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Frontiers of Chemical Science and Engineering

ISSN 2095-0179

ISSN 2095-0187(Online)

CN 11-5981/TQ

邮发代号 80-969

2019 Impact Factor: 3.552

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Frontiers of Chemical Science and Engineering  2016, Vol. 10 Issue (2): 203-212   https://doi.org/10.1007/s11705-016-1572-4
  本期目录
Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
Liaoran Cao1,Hong Ren2,Jing Miao1,Wei Guo1,Yan Li1,Guohui Li1,*()
1. Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
2. Department of Ophthalmology, Aerospace Center Hospital, Beijing 100049, China
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文章导读  
Abstract：

Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.
Key words： nucleic acid    polarizable force field    AMOEBA
收稿日期: 2015-12-31      出版日期: 2016-05-19
Corresponding Author(s): Guohui Li   
 引用本文:   
. [J]. Frontiers of Chemical Science and Engineering, 2016, 10(2): 203-212.
Liaoran Cao,Hong Ren,Jing Miao,Wei Guo,Yan Li,Guohui Li. Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions. Front. Chem. Sci. Eng., 2016, 10(2): 203-212.
 链接本文:  
https://academic.hep.com.cn/fcse/CN/10.1007/s11705-016-1572-4
https://academic.hep.com.cn/fcse/CN/Y2016/V10/I2/203
Fig.1  
Acetic acid Benzene Methane Methanol Water
BSSE /(kcal·mol?1) 0.113 0.0677 0.422 0.098 0.147
Tab.1  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.914 0.969 0.0261 ?0.956 0.0507
AMBER 0.933 1.054 0.0248 ?0.913 0.0483
CHARMM 0.914 0.965 0.0259 ?0.871 0.0505
DNA AMOEBA 0.899 0.969 0.0257 0.787 0.0525
AMBER 0.893 1.004 0.0275 0.820 0.0562
CHARMM 0.893 0.964 0.0264 0.980 0.0540
Tab.2  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.895 1.109 0.0333 ?0.007 0.0413
AMBER 0.863 1.038 0.0363 ?0.101 0.0450
CHARMM 0.808 1.011 0.0433 ?0.825 0.0536
DNA AMOEBA 0.904 0.966 0.0254 ?0.331 0.0293
AMBER 0.897 0.963 0.0258 ?0.381 0.0297
CHARMM 0.898 0.966 0.0259 ?0.401 0.0298
Tab.3  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.878 1.020 0.0334 ?0.940 0.0207
AMBER 0.872 1.010 0.0340 ?0.853 0.0210
CHARMM 0.872 0.980 0.0330 ?0.144 0.0204
DNA AMOEBA 0.863 1.001 0.0315 ?0.318 0.0296
AMBER 0.845 0.933 0.0316 ?0.355 0.0296
CHARMM 0.856 0.983 0.0321 ?0.271 0.0201
Tab.4  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.894 0.996 0.0301 ?0.167 0.0372
AMBER 0.907 0.997 0.0281 ?0.168 0.0347
CHARMM 0.905 1.023 0.0291 ?0.160 0.0360
DNA AMOEBA 0.895 0.979 0.0265 0.0997 0.0358
AMBER 0.899 1.003 0.0266 0.0861 0.0359
CHARMM 0.884 0.972 0.0278 0.0618 0.0376
Tab.5  
Fig.2  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.948 0.741 0.0109 0.0664 0.0229
AMBER 0.946 1.049 0.0157 0.363 0.0329
CHARMM 0.933 1.023 0.0172 0.351 0.0360
DNA AMOEBA 0.978 0.794 0.0074 0.104 0.0156
AMBER 0.948 1.017 0.0149 0.366 0.0314
CHARMM 0.921 0.994 0.0183 0.357 0.0383
Tab.6  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.742 0.792 0.0255 0.199 0.122
AMBER 0.872 0.963 0.0200 0.937 0.0962
CHARMM 0.853 0.853 0.0193 0.423 0.0932
DNA AMOEBA 0.927 0.958 0.0146 0.842 0.0698
AMBER 0.945 0.904 0.0112 0.627 0.0566
CHARMM 0.832 0.756 0.0108 0.123 0.0886
Tab.7  
Fig.3  
Fig.4  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.846 0.808 0.0215 ?5.419 1.065
AMBER 0.909 0.993 0.0197 5.722 0.974
CHARMM 0.856 0.929 0.0238 1.892 1.176
DNA AMOEBA 0.939 0.884 0.0141 ?1.074 0.708
AMBER 0.891 0.969 0.0212 5.630 1.064
CHARMM 0.837 0.906 0.0250 1.813 1.250
Tab.8  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.825 0.804 0.0231 ?6.500 1.126
AMBER 0.908 0.933 0.0185 3.136 0.901
CHARMM 0.886 0.906 0.0206 1.011 0.967
DNA AMOEBA 0.953 0.852 0.0666 ?3.509 0.324
AMBER 0.928 0.928 0.0642 2.660 0.061
CHARMM 0.905 0.869 0.0609 ?1.028 0.297
Tab.9  
Fig.5  
Fig.6  
Nucleic Force Adj. R-square Slope Intercept /(kcal·mol?1)
Value Standard error Value Standard error
