Paper Citing NAMD - Abstract
Woelke, Anna Lena; Galstyan, Gegham; Galstyan, Artur; Meyer, Tim; Heberle, Joachim; Knapp, Ernst-Walter
Exploring the Possible Role of Glu286 in CcO by Electrostatic Energy Computations Combined with Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12432-12441, OCT 17 2013
Cytochrome c oxidase (CcO) is a central enzyme in aerobic life catalyzing the conversion of molecular oxygen to water and utilizing the chemical energy to pump protons and establish an electrochemical gradient. Despite intense research, it is not understood how CcO achieves unidirectional proton transport and avoids short circuiting the proton pump. Within this work, we analyzed the potential role of Glu286 as a proton valve. We performed unconstrained MD simulations of CcO with an explicit membrane for up to 80 ns. Those MD simulations revealed that deprotonated Glu286 (Glu286-) is repelled by the negatively charged propionic acid PRD of heme a(3). Thus, it destabilizes a potential linear chain of waters in the hydrophobic cavity connecting Glu286 with PR]) and the binuclear center (BNC). Conversely, protonated Glu286 (Glu286H) may remain in an upward position (oriented toward PR])) and can stabilize the connecting linear water chain in the hydrophobic cavity. We calculated the pK(a) of Glu286 under physiological conditions to be above 12, but this value decreases to about 9 under increased water accessibility of Glu286. The latter value is in accordance with experimental measurements. In the time course of MD simulation, we also observed conformations where Glu286 bridges between water molecules located on both sides (the D channel being connected to the N side and the hydrophobic cavity), which might lead to proton backflow.
