The α/β3 complex of human voltage-gated sodium channel hNa1.7 to study mechanistic differences in presence and absence of auxiliary subunit β3.

CONTEXT

In the context of structural interactomics, we generated a 3D model between α and β3 subunits for the hitherto unknown human voltage-gated sodium channel complex (hNa 1.7α/β3). We embedded our 3D model in a membrane lipid bilayer for molecular dynamics (MD) simulations of the sodium cation passage from the outer vestibule through the inner pore segment of our hNa 1.7 complex in presence and absence of auxiliary subunit β3 with remarkable changes close to electrophysiological study results. A complete passage could not be expected due to because the inactivated state of the underlying 3D template. A complete sodium ion passage would require an open state of the channel. The computed observations concerning side chain rearrangements for favorable cooperativity under evolutionary neighborhood conditions, favorable and unfavorable amino acid interactions, proline kink, loop, and helix displacements were all found in excellent keeping with the extant literature without any exception nor contradiction. Complex-stabilizing pairs of interacting amino acids with evolutionary neighborhood complementary were identified.

METHODS

The following tools were used: sequence search and alignment by FASTA and Clustal Omega; 3D model visualization and homology modeling by Vega ZZ, SPDBV, Chimera and Modeller, respectively; missing sections (loops) by Alphafold; geometry optimization prior to MD runs by GROMACS 2021.4 under the CHARMM 36 force field; local healing of bad contacts by SPDBV based on its Ramachandran plots; protein-protein docking by HDOCK 2.4; membrane insertion assisted by OPM; Berendsen V-rescaling for NVT; Parrinello-Rahman and Nose-Hoover for MPT; MD analyses by VMD and XMGRACE.