Mechanisms Underlying Proton Release in CLC-type F^–/H⁺ Antiporters

Abstract

The CLC family of anion channels and transporters includes Cl–/H+ exchangers (blocked by F–) and F–/H+ exchangers (or CLCFs). CLCFs contain a glutamate (E318) in the central anion-binding site that is absent in CLC Cl–/H+ exchangers. The X-ray structure of the protein from Enterococcus casseliflavus (CLCF-eca) shows that E318 tightly binds to F– when the gating glutamate (E118; highly conserved in the CLC family) faces the extracellular medium. Here, we use classical and DFT-based QM/MM metadynamics simulations to investigate proton transfer and release by CLCF-eca. After up to down movement of protonated E118, both glutamates combine with F– to form a triad, from which protons and F– anions are released as HF. Our results illustrate how glutamate insertion into the central anion-binding site of CLCF-eca permits the release of H+ to the cytosol as HF, thus enabling a net 1:1 F–/H+ stoichiometry.

Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter

“…4 performed a series of calculations on the crystal structures of wild type CLC F and its mutants which determined Glu int should remain deprotonated during the transport process and agreed with Last et al 6 that Glu ext is directly interacting with the extracellular and intracellular solutions. Later that same year, however, Chiariello et al 5 concluded, through QM/MM simulations, that Glu int is a part of the proton transport, but that while F - is exported in its anionic form, the proton is released to the intracellular solution in the form of HF.…”

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

“…18 MiMiC has displayed excellent scalability over more than thousands of cores, paving the way toward routine subnanosecond QM/MM MD of large biological systems. 19,20 MiMiC QM/MM requires one input file for GROMACS and one for CPMD. The definition of the QM region must be added to both.…”

“…In addition, support for CFOUR will be available soon, allowing for high-level wave function-based QM/MM simulations . MiMiC has displayed excellent scalability over more than thousands of cores, paving the way toward routine subnanosecond QM/MM MD of large biological systems. , …”

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations

“…In this respect, non-empirical density functional theory (DFT) is a rather general (and relatively accurate) approach, and it comes at a far minor computational cost than wavefunction-based methods including electronic correlation. 4 As such, DFT-based QM/MM MD simulations are nowadays the method of choice in many state of the art in-silico studies of biochemical processes, including enzymatic reactions, [5][6][7][8][9][10][11][12][13][14][15][16] transition metals binding to proteins, [17][18][19][20] proton transfer [21][22][23][24] and photophysical processes. [25][26][27][28] Applications to drug design, on the other hand, have not been sufficiently explored, apart from notable exceptions.…”