Noy A, Perez A, Lankas F, Javier Luque F, Orozco M 2004 J. Mol. Biol. 343 627

    [83]

    Ma N, van der Vaart A 2016 J. Am. Chem. Soc. 138 9951

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  • 收稿日期:  2018-02-12
  • 修回日期:  2018-03-09
  • 刊出日期:  2018-05-20

脱氧核糖核酸柔性的分子动力学模拟:Amber bsc1和bsc0力场的对比研究

    基金项目: 

    国家自然科学基金(批准号:11575128,11774272,11647312)资助的课题.

摘要: 脱氧核糖核酸(DNA)的结构柔性对DNA生物功能的实现具有重要作用,全原子分子动力学模拟是一种研究DNA结构柔性的重要方法.DNA的分子动力学力场在Amber bsc0基础上有了进一步的发展,即Amber bsc1.本文采用基于最新bsc1力场和先前bsc0力场的分子动力学模拟对DNA的宏观柔性和微观柔性进行对比研究,发现力场的改进对DNA宏观柔性参量的预测有一定改善,即所预测的拉伸模量和扭转-伸缩耦合比与实验值更为接近,而弯曲持久长度和扭转持久长度两种力场结果皆与实验值一致.微观分析发现,除了滑移量稍变大,bsc1力场得到的微观结构参量如扭转角和倾斜角与实验值更为接近,且新力场下DNA宏观柔性的改善与DNA的微观结构参量及其涨落紧密相关.

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