Structural modeling of calcium binding in the selectivity filter of the L-type calcium channel

Abstract

Calcium channels play crucial physiological roles. In the absence of high-resolution structures of the channels, the mechanism of ion permeation is unknown. Here we used a method proposed in an accompanying paper (Cheng and Zhorov in Eur Biophys J, 2009) to predict possible chelation patterns of calcium ions in a structural model of the L-type calcium channel. We compared three models in which two or three calcium ions interact with the four selectivity filter glutamates and a conserved aspartate adjacent to the glutamate in repeat II. Monte Carlo energy minimizations yielded many complexes with calcium ions bound to at least two selectivity filter carboxylates. In these complexes calcium-carboxylate attractions are counterbalanced by calcium-calcium and carboxylate-carboxylate repulsions. Superposition of the complexes suggests a high degree of mobility of calcium ions and carboxylate groups of the glutamates. We used the predicted complexes to propose a permeation mechanism that involves single-file movement of calcium ions. The key feature of this mechanism is the presence of bridging glutamates that coordinate two calcium ions and enable their transitions between different chelating patterns involving four to six oxygen atoms from the channel protein. The conserved aspartate is proposed to coordinate a calcium ion incoming to the selectivity filter from the extracellular side. Glutamates in repeats III and IV, which are most distant from the repeat II aspartate, are proposed to coordinate the calcium ion that leaves the selectivity filter to the inner pore. Published experimental data and earlier proposed permeation models are discussed in view of our model.

Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels

“…ing in the calcium channel selectivity filter, which predicts multiple Ca 2ϩ chelation patterns involving long flexible side chains in the EEEE ring (6). Our present model of the sodium channel suggests the importance of the inter-repeat H-bonds involving conserved tryptophans for outer-pore stability and ion permeation.…”

“…The incoming Ca 2ϩ ion would exchange its waters to the water molecules in the tryptophan ring, which along with the highly conserved D 2p51 would coordinate the ion. Vacancies in the first coordination spheres of other Ca 2ϩ ions would be also filled by waters (6). Thus, our model suggests that the tryptophan ring participates in the permeation process by stabilizing the conducting conformation of the outer pore and by helping to deliver the external Ca 2ϩ ion to the selectivity filter.…”

“…The backbones of the ascending limbs were initially folded as in Ref. 5,6. All calculations were performed using the ZMM program.…”

“…A notable exception is a highly conserved D 2p51 next to the selectivity filter glutamate E 2p50 . Residue D 2p51 was proposed by us to play an important role in calcium permeation (6).…”

“…Analysis of these alignments allowed us to propose a network of hydrophobic, hydrogen bonding, and knob-into-the-hole contacts involving conserved residues, which stabilize the outer-pore region. Using available experimental data and the above contacts as distance constraints, we elaborated our homology models (5,6,9). The new inter-repeat contacts suggest new important roles for some of the exceptionally conserved residues.…”