Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials

doi:10.1021/acs.jctc.5b00903

	Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials
	Zhang, Dinglin; Wang, Honglei; Li, Guohui; Shen, Hujun; Li, Yan
刊名	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
	2016-02-01
卷号	12 期号:2 页码:676-693
ISSN号	1549-9618
DOI	10.1021/acs.jctc.5b00903
文献子类	Article
英文摘要	In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths.
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; PACE FORCE-FIELD ; STRUCTURAL BASIS ; BASE-PAIRS ; DNA ; RNA ; PROTEINS ; COMPLEX ; WOBBLE ; DUPLEX
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000370112900021
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/171254]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Li, Guohui
作者单位	Chinese Acad Sci, Dalian Inst Chem Phys, Lab Mol Modeling & Design, State Key Lab Mol React Dynam, Dalian 116023, Liaoning Provin, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Dinglin,Wang, Honglei,Li, Guohui,et al. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2016,12(2):676-693.
APA	Zhang, Dinglin,Wang, Honglei,Li, Guohui,Shen, Hujun,&Li, Yan.(2016).Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,12(2),676-693.
MLA	Zhang, Dinglin,et al."Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12.2(2016):676-693.