Paper Citing NAMD - Abstract
Weidemueller, Christian; Hauser, Karin
Ion transport and energy transduction of P-type ATPases: Implications from electrostatic calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1787:721-729, JUN 2009
This paper summarizes our present electrostatic calculations on P-type ATPases and their contribution to understand the molecular details of the reaction mechanisms. One focus was set on analyzing the proton countertransport of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1a). Protonation of acidic residues was calculated in dependence of pH for different enzyme states in the reaction cycle of the Ca(2+)-ATPase. We proposed that the acidic Ca(2+) ligands Glu 771, Asp 800 and Glu 908 participate in the proton countertransport whereas Glu 309 is more likely to serve as a proton shuttle between binding site I and the cytoplasm. Complementary to infrared measurements, we assigned infrared bands to specific Ca(2+) ligands that are hydrogen bonded. Ion pathways were proposed based on the calculations and structural data. Another focus was set on analyzing the energy transduction mechanism of P-type ATPases. In accordance to electrophysiological experiments, we simulated an electric field across the membrane. The impact of the electric field was studied by an accumulated number of residue conformational and ionization changes on specific transmembrane helices. Our calculations on the Ca(2+)-ATPase and the Na(+)/K(+)-ATPase indicated that the highly conserved transmembrane helix M5 is one structural element that is likely to act as energy transduction element in P-type ATPases. Perspectives and limitations of the electrostatic calculations for future computational studies are pointed out. (C) 2009 Elsevier B.V. All rights reserved.
