Molecular dynamics simulations of metal ion binding to the His-tag motif

Chin W. Chen, Hsuan Liang Liu, Jin Chung Lin, Yih Ho

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

In our previous study, we have observed that the chelation of various metal ions to the His-tag motifs mostly involves the i and i+2 His residues for Ni2+, Cu2+, Zn2+ and Co2+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His-tag motif with 6 His residues (His-tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His-tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni2+ and Cu2+. K + was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe3+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni2+ exhibits the highest binding affinity towards His-tag6 over the other metal ions. Most of the structural variations of the His-tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.

Original languageEnglish
Pages (from-to)1281-1290
Number of pages10
JournalJournal of the Chinese Chemical Society
Volume52
Issue number6
Publication statusPublished - 2005

Fingerprint

Metal ions
Molecular dynamics
Computer simulation
His-His-His-His-His-His
Chelation
Metals
Potential energy

Keywords

  • Affinity
  • Chelation
  • His-tag
  • IMAC
  • Metal ion
  • Molecular dynamics simulations

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Molecular dynamics simulations of metal ion binding to the His-tag motif. / Chen, Chin W.; Liu, Hsuan Liang; Lin, Jin Chung; Ho, Yih.

In: Journal of the Chinese Chemical Society, Vol. 52, No. 6, 2005, p. 1281-1290.

Research output: Contribution to journalArticle

Chen, Chin W. ; Liu, Hsuan Liang ; Lin, Jin Chung ; Ho, Yih. / Molecular dynamics simulations of metal ion binding to the His-tag motif. In: Journal of the Chinese Chemical Society. 2005 ; Vol. 52, No. 6. pp. 1281-1290.
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N2 - In our previous study, we have observed that the chelation of various metal ions to the His-tag motifs mostly involves the i and i+2 His residues for Ni2+, Cu2+, Zn2+ and Co2+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His-tag motif with 6 His residues (His-tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His-tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni2+ and Cu2+. K + was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe3+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni2+ exhibits the highest binding affinity towards His-tag6 over the other metal ions. Most of the structural variations of the His-tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.

AB - In our previous study, we have observed that the chelation of various metal ions to the His-tag motifs mostly involves the i and i+2 His residues for Ni2+, Cu2+, Zn2+ and Co2+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His-tag motif with 6 His residues (His-tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His-tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni2+ and Cu2+. K + was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe3+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni2+ exhibits the highest binding affinity towards His-tag6 over the other metal ions. Most of the structural variations of the His-tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.

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