RNA AMOEBA 0.816 0.849 0.0360 ?6.386 1.754
AMBER 0.938 1.006 0.0094 4.207 0.199
CHARMM 0.910 0.974 0.0440 1.931 1.689
DNA AMOEBA 0.954 0.906 0.0336 ?3.183 0.161
AMBER 0.953 0.999 0.0173 3.576 0.141
CHARMM 0.928 0.934 0.0850 ?0.216 0.170
Tab.10  
Fig.7  
1 Kumar G S, Maiti M. DNA polymorphism under the influence of low pH and low-temperature. Journal of Biomolecular Structure & Dynamics, 1994, 12(1): 183–201
https://doi.org/10.1080/07391102.1994.10508096
2 Ali N, Ali R. High salt and solvent induced Z-conformation in native calf thymus DNA. Biochemistry and Molecular Biology International, 1997, 41: 1227–1235
3 Jones S, van Heyningen P, Berman H M, Thornton J M. Protein-DNA interactions: A structural analysis. Journal of Molecular Biology, 1999, 287(5): 877–896
https://doi.org/10.1006/jmbi.1999.2659
4 Reinert K E. DNA multimode interaction with berenil and pentamidine; Double helix stiffening, unbending and bending. Journal of Biomolecular Structure & Dynamics, 1999, 17(2): 311–331
https://doi.org/10.1080/07391102.1999.10508364
5 Levitt M. Computer-simulation of DNA double-helix dynamics. Cold Spring Harbor Symposia on Quantitative Biology, 1983, 47: 251–262
https://doi.org/10.1101/SQB.1983.047.01.030
6 Tidor B, Irikura K K, Brooks B R, Karplus M. Dynamics of DNA oligomers. Journal of Biomolecular Structure & Dynamics, 1983, 1(1): 231–252
https://doi.org/10.1080/07391102.1983.10507437
7 Condon D E, Yildirim I, Kennedy S D, Mort B C, Kierzek R, Turner D H. Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU). Journal of Physical Chemistry B, 2014, 118(5): 1216–1228
https://doi.org/10.1021/jp408909t
8 Perez A, Marchan I, Svozil D, Sponer J, Cheatham T E 3rd, Laughton C A, Orozco M. Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophysical Journal, 2007, 92(11): 3817–3829
https://doi.org/10.1529/biophysj.106.097782
9 Soares T A, Hunenberger P H, Kastenholz M A, Krautler V, Lenz T, Lins R D, Oostenbrink C, Van Gunsteren W F. An improved nucleic acid parameter set for the GROMOS force field. Journal of Computational Chemistry, 2005, 26(7): 725–737
https://doi.org/10.1002/jcc.20193
10 Hart K, Foloppe N, Baker C M, Denning E J, Nilsson L, MacKerell A D Jr. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. Journal of Chemical Theory and Computation, 2012, 8(1): 348–362
https://doi.org/10.1021/ct200723y
11 Langley D R. Environmentally dependent molecular dynamic simulations of DNA using the BMS nucleic acid force field. Abstracts of Papers of the American Chemical Society, 1997, 213: 135
12 Langley D R. Molecular dynamic simulations of environment and sequence dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results. Journal of Biomolecular Structure & Dynamics, 1998, 16(3): 487–509
https://doi.org/10.1080/07391102.1998.10508265
13 Anisimov V M, Lopes P E M, MacKerell A D. COMP 382-classical CHARMM drude oscillator polarizable force field for nucleic acid bases. Abstracts of Papers of the American Chemical Society, 2007, 234
14 Baker C M, Anisimov V M, MacKerell A D Jr. Development of CHARMM polarizable force field for nucleic acid bases based on the classical drude oscillator model. Journal of Physical Chemistry B, 2011, 115(3): 580–596
https://doi.org/10.1021/jp1092338
15 Rick S W, Stuart S J. Potentials and algorithms for incorporating polarizability in computer simulations. Reviews in Computational Chemistry, 2002, 18: 89–146
16 Ren P Y, Ponder J W. Polarizable atomic multipole water model for molecular mechanics simulation. Journal of Physical Chemistry B, 2003, 107(24): 5933–5947
https://doi.org/10.1021/jp027815+
17 Ren P Y, Ponder J W. Temperature and pressure dependence of the AMOEBA water model. Journal of Physical Chemistry B, 2004, 108(35): 13427–13437
https://doi.org/10.1021/jp0484332
