Atomistic modeling and molecular dynamics analysis of human Ca1.2 channel using external electric field and ion pulling simulations.

BACKGROUND

Human Ca1.2 (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 hCa1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCa1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCa1.2 model and studying calcium influx using computational approaches.

METHODS

We employed homology modeling and molecular dynamics (MD) to build the structure of hCa1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCa1.2.

RESULTS

We report a comprehensive three-dimensional model of a closed state hCa1.2 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 hCa1.2.

CONCLUSIONS

Our results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCa1.2. 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.

Copyright © 2019. Published by Elsevier B.V.