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

Computer Engineering | 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
- Frontiers of Information Technology & Electronic Engineering Vol. 14, Issue 2, Pages: 118-124(2013)
- 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：
- DOI：10.1631/jzus.C1200072
  CLC： R857.3
- Received：15 March 2012，
  
  Revised：2013-;1-23，
  
  Published：2013-02
- Accepted：
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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：

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.

关键词

Keywords

references

V.S. Ananthanarayanan , , , A. Kerman . . Role of metal ions in ligand receptor interaction:insights from structural studies . . Mol.Cell.Endocr. , , 2006 . . 246 ( ( 1-2 ): ): 53 - - 59 . . DOI: 10.1016/j.mce.2005.11.023 http://doi.org/10.1016/j.mce.2005.11.023 . .

C. Bissantz , , , G. Folkers , , , D. Rognan . . Protein-based virtual screening of chemical databases.Ⅰ.Evaluation of different docking/scoring combinations . . J.Med.Chem. , , 2000 . . 43 ( ( 25 ): ): 4759 - - 4767 . . DOI: 10.1021/jm001044l http://doi.org/10.1021/jm001044l . .

H.J. Bhm . . Prediction of binding constants of protein ligands:a fast method for the prioritization of hits obtained from de novo design or 3D database search programs . . J.Comput.Aided Mol.Des. , , 1998 . . 12 ( ( 4 ): ): 309 - - 323 . . DOI: 10.1023/A:1007999920146 http://doi.org/10.1023/A:1007999920146 . .

D. Chen , , , G. Menche , , , T.D. Power , , , L. Sower , , , J.W. Peterson , , , C.H. Schein . . Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins . . Proteins , , 2007 . . 67 ( ( 3 ): ): 593 - - 605 . . DOI: 10.1002/prot.21249 http://doi.org/10.1002/prot.21249 . .

P. Ferrara , , , H. Gohlke , , , D.J. Price , , , G. Klebe , , , C.L.I. Brooks . . Assessing scoring functions for protein-ligand interactions . . J.Med.Chem. , , 2004 . . 47 ( ( 12 ): ): 3032 - - 3047 . . DOI: 10.1021/jm030489h http://doi.org/10.1021/jm030489h . .

R.A. Friesner , , , J.L. Banks , , , R.B. Murphy , , , T.A. Halgren , , , J.J. Klicic , , , D.T. Mainz , , , M.P. Repasky , , , E.H. Knoll , , , M. Shelley , , , J.K. Perry , , , 等 . . Glide:a new approach for rapid, accurate docking and scoring.Ⅰ.Method and assessment of docking accuracy . . J.Med.Chem. , , 2004 . . 47 ( ( 7 ): ): 1739 - - 1749 . . DOI: 10.1021/jm0306430 http://doi.org/10.1021/jm0306430 . .

T.A. Halgren , , , R.B. Murphy , , , R.A. Friesner , , , H.S. Beard , , , L.L. Frye , , , W.T. Pollard , , , J.L. Banks . . Glide:a new approach for rapid, accurate docking and scoring.Part 2:Enrichment factors in database screening . . J.Med.Chem. , , 2004 . . 47 ( ( 7 ): ): 1750 - - 1759 . . DOI: 10.1021/jm030644s http://doi.org/10.1021/jm030644s . .

I. Halperin , , , B.Y. Ma , , , H. Wolfson , , , R. Nussinov . . Principles of docking:an overview of search algorithms and a guide to scoring functions . . Proteins , , 2002 . . 47 ( ( 4 ): ): 409 - - 443 . . DOI: 10.1002/prot.10115 http://doi.org/10.1002/prot.10115 . .

X. Hu , , , W.H. Shelver . . Docking studies of matrix metalloproteinase inhibitors:zinc parameter optimization to improve the binding free energy prediction . . J.Mol.Graph.Model. , , 2003 . . 22 ( ( 2 ): ): 115 - - 126 . . DOI: 10.1016/S1093-3263(03)00153-0 http://doi.org/10.1016/S1093-3263(03)00153-0 . .

