Molecular Dynamics Simulation Reveals Specific Interaction Sites between Scorpion Toxins and Kv1.2 Channel: Implications for Design of Highly Selective Drugs

Abstract

The Kv1.2 channel plays an important role in the maintenance of resting membrane potential and the regulation of the cellular excitability of neurons, whose silencing or mutations can elicit neuropathic pain or neurological diseases (e.g., epilepsy and ataxia). Scorpion venom contains a variety of peptide toxins targeting the pore region of this channel. Despite a large amount of structural and functional data currently available, their detailed interaction modes are poorly understood. In this work, we choose four Kv1.2-targeted scorpion toxins (Margatoxin, Agitoxin-2, OsK-1, and Mesomartoxin) to construct their complexes with Kv1.2 based on the experimental structure of ChTx-Kv1.2. Molecular dynamics simulation of these complexes lead to the identification of hydrophobic patches, hydrogen-bonds, and salt bridges as three essential forces mediating the interactions between this channel and the toxins, in which four Kv1.2-specific interacting amino acids (D353, Q358, V381, and T383) are identified for the first time. This discovery might help design highly selective Kv1.2-channel inhibitors by altering amino acids of these toxins binding to the four channel residues. Finally, our results provide new evidence in favor of an induced fit model between scorpion toxins and K+ channel interactions.

Dual-Site Binding of Quaternary Ammonium Ions as Internal K+-Ion Channel Blockers: Nonclassical (C–H···O) H Bonding vs Dispersive (C–H···H–C) Interaction

“…The system is solvated by the truncated octahedron TIP3PBOX at 12 Å distance from the edge of the octahedron. Note that the amino acid residues TRP-26 and TRP-113, at the intracellular ends of transmembrane α helices M1 and M2, respectively, and TRP-87 at the extracellular end of M2, which are involved in the interaction with the lipid bilayer, are not involved in the internal blocking action of QA. , Previous reports indicated that binding of blocker molecules hardly affects the overall stability of the K + channels and the interaction is hardly affected by the membrane. − Also, many simulation studies on the binding of blocker molecules and K + channels without a membrane have achieved good agreement with the experimental data. ,− Moreover, discarding the lipid–protein interactions has also contributed to the reduction of the computational time. Thus, we did not add the membrane into the simulation, but rather perform the simulation by maintaining a restraint weight of 0.5 kcal/mol/Å 2 on the C α atom of protein during the production runs to mimic the stabilizing effect of the lipid bilayer on the tetrameric ion channel, while the side chains and QAs are allowed to move freely.…”

“…Note that the amino acid residues TRP-26 and TRP-113, at the intracellular ends of transmembrane α helices M1 and M2, respectively, and TRP-87 at the extracellular end of M2, which are involved in the interaction with the lipid bilayer, are not involved in the internal blocking action of QA. 58,59 Previous reports indicated that binding of blocker molecules hardly affects the overall stability of the K + channels and the interaction is hardly affected by the membrane. 60−63 Also, many simulation studies on the binding of blocker molecules and K + channels without a membrane have achieved good agreement with the experimental data.…”

Scorpion Toxins: Positive Selection at a Distal Site Modulates Functional Evolution at a Bioactive Site

“…In this work, we carried out mutational analysis of site 52 in three α-ScNaTxs. In combination with molecular dynamics simulations (Yuan et al 2017) and statistical coupling analysis (SCA) (Halabi et al 2009), our experimental data demonstrated that the accelerated substitutions of site 52 is a result of adaptation to the evolutionary change of the bioactive PSSs, and that such coevolution may help the substituted bioactive sites to maintain an active conformation for receptor binding. Our study thus suggests that within one nonenzymatic protein, there exists also allosteric communication between its bioactive and nonbioactive distant sites.…”

Back to basics with receptors and ligands – molecules, mechanisms and medicine

“…These toxins typically consist of 23-43 amino acid residues and are classified into four subfamilies, of which α-KTx is the largest subfamily that shares a common cysteine-stabilized α/β motif 53 . Given the high specificity and affinity of scorpion toxins for K + and other ion channels, their potential as lead candidates for drug discovery for ion channelopathies has been widely recognized 5,52,54 .…”