18 Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder J W, Ren P. The polarizable atomic multipole-based AMOEBA force field for proteins. Journal of Chemical Theory and Computation, 2013, 9(9): 4046–4063
https://doi.org/10.1021/ct4003702
19 Case D A, Berryman J T, Betz R M, Cerutti D S, Cheatham T E, Darden III T A, Duke R E, Giese T J, Gohlke H, Goetz A W, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee T S, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz K M, Monard G, Needham P, Nguyen H, Nguyen H T, Omelyan I, Onufriev A, Roe D R, Roitberg A, Salomon-Ferrer R, Simmerling C L, Smith W, Swails J, Walker R C, Wang J, Wolf R M, Wu X, York D M, Kollman P A. AMBER 2015, University of California, San Francisco
20 PetaChem. (accessed on <Date>12 Jan, 2015</Date>)
21 Gaussian 09. Wallingford, CT, USA: Gaussian, Inc., 2009
22 Best R B, Zhu X, Shim J, Lopes P E M, Mittal J, Feig M, MacKerell A D Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles. Journal of Chemical Theory and Computation, 2012, 8(9): 3257–3273
https://doi.org/10.1021/ct300400x
23 Wang J M, Wolf R M, Caldwell J W, Kollman P A, Case D A. Development and testing of a general amber force field. Journal of Computational Chemistry, 2004, 25(9): 1157–1174
https://doi.org/10.1002/jcc.20035
24 Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell A D. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 2010, 31: 671–690
25 Yu W B, He X B, Vanommeslaeghe K, MacKerell A D Jr. Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of Computational Chemistry, 2012, 33(31): 2451–2468
https://doi.org/10.1002/jcc.23067
26 Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kale L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 2005, 26(16): 1781–1802
https://doi.org/10.1002/jcc.20289
27 Izvekov S, Parrinello M, Burnham C J, Voth G A. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching. Journal of Chemical Physics, 2004, 120(23): 10896–10913
https://doi.org/10.1063/1.1739396
28 Akin-Ojo O, Song Y, Wang F. Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method. Journal of Chemical Physics, 2008, 129(6):  064108
29 Wang L P, Chen J H, Van TVoorhis. Systematic parametrization of polarizable force fields from quantum chemistry data. Journal of Chemical Theory and Computation, 2013, 9(1): 452–460
https://doi.org/10.1021/ct300826t
30 Laury M L, Wang L P, Pande V S, Head-Gordon T, Ponder J W. Revised parameters for the AMOEBA polarizable atomic multipole water model. Journal of Physical Chemistry B, 2015, 119(29): 9423–9437
https://doi.org/10.1021/jp510896n
31 Mackerell A D, Wiorkiewiczkuczera J, Karplus M. An all-atom empirical energy function for the simulation of nucleic-acids. Journal of the American Chemical Society, 1995, 117(48): 11946–11975
https://doi.org/10.1021/ja00153a017
32 MacKerell A D, Banavali N, Foloppe N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 2001, 56(4): 257–265
https://doi.org/10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
33 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. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 1996, 118(9): 2309–2309
https://doi.org/10.1021/ja955032e
34 Badawi H M, Forner W, Al-Saadi A A. DFT-B3LYP versus MP2, MP3 and MP4 calculations of the structural stability of azidoketene O=C=CH‒NNN. Journal of Molecular Structure THEOCHEM, 2004, 712(1-3): 131–138
https://doi.org/10.1016/j.theochem.2004.08.047
35 Badawi H M. MP2, MP3 and MP4 versus DFT-B3LYP energies and vibrational assignments of near-planar carbamoyl azide and ketene. Journal of Molecular Structure, 2008, 888(1-3): 379–385
https://doi.org/10.1016/j.molstruc.2008.01.018
36 Neese F. The ORCA program system. Wiley Interdisciplinary Reviews. Computational Molecular Science, 2012, 2(1): 73–78
https://doi.org/10.1002/wcms.81
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