An empirical molecular docking study of a di-iron binding protein with iron ions

Huan WANG; Ping LIU; Hao XIE

doi:10.1631/jzus.C1200072

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An empirical molecular docking study of a di-iron binding protein with iron ions

计算机工程 | Updated：2022-05-19

- An empirical molecular docking study of a di-iron binding protein with iron ions
- An empirical molecular docking study of a di-iron binding protein with iron ions
- 信息与电子工程前沿（英文） 2013年14卷第2期页码：118-124
- Affiliations：
  
  1.School of Computer Science and Technology, Wuhan University of Technology, Wuhan 430070, China
  2.Institute of Sciences, Wuhan University of Technology, Wuhan 430070, China
  3.School of Information Management, Wuhan University, Wuhan 430072, China
- Author bio：
  
  [ "WANG Huan, E-mail:shrekwang1@gmail.com" ]
  XIE Hao, E-mail:drxiehao@126.com
- Funds：
  
  Project (No. 2011-Ⅱ-010) supported by the Fundamental Research Funds for the Central Universities, China
- DOI：10.1631/jzus.C1200072
  中图分类号： R857.3
- 收稿：2012-03-15，
  
  修回：2013-;1-23，
  
  纸质出版：2013-02
- Accepted：
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An empirical molecular docking study of a di-iron binding protein with iron ions[J]. 信息与电子工程前沿（英文）, 2013,14(2):118-124.

Huan WANG, Ping LIU, Hao XIE. An empirical molecular docking study of a di-iron binding protein with iron ions[J]. Frontiers of Information Technology & Electronic Engineering, 2013, 14(2): 118-124.
An empirical molecular docking study of a di-iron binding protein with iron ions[J]. 信息与电子工程前沿（英文）, 2013,14(2):118-124. DOI： 10.1631/jzus.C1200072.

Huan WANG, Ping LIU, Hao XIE. An empirical molecular docking study of a di-iron binding protein with iron ions[J]. Frontiers of Information Technology & Electronic Engineering, 2013, 14(2): 118-124. DOI： 10.1631/jzus.C1200072.

摘要

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.

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references

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