Paper Citing NAMD - Abstract
Michel Espinoza-Fonseca, L.; Autry, Joseph M.; Lizbeth Ramirez-Salinas, G.; Thomas, David D.
Atomic-Level Mechanisms for Phospholamban Regulation of the Calcium Pump
BIOPHYSICAL JOURNAL, 108:1697-1708, APR 7 2015
We performed protein pKa calculations and molecular dynamics (MD) simulations of the calcium pump (sarco-plasmic reticulum Ca2+-ATPase (SERCA)) in complex with phospholamban (PLB). X-ray crystallography studies have suggested that PLB locks SERCA in a low-Ca2+-affinity E2 state that is incompatible with metal-ion binding, thereby blocking the conversion toward a high-Ca2+-affinity E1 state. Estimation of pKa values of the acidic residues in the transport sites indicates that at normal intracellular pH (7.1-7.2), PLB-bound SERCA populates an E1 state that is deprotonated at residues E309 and D800 yet protonated at residue E771. We performed three independent microsecond-long MD simulations to evaluate the structural dynamics of SERCA-PLB in a solution containing 100 mM K+ and 3 mM Mg2+. Principal component analysis showed that PLB-bound SERCA lies exclusively along the structural ensemble of the E1 state. We found that the transport sites of PLB-bound SERCA are completely exposed to the cytosol and that K+ ions bind transiently (<= 5 ns) and nonspecifically (nine different positions) to the two transport sites, with a total occupancy time of K+ in the transport sites of 80%. We propose that PLB binding to SERCA populates a novel (to our knowledge) E1 intermediate, E1.H-771(+). This intermediate serves as a kinetic trap that controls headpiece dynamics and depresses the structural transitions necessary for Ca2+-dependent activation of SERCA. We conclude that PLB-mediated regulation of SERCA activity in the heart results from biochemical and structural transitions that occur primarily in the E1 state of the pump.
