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

Abstract

A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C–H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl−π and hydrophobic interactions (C–H···H–C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (−16.4 kcal/mol) to octyl (−65.5 kcal/mol), due to an almost linear increase in dispersive interaction.

Quantum Calculations on Ion Channels: Why Are They More Useful Than Classical Calculations, and for Which Processes Are They Essential?

“…There is also the possibility of doing QM/MM calculations (QM = quantum mechanics, MM = molecular mechanics, which is classical); this allows the key section of the protein to be done properly as a QM calculation, while the background is approximated much better than a vacuum; a pure QM calculation of a section of protein has a vacuum outside, albeit at a greater distance than the boundary between the QM and MM sections of the QM/MM calculations [9][10][11]. This is not the only multiscale method; the development of multiscale methods is ongoing, from many laboratories.…”

Effect of geometrical and electronic alteration on the n → π* vertical excitation energy and thermodynamic stability of locked azobenzene (LAB) with protein confinement

“…The TEA pointing down with respect to the ion channel or pointing towards the channel gate in Z cg and E cg . These are two possible binding sites reported for free TEA [62, 63]. Throughout the simulation, the E ‐isomers retained in its initial orientations ( E cg and E sf ) inside the channel cavity.…”

Deciphering the shape selective conformational equilibrium of E- and Z-locked azobenzene–tetraethylammonium ion in regulating photo-switchable K+-ion channel blocking

“…Internal channel blockers have been reported to enter the channel through the open channel gate (CG) and bind to the channel cavity (CC). 71,[93][94][95][96][97] As a result, these gate and cavity residues are involved in the passage and binding of internal blockers via significant interaction with them. The channel cavity consists of ten amino acid residues with the polar hydroxyl side chain of threonine at the top (THR-75) and the bottom (THR-107) of the central cavity.…”

“…Consequently, the TEA moiety binds to the CG residues and eventually detaches from the CG and moves to the intracellular region (Movie S1, ESI †). 93 The above binding and unbinding process keeps repeating during the simulation. Only in one of the simulations it does move into the CC.…”