R. Huey , , , G.M. Morris , , , A.J. Olson , , , D.S. Goodsell . . A semiempirical free energy force field with charge-based desolvation . . J.Comput.Chem. , , 2007 . . 28 ( ( 6 ): ): 1145 - - 1152 . . DOI: 10.1002/jcc.20634 http://doi.org/10.1002/jcc.20634 . .

G. Jones , , , P. Willett , , , R.C. Glen , , , A.R. Leach , , , R. Taylor . . Development and validation of a genetic algorithm for flexible docking . . J.Mol.Biol. , , 1997 . . 267 ( ( 3 ): ): 727 - - 748 . . DOI: 10.1006/jmbi.1996.0897 http://doi.org/10.1006/jmbi.1996.0897 . .

A. Khandelwal , , , V. Lukacova , , , D. Comez , , , D. Kroll , , , S. Raha , , , S. Balaz . . A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands . . J.Med.Chem. , , 2005 . . 48 ( ( 17 ): ): 5437 - - 5447 . . DOI: 10.1021/jm049050v http://doi.org/10.1021/jm049050v . .

B. Kramer , , , M. Rarey , , , T. Lengauer . . Evaluation of the FLEXX incremental construction algorithm for protein- ligand docking . . Proteins , , 1999 . . 37 ( ( 2 ): ): 228 - - 241 . . DOI: 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8 http://doi.org/10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8 . .

D.M.Jr. Kurtz . . Structural similarity and functional diversity in diiron-oxo proteins . . J.Biol.Inorg.Chem. , , 1997 . . 2 ( ( 2 ): ): 159 - - 167 . . DOI: 10.1007/s007750050120 http://doi.org/10.1007/s007750050120 . .

G.M. Morris , , , D.S. Goodsell , , , R. Huey , , , A.J. Olson . . Distributed automated docking of flexible ligands to proteins:parallel applications of AutoDock 2.4 . . J.Comput.Aided Mol.Des. , , 1996 . . 10 ( ( 4 ): ): 293 - - 304 . . DOI: 10.1007/BF00124499 http://doi.org/10.1007/BF00124499 . .

G.M. Morris , , , D.S. Goodsell , , , R.S. Halliday , , , R. Huey , , , W.E. Hart , , , R.K. Belew , , , A.J. Olson . . Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function . . J.Comput.Chem. , , 1998 . . 19 ( ( 14 ): ): 1639 - - 1662 . . DOI: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B http://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B . .

F. Spyrakis , , , A. Amadasi , , , M. Fornabaio , , , D.J. Abraham , , , A. Mozzarelli , , , G.E. Kellogg , , , P. Cozzini . . The consequences of scoring docked ligand conformations using free energy correlations . . Eur.J.Med.Chem. , , 2007 . . 42 ( ( 7 ): ): 921 - - 933 . . DOI: 10.1016/j.ejmech.2006.12.037 http://doi.org/10.1016/j.ejmech.2006.12.037 . .

C.M. Venkatachalam , , , X. Jiang , , , T. Oldfield , , , M. Waldman . . LigandFit:a novel method for the shape-directed rapid docking of ligands to protein active sites . . J.Mol.Graph.Model. , , 2003 . . 21 ( ( 4 ): ): 289 - - 307 . . DOI: 10.1016/S1093-3263(02)00164-X http://doi.org/10.1016/S1093-3263(02)00164-X . .

G.L. Warren , , , C.W. Andrews , , , A.M. Capelli , , , B. Clarke , , , J. LaLonde , , , M.H. Lambert , , , M. Lindvall , , , N. Nevins , , , S.F. Semus , , , S. Senger , , , 等 . . A critical assessment of docking programs and scoring functions . . J.Med.Chem. , , 2006 . . 49 ( ( 20 ): ): 5912 - - 5931 . . DOI: 10.1021/jm050362n http://doi.org/10.1021/jm050362n . .

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