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Front. Inform. Technol. Electron. Eng.  2013, Vol. 14 Issue (2): 118-124    DOI: 10.1631/jzus.C1200072
    
An empirical molecular docking study of a di-iron binding protein with iron ions
Huan Wang, Ping Liu, Hao Xie
School of Computer Science and Technology, Wuhan University of Technology, Wuhan 430070, China; Institute of Sciences, Wuhan University of Technology, Wuhan 430070, China; School of Information Management, Wuhan University, Wuhan 430072, China
An empirical molecular docking study of a di-iron binding protein with iron ions
Huan Wang, Ping Liu, Hao Xie
School of Computer Science and Technology, Wuhan University of Technology, Wuhan 430070, China; Institute of Sciences, Wuhan University of Technology, Wuhan 430070, China; School of Information Management, Wuhan University, Wuhan 430072, China
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摘要： Various molecular docking software packages are available for modeling interactions between small molecules and proteins. However, there have been few reports of modeling the interactions between metal ions and metalloproteins. In this study, the AutoDock package was employed to example docking into a di-iron binding protein, bacterioferritin. Each binding site of this protein was tested for docking with iron ions. Blind docking experiments showed that all docking conformations converged into two clusters, one for internal iron binding in sites within the metalloprotein and the other for external iron binding on the protein surface. Local docking experiments showed that there were significant differences between two internal iron binding sites. Docking at one site gave a reasonable root-mean-square deviation (RMSD) distribution with relatively low binding energy. Analysis of the binding mode quality for this site revealed that more than half of the docking conformations were categorized as having good binding geometry, while no good conformations were found for the other site. Further investigations indicated that coordinating water molecules contributed to the stability of binding geometries. This study provides an empirical approach towards the study of molecular docking in metalloproteins.
关键词： AutoDock;  Docking;  Iron ions;  Metalloproteins;  Binding modes    
Abstract: Various molecular docking software packages are available for modeling interactions between small molecules and proteins. However, there have been few reports of modeling the interactions between metal ions and metalloproteins. In this study, the AutoDock package was employed to example docking into a di-iron binding protein, bacterioferritin. Each binding site of this protein was tested for docking with iron ions. Blind docking experiments showed that all docking conformations converged into two clusters, one for internal iron binding in sites within the metalloprotein and the other for external iron binding on the protein surface. Local docking experiments showed that there were significant differences between two internal iron binding sites. Docking at one site gave a reasonable root-mean-square deviation (RMSD) distribution with relatively low binding energy. Analysis of the binding mode quality for this site revealed that more than half of the docking conformations were categorized as having good binding geometry, while no good conformations were found for the other site. Further investigations indicated that coordinating water molecules contributed to the stability of binding geometries. This study provides an empirical approach towards the study of molecular docking in metalloproteins.
Key words: AutoDock    Docking    Iron ions    Metalloproteins    Binding modes
收稿日期: 2012-03-15 出版日期: 2013-01-31
CLC:  R857.3  
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Huan Wang
Ping Liu
Hao Xie

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Huan Wang, Ping Liu, Hao Xie. An empirical molecular docking study of a di-iron binding protein with iron ions. Front. Inform. Technol. Electron. Eng., 2013, 14(2): 118-124.

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http://www.zjujournals.com/xueshu/fitee/CN/10.1631/jzus.C1200072    或    http://www.zjujournals.com/xueshu/fitee/CN/Y2013/V14/I2/118

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