Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

• Published in: Journal of chemical theory and computation Vol. 15; no. 2; pp. 892 - 905
• Main Authors: Duster, Adam W, Garza, Christina M, Aydintug, Baris O, Negussie, Mikias B, Lin, Hai
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 12.02.2019
• Subjects: Binding sites; Chloride ions; Computer simulation; E coli; Ion channels; Mechanics (physics); Migration; Molecular dynamics; Pictures; Proteins; Simulation; Subsystems; Trajectories; Water chemistry
• DOI: 10.1021/acs.jctc.8b01128
• ISSN: 1549-9618

Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories are propagated. This allows one to use small, mobile QM subsystems, the contents of which are dynamically updated as needed. In this work, we report the first adaptive QM/MM simulations of H+ transfer through a biological channel, in particular, the protein EcCLC, a chloride channel (CLC) Cl–/H+ antiporter derived from E. coli. To this end, the H+ indicator previously formulated for approximating the location of an excess H+ in bulk water was extended to include Cl– ions and carboxyl groups as H+ donors/acceptors. Furthermore, when setting up buffer groups, a new “sushi-roll” scheme was employed to group multiple water molecules, ions, and titratable residues along the one-dimensional channel for adaptive partitions. Our simulations reveal that the H+ relay path, which consists of water molecules in the pore, a bound Cl– ion at the central binding site (Cl– cen) of the protein, and the external gating residue E148, exhibits certain mobility within the channel. A two-stage journey of H+ migration was observed: the H+ moves toward Cl– cen and is then shared between Cl– cen and nearby water molecules in the first stage and departs from Cl– cen via nearly concerted transfer to protonate E148 in the second stage. Most of the simulated trajectories show the bound Cl– ion in the channel to be transiently protonated, a possibility that was previously suggested by experiments and computations. Comparisons with conventional QM/MM simulations revealed that both adaptive and conventional treatments yield similar qualitative pictures. This work demonstrates the feasibility of adaptive QM/MM in the simulations of H+ migration through biological channels.