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Keywords:

  • three-fold channel;
  • four-fold channel;
  • ion channels;
  • all atom MD;
  • catalytic site

Abstract

We study via all atom classical molecular dynamics (MD) simulation the process of uptake of ferrous ions (Fe2+) into the human ferritin protein and the catalytic ferroxidase sites via pores (“channels”) in the interior of the protein. We observe that the three-fold hydrophilic channels serve as the main entrance pathway for the Fe2+ ions. The binding sites along the ion pathway are investigated. Two strong binding sites, at the Asp131 and Glu134 residues and two weak binding sites, at the His118 and Cys130 are observed inside the three-fold channel. We also identify an explicit pathway for an ion exiting the channel into the central core of the protein as it moves to the ferroxidase site. The diffusion of an Fe2+ ion from the inner opening of the channel to a ferroxidase site located in the interior region of the protein coat is assisted by Thr135, His136 and Tyr137. The Fe2+ ion binds preferentially to site A of the ferroxidase site. © 2013 Wiley Periodicals, Inc.