Molecular Modeling of L-Type Calcium Channel with Calcium Ions and Ligands

Abstract

In the absence of X-ray structure of L-type Ca²⁺ channel (LCC), we have built a homology model of LCC based on the crystal structure of KcsA channel and have performed a series 0° docking simulations. The search for lowest-energy conformations was performed by the Monte Carlo energy-minimization method. To obtain the conformation with the lowest energy where dihydropyridine (DHP) ligand forms optimal contacts with the DHP-sensing residues of the channel, we have tested different sequence alignments between KcsA and LCC, and have docked the ligand inside the pore of the channel as well as into the interface between repeats IIIS5-IIIS6-IVS6. The LCC ligand tetrandrine was used during the studies of the selectivity filter of the channel. Conformational studies of the drug and its interaction with Ca²⁺ ions in a non-polar solution were performed by NMR spectroscopy. These experiments have demonstrated the binding of Ca²⁺ ions to the ligand. In the model based on the alignment proposed by Lipkind and Fozzard (2000), the DHP ligand nifedipine fits inside the pore and forms favorable contacts with several hydrophobic DHP-sensing residues, and forms hydrogen bonds with conserved tyrosines in repeats HI and IV. These interactions stabilize the portside-down docking mode of nifedipine, in which this blocker exposes its hydrophobic methoxy group to the bracelet of hydrophobic residues forming the gate of the channel near the crossing of the bundle of helices. The stabilizes the closed state of the channel. In contrast, the agonist has the hydrophilic group at its portside. The favorable interaction of this group with hydrated Ca²⁺ ion facilitates its permeation through hydrophobic gate. We have simulated the passage of the hydrated ion along the pore with the agonist bound inside and determined several residues crucial for this passage. The role of these residues can be tested experimentally.