Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca²⁺‐ATPase

Abstract

Sarco(endo)plasmic reticulum Ca(2+)-ATPase transports two Ca(2+) per ATP-hydrolyzed across biological membranes against a large concentration gradient by undergoing large conformational changes. Structural studies with X-ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and the transmembrane helices in individual reaction steps. Here, we employed "Motion Tree (MT)," a tree diagram that describes a conformational change between two structures, and applied it to representative Ca(2+) -ATPase structures. MT provides information of coupled rigid-body motions of the ATPase in individual reaction steps. Fourteen rigid structural units, "common rigid domains (CRDs)" are identified from seven MTs throughout the whole enzymatic reaction cycle. CRDs likely act as not only the structural units, but also the functional units. Some of the functional importance has been newly revealed by the analysis. Stability of each CRD is examined on the morphing trajectories that cover seven conformational transitions. We confirmed that the large conformational changes are realized by the motions only in the flexible regions that connect CRDs. The Ca(2+) -ATPase efficiently utilizes its intrinsic flexibility and rigidity to response different switches like ligand binding/dissociation or ATP hydrolysis. The analysis detects functional motions without extensive biological knowledge of experts, suggesting its general applicability to domain movements in other membrane proteins to deepen the understanding of protein structure and function.

Probing the effects of nonannular lipid binding on the stability of the calcium pump SERCA

“…We have recently shown that activation of the E2-to-E1 transition is largely determined by changes in the hierarchical organization of the headpiece structural dynamics that ultimately shift the equilibrium between the E1 and E2 states 10 . In the present study, we did not find any evidence suggesting changes in the hierarchical organization of the E2 state, because the essential phase space of SERCA (e.g., the functional motions that determine the pump’s function 10,44 ) is similar in the presence and absence of the nonannular lipid. Together, these findings indicate that binding of a nonannular lipid molecule to SERCA is not required for the stability of the E2 intermediate state, that occupancy of a lipid molecule at this site does not induce destabilization of this state, and that lipid binding has no effect on the structural dynamics of this biochemical intermediate.…”

Probing the effects of nonannular lipid binding on the stability of the calcium pump SERCA

“…Recent studies by our group have shown that activation of the E2-to-E1 transition is largely determined by changes in the hierarchical organization and amplitude of rigid-body motions of the headpiece that ultimately shift the equilibrium between the E1 and E2 states. We found that the intrinsic structural dynamics of SERCA (e.g., the functional motions that determines the pump's function 10, 45 ) are virtually identical in the presence and absence of the nonannular lipid. Together, these findings not only indicate that binding of a nonannular lipid molecule to SERCA is not required for the stability of the E2 intermediate state, but also suggest that occupancy of a lipid molecule at this site does not induce destabilization of this state.…”

Normal Mode Analysis: A Tool for Better Understanding Protein Flexibility and Dynamics with Application to Homology Models

“…Conventionally, the Ca 2þ -ATPase is thought to take two different states: E1, which has high affinity for Ca 2þ , and E2, which has much lower affinity [60,61]. In addition to the binding and dissociation of Ca 2þ , ATP hydrolysis and dephosphorylation of the resulting phosphorylated Asp351 result in the presence of 4-7 different physiological states [62]. At least 54 crystal structures have been determined since the first one in 2000 [63] and they cover nearly all the conformations of the different physiological states.…”

“…At least 54 crystal structures have been determined since the first one in 2000 [63] and they cover nearly all the conformations of the different physiological states. They show large conformational rearrangements during the reaction cycle and have been investigated by a number of computational methods [62]. Most of the NMA studies occurred soon after the initial structures by Toyoshima et al [63,64] had been reported, but before the final ones had become available [65,66], making this a good situation for illustrating both the abilities and limitations of NMA.…”