Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca²⁺‐ATPase

Abstract

Calcium ATPase is a member of the P-type ATPase, and it pumps calcium ions from the cytoplasm into the reticulum against a concentration gradient. Several X-ray structures of different conformations have been solved in recent years, providing basis for elucidating the active transport mechanism of Ca2+ ions. In this work, molecular dynamics (MD) simulations were performed at atomic level to investigate the dynamical process of calcium ions moving from the outer mouth of the protein to their binding sites. Five initial locations of Ca2+ ions were considered, and the simulations lasted for 2 or 6 ns, respectively. Specific pathways leading to the binding sites and large structural rearrangements around binding sites caused by uptake of calcium ions were identified. A cooperative binding mechanism was observed from our simulation. Firstly, the first Ca2+ ion binds to site I, and then, the second Ca2+ ion approaches. The interactions between the second Ca2+ and the residues around site I disturb the binding state of site I and weaken its binding ability for the first bound Ca2+. Because of the electrostatic repulsion of the second Ca2+ and the electrostatic attraction of site II, the first bound Ca2+ shifts from site I to site II. Concertedly, the second Ca2+ binds to site I, forming a binding state with two Ca2+ ions, one at site I and the other at site II. Both of Glu908 and Asp800 coordinate with the two Ca2+ ions simultaneously during the concerted binding process, which is believed to be the hinge to achieve the concerted binding. In our simulations, four amino acid residues that serve as the channel to link the outer mouth and the binding sites during the binding process were recognized, namely Tyr837, Tyr763, Asn911, and Ser767. The analyses regarding the activity of the proteins via mutations of some key residues also supported our cooperative mechanism.

Microsecond Molecular Dynamics Simulations of Mg2+- and K+- Bound E1 Intermediate States of the Calcium Pump

“…We found that K + (I) and K + (I′) binding to the TM sites follow TM1 pathway [33], where K + ions are guided by E55, E58, E59 and E109 toward site II before reaching sites I and I′, respectively. We did not find any evidence of another entry site to the TM domains (i.e., via TM8-9 [34]). K + (I) interacts with residues E771, T799, D800 and E908 in a location that virtually overlaps with the site occupied by Ca 2+ (I) in E1•2Ca 2+ .…”

Finite-element estimation of protein–ligand association rates with post-encounter effects: applications to calcium binding in troponin C and SERCA

“…Previous simulations [32, 21, 13] have explored possible pathways of Ca 2+ entry. Borrowing the convention proposed in [21] the L3 region (near E309, Fig. 1b) has been suggested as a predominant entryway for Ca 2+ binding based on molecular dynamics (MD) and solutions of the Poisson Boltzmann equation.…”

Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca2+ ATPase

“…Binding of calcium to site I increases the calcium affinity of site II, whereupon binding of a second Ca 2+ is necessary for ATP hydrolysis and continuation of the reaction cycle 1. Simulations of Ca 2+ binding to SERCA8 also indicate that Ca 2+ binds first at site I, then site II. Bridging site II and the cytoplasm are solvent‐exposed acidic residues thought to be involved in Ca 2+ gating (M4: E309),9 or recognition (M1: E51, E55, E58, D5910 and M2: D10911) Fig.…”

“…Molecular dynamics simulations of SERCA have provided substantial insight into the relationship between protein structure and mechanisms of substrate binding, selectivity, and conformational motions. Simulations by Musgaard et al, 18 Huang et al, 8 and Costa et al, 14 have explored possible pathways of Ca 2+ entry. Specifically, the regions near L67/L89 and M1/M2/M4 have been suggested as predominant pathways for Ca 2+ binding, which we describe as L1 and L3, respectively (according to the convention in Huang et al .…”