Molecular dynamics simulations on DNA flexibility: a comparative study of Amber bsc1 and bsc0 force fields

Xiong Kai-Xin; Xi Kun; Bao Lei; Zhang Zhong-Liang; Tan Zhi-Jie

doi:10.7498/aps.67.20180326

Abstract

The structural flexibility of DNA plays a key role in many biological processes of DNA, such as protein-DNA interactions, DNA packaging in viruses and nucleosome positioning on genomic DNA. Some experimental techniques have been employed to investigate the structural flexibility of DNA with the combination of elastic models, but these experiments could only provide the macroscopic properties of DNA, and thus, it is still difficult to understand the corresponding microscopic mechanisms. Recently, all-atom molecular dynamics (MD) simulation has emerged as a useful tool to investigate not only the macroscopic properties of DNA, but also the microscopic description of the flexibility of DNA at an atomic level. The most important issue in all-atom MD simulations of DNA is to choose an appropriate force field for simulating DNA. Very recently, a new force field for DNA has been developed based on the last generation force field of Amber bsc0, which was named Amber bsc1. In this work, all-atom MD simulations are employed to study the flexibility of a 30-bp DNA with the force fields of Amber bsc1 and Amber bsc0 in a comparative way. Our aim of the research is to examine the improvement of the new development of force field (Amber bsc1) in the macroscopic and microscopic properties of DNA, in comparison with the corresponding experimental measurements. All the MD simulations are performed with Gromacs 4.6 and lasted with a simulation time of 600 ns. The MD trajectories are analyzed with Curves+ for the last 500 ns, since the system reaches equilibrium approximately after ~100 ns. Our results show that the new force field (Amber bsc1) can lead to the improvements in the macroscopic parameters of DNA flexibility, i.e., stretch modulus S and twist-stretch coupling D become closer to experimental measurements, while bending persistence lengths lp and torsional persistence lengths C from the two force fields (bsc1 and bsc0) are both in good agreement with experimental data. Our microscopic analyses show that the microscopic structure parameters of DNA from the MD simulation with the Amber bsc1 force field are closer to the experimental values than those with the Amber bsc0 force field, except for slide, and the obvious improvements are observed in some microscopic parameters such as twist and inclination. Our further analyses show that the improvements in macroscopic flexibility from the Amber bsc1 force field are tightly related to the microscopic parameters and their fluctuations. This study would be helpful in understanding the performances of Amber bsc1 and bsc0 force fields in the description of DNA flexibility at both macroscopic and microscopic level.

Keywords:

Authors and contacts

1.
School of Physics and Technology, Wuhan University, Wuhan 430072, China

Corresponding author: Zhang Zhong-Liang, zhongliang_z@whu.edu.cn;zjtan@whu.edu.cn ; Tan Zhi-Jie, zhongliang_z@whu.edu.cn;zjtan@whu.edu.cn

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11575128, 11774272, 11647312).

References

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

Cited By

[1]	Peters J P, Maher L J 2010 Q. Rev. Biophys. 43 23
[2]	Bao L, Zhang X, Jin L, Tan Z J 2015 Chin. Phys. B 24 018703
[3]	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]	Ivani I, Dans P D, Noy A, Perez A, Faustino I, Hospital A, Walther J, Andrio P, Goni R, Balaceanu A, Portella G, Battistini F, Gelpi J L, Gonzalez C, Vendruscolo M, Laughton C A, Harris S A, Case D A, Orozco M 2016 Nat. Methods 13 55
[61]	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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Vol. 67, Issue 10 - 2018-05-20

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