Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin

Bio Systems
Slawomir Orlowski, Wieslaw Nowak

Abstract

The physiological role of recently discovered human neuroglobin (Ngb) is still unknown. Sound hypothesis says that it protects brain during hypoxia. In this paper the advanced potential of mean force by implicit ligand sampling (PMF/ILS) method is used to study the free energy landscape of Ngb for O(2), NO and CO ligands. The multiple diffusion paths are discovered and four ligand binding cavities are determined. The data show that certain regions are easily accessible by O(2) and NO but are protected from CO. Free energy landscapes provide realistic data for stochastic models of ligand diffusion in proteins.

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Citations

May 11, 2011·Journal of the American Chemical Society·Anthony BocahutSophie Sacquin-Mora
Oct 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Stefania AbbruzzettiCristiano Viappiani
Aug 4, 2012·The Journal of Biological Chemistry·Mallory D SalterJohn S Olson
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Mar 19, 2016·Journal of Chemical Theory and Computation·Jakub Mateusz Rydzewski, Wieslaw Nowak
Nov 9, 2016·Molecular Aspects of Medicine·Paolo AscenziMaria Marino
Jul 6, 2014·Physiological Reviews·Dmitry B ZorovSteven J Sollott
Nov 19, 2009·The Journal of Physical Chemistry. B·Anthony BocahutSophie Sacquin-Mora
Apr 16, 2017·Physics of Life Reviews·J Rydzewski, W Nowak

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