Probing ion binding in the selectivity filter of the Cav1.1 channel with molecular dynamics

Cav1.1 is the voltage-gated calcium channel essential for the contraction of skeletal muscles upon membrane potential changes. Structural determination of the Cav1.1 channel opens the avenue toward understanding of the structure-function relationship of voltage-gated calcium channels. Here, we show that there exist two Ca2+-binding sites, termed S1 and S2, within the selectivity filter of Cav1.1 through extensive molecular dynamics simulations on various initial ion arrangement configurations. The formation of both binding sites is associated with the four Glu residues (Glu292/614/1014/1323) that constitute the so-called EEEE locus. At the S1 site near the extracellular side, the Ca2+ ion is coordinated with the negatively charged carboxylic groups of these Glu residues and of the Asp615 residue either in a direct way or via an intermediate water molecule. At the S2 site, Ca2+ binding shows two distinct states: an upper state involving two out of the four Glu residues in the EEEE locus and a lower state involving only one Glu residue. In addition, there exist two recruitment sites for Ca2+ above the entrance of the filter. These findings promote the understanding of mechanism for ion permeation and selectivity in calcium channels.

Terahertz Wave Enhances Permeability of the Voltage-Gated Calcium Channel

A deficiency of Ca²⁺ fluxes arising from dysfunctional voltage-gated calcium channels has been associated with a list of calcium channelopathies such as epilepsy, hypokalemic periodic paralysis, episodic ataxia, etc. Apart from analyzing the pathogenic channel mutations, understanding how the channel regulates the ion conduction would be instructive to the treatment as well. In the present work, in relating the free energetics of Ca²⁺ transport to the calcium channel, we demonstrate the importance of bridging Ca²⁺ hydration waters, which form hydrogen bonds with channel -COO^- and -C═O groups and enable a long-distance effect on the Ca²⁺ permeation. By firing a terahertz wave which resonates with the stretching mode of either the -COO^- or the -C═O group, we obtain significantly enhanced selectivity and conductance of Ca²⁺. The Ca²⁺ free energy negatively grows nearly 5-fold. The direct evidence is the reinforced hydrogen bonds. In addition, thanks to forced vibrations, -COO^- contributes to raised permeation as well even under a field in resonance with -C═O, and vice versa. Since the resonant terahertz field could manipulate the conduction of calcium channels, it has potential applications in therapeutic intervention such as rectifying a Ca²⁺ deficiency in degraded calcium channels, inducing apoptosis of tumor cells with overloaded calcium etc.

Effects of selective calcium channel blockers on ions' permeation through the human Cav1.2 ion channel: A computational study

Selective calcium channel antagonists are widely used in the treatment of cardiovascular disorders. They are mainly classified into 1,4-dihydropyridine (1,4-DHPs) and non-DHPs. The non-DHPs class is further classified into phenylalkylamines (PAAs) and benzothiazepines (BZTs) derivatives. These blockers are used for the treatment of hypertension, angina pectoris, and cardiac arrhythmias. Despite their well-established efficiency, the structural basis behind their activity is not very clear. Here we report the use of a near-open confirmation (NOC) model of the Cav1.2 cardiac ion channel to examine the mode of binding of these antagonists within the pore domain as well as the fenestration of the pore-forming domains. Effects of calcium ion permeation in the presence of drug molecules were assessed using steered molecular dynamics (SMD) simulations. These studies reveal that nicardipine, a DHP derivative, shows a strong Cav1.2 blocking activity, requiring more 2500 pN force to pull calcium ion towards the channel's pore in the presence of the compound. Similar blocking activity was observed for verapamil, a PAA derivative, requiring almost 2300 pN of force. The least blocking activity was observed for Diltiazem, a BZT derivative. Our results explain the structural basis and the binding details of 1,4-DHPs, PAAs and BZTs at their distinct Cav1.2 sites and offer detailed insights into their mechanism of action in modulating the Cav1.2 channel.

Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations

BACKGROUND

Human Ca_V1.2 (hCav1.2), a calcium selective voltage-gated channel, plays important roles in normal cardiac and neuronal functions. Calcium influx and gating mechanisms leading to the activation of hCa_V1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCa_V1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCa_V1.2 model and studying calcium influx using computational approaches.

METHODS

We employed homology modeling and molecular dynamics (MD) to build the structure of hCa_V1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCa_V1.2.

RESULTS

We report a comprehensive three-dimensional model of a closed state hCa_V1.2 refined under physiological membrane-bound conditions using MD simulations. Our SMD simulations on the model revealed four important barriers for ion permeation: this includes three calcium binding sites formed by the EEEE- and TTTT- rings within the selectivity filter region and a large barrier rendered by the hydrophobic internal gate. Our results also revealed that the first hydration shell of calcium remained intact throughout the simulations, thus playing an important role in ion permeation in hCa_V1.2.

CONCLUSIONS

Our results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCa_V1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation.