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Treating hydrogen bonding in ab initio calculation of biopolymers
Mei, Y; Wu, EL; Han, KL; Zhang, JZH; Zhang ZH(张增辉); Zhang ZH(张增辉)
关键词Ab Initio Protein Hydrogen Bonding Alpha-helix Beta-sheet Polarization
刊名INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
2006-04-05
DOI10.1002/qua.20875
106期:5页:1267-1276
收录类别SCI
文章类型Article
部门归属11
项目归属1101
产权排名2;2
WOS标题词Science & Technology ; Physical Sciences
类目[WOS]Chemistry, Physical ; Mathematics, Interdisciplinary Applications ; Physics, Atomic, Molecular & Chemical
研究领域[WOS]Chemistry ; Mathematics ; Physics
关键词[WOS]QUANTUM-MECHANICAL CALCULATION ; INTERACTION ENERGY ; MOLECULAR-DYNAMICS ; ELECTRON-DENSITY ; FORCE-FIELD ; PROTEIN ; FRACTIONATION ; POLYPEPTIDES ; COMPUTATION ; PROGRAM
英文摘要We present a general scheme to treat backbone hydrogen bonding in protein using the molecular fractionation with conjugate caps (MFCC) approach. In this approach, molecular caps are employed to mimic the hydrogen bonding environment of protein fragments that are calculated individually. Using this scheme in the MFCC method, we carried out explicit numerical calculations for a number of secondary structures of proteins, including the alpha-helix and beta-sheet. The calculated electron densities, electrostatic potentials, and dipole moment are compared with those from the standard full system ab initio calculations. The result shows that the current treatment using the hydrogen bond cap gives an accurate description of the hydrogen bonding effect and accurate dipole moment. In contrast, calculation using the standard force field (FF) approach gives dipole moments that are in huge error (i.e., significantly smaller) than the quantum result for helix structures due to the lack of polarization effect with fixed partial charges. The present study demonstrates that the MFCC approach can quantitatively describe hydrogen bonding in practical ab initio Calculation of proteins. Our result also underscores the importance of the polarization effect in backbone hydrogen bonding of protein. This could have significant implication in studying the electrostatic interaction of proteins, such as protein solvation. (c) 2005 Wiley Periodicals, Inc.
语种英语
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WOS记录号WOS:000235537700021
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被引频次:25[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/97315
专题中国科学院大连化学物理研究所
通讯作者Zhang ZH(张增辉); Zhang ZH(张增辉)
作者单位1.Nanjing Univ, Inst Theoret & Computat Chem, Coll Chem & Chem Engn, Nanjing 210093, Peoples R China
2.Chinese Acad Sci, Ctr Computat Chem, Dalian 116023, Peoples R China
3.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
4.NYU, Dept Chem, New York, NY 10003 USA
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Mei, Y,Wu, EL,Han, KL,et al. Treating hydrogen bonding in ab initio calculation of biopolymers[J]. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY,2006,106(5):1267-1276.
APA Mei, Y,Wu, EL,Han, KL,Zhang, JZH,张增辉,&张增辉.(2006).Treating hydrogen bonding in ab initio calculation of biopolymers.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY,106(5),1267-1276.
MLA Mei, Y,et al."Treating hydrogen bonding in ab initio calculation of biopolymers".INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 106.5(2006):1267-1276.
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