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CLC number: R857.3

On-line Access: 2013-01-31

Received: 2012-03-15

Revision Accepted: 2012-09-28

Crosschecked: 2013-01-23

Cited: 1

Clicked: 3319

Citations:  Bibtex RefMan EndNote GB/T7714

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Journal of Zhejiang University SCIENCE C 2013 Vol.14 No.2 P.118-124


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

Author(s):  Huan Wang, Ping Liu, Hao Xie

Affiliation(s):  School of Computer Science and Technology, Wuhan University of Technology, Wuhan 430070, China; more

Corresponding email(s):   shrekwang1@gmail.com, drxiehao@126.com

Key Words:  AutoDock, Docking, Iron ions, Metalloproteins, Binding modes

Huan Wang, Ping Liu, Hao Xie. An empirical molecular docking study of a di-iron binding protein with iron ions[J]. Journal of Zhejiang University Science C, 2013, 14(2): 118-124.

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author="Huan Wang, Ping Liu, Hao Xie",
journal="Journal of Zhejiang University Science C",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T An empirical molecular docking study of a di-iron binding protein with iron ions
%A Huan Wang
%A Ping Liu
%A Hao Xie
%J Journal of Zhejiang University SCIENCE C
%V 14
%N 2
%P 118-124
%@ 1869-1951
%D 2013
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.C1200072

T1 - An empirical molecular docking study of a di-iron binding protein with iron ions
A1 - Huan Wang
A1 - Ping Liu
A1 - Hao Xie
J0 - Journal of Zhejiang University Science C
VL - 14
IS - 2
SP - 118
EP - 124
%@ 1869-1951
Y1 - 2013
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.C1200072

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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


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