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Keywords:

  • ligand migration;
  • O2;
  • NO;
  • CO;
  • implicit ligand sampling;
  • multiple steered molecular dynamics;
  • free energy profile;
  • molecular dynamics;
  • proteins;
  • cavities;
  • tunnels;
  • nitrophorin;
  • truncated haemoglobin;
  • xenon sites;
  • docking sites;
  • AMBER;
  • MSMD;
  • ILS;
  • MD

Abstract

The ubiquitous heme proteins perform a wide variety of tasks that rely on the subtle regulation of their affinity for small ligands like O2, CO, and NO. Ligand affinity is characterized by kinetic association and dissociation rate constants, that partially depend on ligand migration between the solvent and active site, mediated by the presence of internal cavities or tunnels. Different computational methods have been developed to study these processes which can be roughly divided in two strategies: those costly methods in which the ligand is treated explicitly during the simulations, and the free energy landscape of the process is computed; and those faster methods that use prior computed Molecular Dynamics simulation without the ligand, and incorporate it afterwards, called implicit ligand sampling (ILS) methods. To compare both approaches performance and to provide a combined protocol to study ligand migration in heme proteins, we performed ILS and multiple steered molecular dynamics (MSMD) free energy calculations of the ligand migration process in three representative and well theoretically and experimentally studied cases that cover a wide range of complex situations presenting a challenging benchmark for the aim of the present work. Our results show that ILS provides a good description of the tunnel topology and a reasonable approximation to the free energy landscape, while MSMD provides more accurate and detailed free energy profile description of each tunnel. Based on these results, a combined strategy is presented for the study of internal ligand migration in heme proteins. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011