Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods
文献类型：期刊论文
| 作者 | Zou, Hanjun; Luo, Cheng ; Zheng, Suxin; Luo, Xiaomin; Zhu, Weiliang; Chen, Kaixian; Shen, Jianhua; Jiang, Hualiang
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| 刊名 | JOURNAL OF PHYSICAL CHEMISTRY B
 |
| 出版日期 | 2007-08-02 |
| 卷号 | 111期号:30页码:9104-9113 |
| ISSN号 | 1520-6106 |
| DOI | 10.1021/jp0713763 |
| 文献子类 | Article |
| 英文摘要 | The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details. Equally spaced snapshots along the trajectory were chosen to perform the binding free energy calculation, which yields a result highly consistent with experimental value with a deviation of 0.4 kcal/mol. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in IFABP to alanine and recomputing the Delta Delta G(binding). By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated Delta Delta G(binding) is below 1.5 kcal/mol for most of the alanine mutations of the noncharged residues (67% in total). To further investigate some particular mutants, three additional dynamical simulations of IFABP Arg126Ala, Arg106Ala, and Arg106Gln mutants were conducted. Recalculated binding free energies are well consistent with the experimental data. Moreover, the ambiguous role of Arg106 caused by the free energy change of the opposite sign when it is mutated to alanine and glutamine respectively is clarified both structurally and energetically. Typically, this can be attributed to the partial electrostatic compensation mainly from Arg56 and the obvious entropy gain in Arg106Ala mutant while not in Arg106Gln mutant. The presented structural model of IFABP-PA complex could be used to guide future studies. |
| WOS关键词 | FATTY-ACID-BINDING ; FREE-ENERGY CALCULATIONS ; ESCHERICHIA-COLI ; DYNAMICS SIMULATIONS ; PROTEIN INTERACTIONS ; CONTINUUM SOLVENT ; BOUND PALMITATE ; LIGAND-BINDING ; WATER ; THERMODYNAMICS |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:000248315700058 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/273179]  |
| 专题 | 药物发现与设计中心 中科院受体结构与功能重点实验室 新药研究国家重点实验室 |
| 通讯作者 | Shen, Jianhua |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, State Key Lab Drug Res, Shanghai 201203, Peoples R China 2.E China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zou, Hanjun,Luo, Cheng,Zheng, Suxin,et al. Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2007,111(30):9104-9113. |
| APA | Zou, Hanjun.,Luo, Cheng.,Zheng, Suxin.,Luo, Xiaomin.,Zhu, Weiliang.,...&Jiang, Hualiang.(2007).Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods.JOURNAL OF PHYSICAL CHEMISTRY B,111(30),9104-9113. |
| MLA | Zou, Hanjun,et al."Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods".JOURNAL OF PHYSICAL CHEMISTRY B 111.30(2007):9104-9113. |
入库方式： OAI收割
来源：上海药物研究所
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