Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube

The effect of the protonation stateof glutamic acid on its translocationthrough cyclic peptide nanotubes (CPNs) was assessed by using moleculardynamics (MD) simulations. Anionic (GLU-), neutral zwitterionic(GLU0), and cationic (GLU+) forms of glutamic acid were selected asthree different protonation states for an analysis of energetics anddiffusivity for acid transport across a cyclic decapeptide nanotube.Based on the solubility-diffusion model, permeability coefficientsfor the three protonation states of the acid were calculated and comparedwith experimental results for CPN-mediated glutamate transport throughCPNs. Potential of mean force (PMF) calculations reveal that, dueto the cation-selective nature of the lumen of CPNs, GLU-,so-called glutamate, shows significantly high free energy barriers,while GLU+ displays deep energy wells and GLU0 has mild free energybarriers and wells inside the CPN. The considerable energy barriersfor GLU- inside CPNs are mainly attributed to unfavorable interactionswith DMPC bilayers and CPNs and are reduced by favorable interactionswith channel water molecules through attractive electrostatic interactionsand hydrogen bonding. Unlike the distinct PMF curves, position-dependentdiffusion coefficient profiles exhibit comparable frictional behaviorsregardless of the charge status of three protonation states due tosimilar confined environments imposed by the lumen of the CPN. Thecalculated permeability coefficients for the three protonation statesclearly demonstrate that glutamic acid has a strong protonation statedependence for its transport through CPNs, as determined by the energeticsrather than the diffusivity of the protonation state. In addition,the permeability coefficients also imply that GLU- is unlikelyto pass through a CPN due to the high energy barriers inside the CPN,which is in disagreement with experimental measurements, where a considerableamount of glutamate permeating through the CPN was detected. To resolvethe discrepancy between this work and the experimental observations,several possibilities are proposed, including a large concentrationgradient of glutamate between the inside and outside of lipid vesiclesand bilayers in the experiments, the glutamate activity differencebetween our MD simulations and experiments, an overestimation of energybarriers due to the artifacts imposed in MD simulations, and/or finallya transformation of the protonation state from GLU- to GLU0to reduce the energy barriers. Overall, our study demonstrates thatthe protonation state of glutamic acid has a strong effect on thetransport of the acid and suggests a possible protonation state changefor glutamate permeating through CPNs.