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Hydration facilitates oxygenation of hemocyanin: perspectives from molecular dynamics simulations

  • Khair Bux
  • Syed Abid Ali
  • Syed Tarique Moin
Original Article
  • 45 Downloads

Abstract

Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein. The oxygenation effect on the overall structure of the protein or polypeptide subunit was further explored via gyration radii evaluated for the metal-binding domain and for the whole subunit. The evaluation of hydration dynamics was carried out to understand the water mediated role of amino acid residues of the solvent tunnel facilitating the entry of oxygen molecule to the dicopper site of hemocyanin.

Keywords

Molecular dynamics simulations Oxygenation Shutter mechanism Solvent tunnel 

Supplementary material

249_2018_1316_MOESM1_ESM.pdf (364 kb)
Supplementary material 1 (pdf 363 KB)

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Copyright information

© European Biophysical Societies' Association 2018

Authors and Affiliations

  1. 1.H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological SciencesUniversity of KarachiKarachiPakistan

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