Molecular dynamics simulations of valinomycin and its potassium complex in homogeneous solvents

Rethinking Ion Transport by Ionophores: Experimental and Computational Investigation of Single Water Hydration in Valinomycin-K+ Complexes

Valinomycin is a macrocyclic ionophore that transports K⁺ across hydrophobic membranes. Its function depends on selectivity, capture, transport, and release of the ion. While thermodynamics clearly indicate that valinomycin binds K⁺ preferentially over all other alkali ions, characterizing the capture/transport/release of K⁺ by valinomycin at the molecular level remains a challenge. The bracelet-like structure of valinomycin-K⁺ (K⁺VM) has the ion completely enveloped, facilitating transport through the cell membrane. We report that hydration by a single water molecule, (K⁺VM)(H₂O), produces three different conformers, identified by infrared spectroscopy and supporting computational studies. For two minor conformers, the water prevents the ionophore from closing, a conformation that would inhibit diffusion through the membrane. However, the dominant conformer encloses both the ion and the water, replicating the bracelet-like K⁺VM and arguably enhancing diffusion through the membrane. This potential for active participation of water in transport through the hydrophobic cellular membrane has never been previously considered.

Periodic Coulomb Tree Method: An Alternative to Parallel Particle Mesh Ewald

Particle mesh Ewald (PME) is generally the method of choice for handling electrostatics in simulations with periodic boundary conditions. The excellent efficiency of PME on low processor counts is largely due to the use of the fast Fourier transform (FFT). However, due to the FFT's high communication cost, PME scales poorly in parallel. We develop a periodic Coulomb tree (PCT) method for electrostatic interactions in periodic boundary conditions as an alternative to PME in parallel simulations. We verify the accuracy of PCT by comparison of structural and dynamical properties of three different systems obtained via MD simulations using PME and PCT and provide parallel timing comparisons of the two methods on up to 1024 cores.

Visualizing cyclic peptide hydration at the single-molecule level

The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin–water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface.