Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N

Diamantis, Polydefkis and Unke, Oliver T. and Meuwly, Markus. (2017) Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N. PLoS Computational Biology, 13 (3). e1005450.

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In heme proteins, the efficient transport of ligands such as NO or O 2 to the binding site is achieved via ligand migration networks. A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins. For this, Xe migration in truncated hemoglobin N (trHbN) of Mycobacterium Tuberculosis was studied using molecular dynamics simulations. Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol). Depending on the pocket from where Xe enters a particular transition, the conformation of the side chains lining the transition region differs which highlights the coupling between ligand and protein degrees of freedom. Furthermore, comparison of transition probabilities shows that Xe migration in trHbN is a non-Markovian process. Memory effects arise due to protein rearrangements and coupled dynamics as Xe moves through it.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Library of Science
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:17 Apr 2023 08:07
Deposited On:17 Apr 2023 08:07

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