Paper Citing NAMD - Abstract
Musgaard, Maria; Thogersen, Lea; Schiott, Birgit
Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study
BIOCHEMISTRY, 50:11109-11120, DEC 27 2011
The P-type ATPases are responsible for the transport of cations across cell membranes. The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the lumen of the sarco(endo)plasmic reticulum and countertransports two or three protons per catalytic cycle. Two binding sites for Ca2+ ions have been located via protein crystallography, including four acidic amino acid residues that are essential to the ion coordination. In this study, we present molecular dynamics (MD) simulations examining the protonation states of these amino acid residues in a Ca2+-free conformation of SERCA. Such knowledge will be important for an improved understanding of atomistic details of the transport mechanism of protons and Ca2+ ions. Eight combinations of the protonation of four central acidic residues, Glu309, Glu771, Asp800, and Glu908, are tested from 10 ns MD simulations with respect to protein stability and ability to maintain a structure similar to the crystal structure. The trajectories for the most prospective combinations of protonation states were elongated to 50 ns and subjected to more detailed analysis, including prediction of pK(a) values of the four acidic residues over the trajectories. From the simulations we find that the combination leaving only Asp800 as charged is most likely. The results are compared to available experimental data and explain the observed destabilization upon full deprotonation, resulting in the entry of cytoplasmic K+ ions into the Ca2+ binding sites during the simulation in which Ca2+ ions are absent. Furthermore, a hypothesis for the exchange of protons from the central binding cavity is proposed.
