Paper Citing NAMD - Abstract
Pietra, Francesco
From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics
CHEMISTRY & BIODIVERSITY, 10:963-975, JUN 2013
This work deals with two neuroglobins from phylogenetically distant organisms. Deriving from the acoelomorph Symsagittifera roscoffensis, SrNgb is functionally pentacoordinated, and is assumed to function as a reserve of dioxygen (O2). Obtained from mice, mNgb is functionally hexacoordinated, and presumably triggers signals from sensing O2. Here, it is investigated how these two globins are permeated by diatomic gases, SrNgb by O2 and mNgb by CO. With protein atomic coordinates available from high-resolution X-ray diffraction analysis, O2 and CO pathways were traced from molecular-dynamics simulations in H2O solution, which makes no difference between the two gases, accelerated by applying an external randomly-oriented minimal force to the center of mass of the diatomic gas molecule. This allowed us to explore a statistically significant large number of trajectories. It emerged that CO leaves mNgb from preferentially peripheral gates located on the side of the heme propionate chains, whereas O2 leaves SrNgb from the opposite side. This shows no analogy with either the functionally pentacoordinated, O2-transporting, myoglobin (Mgb), or the hexacoordinated, O2-sensing, cytoglobin, despite the same three-over-three typical -helical globin folding. The sole analogy that could be observed was a preference for the shortest diatomic gas pathways with both SrNgb and Mgb. It is tempting to speculate that this fulfills the need of being quick in delivering O2 to depleted organs.
