Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation

Biophysical Journal
Xiaoying LvHaipeng Gong

Abstract

FocA belongs to the formate-nitrate transporter family and plays an essential role in the export and uptake of formate in organisms. According to the available crystal structures, the N-terminal residues of FocA are structurally featureless at physiological conditions but at reduced pH form helices to harbor the cytoplasmic entrance of the substrate permeation pathway, which apparently explains the cessation of electrical signal observed in electrophysiological experiments. In this work, we found by structural analysis and molecular dynamics simulations that those N-terminal helices cannot effectively preclude the substrate permeation. Equilibrium simulations and thermodynamic calculations suggest that FocA is permeable to both formate and formic acid, the latter of which is transparent to electrophysiological studies as an electrically neutral species. Hence, the cease of electrical current at acidic pH may be caused by the change of the transported substrate from formate to formic acid. In addition, the mechanism of formate export at physiological pH is discussed.

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Citations

Jun 3, 2014·Journal of Molecular Biology·Claudia DoberenzR Gary Sawers
Mar 3, 2017·The EMBO Journal·Marie Wiechert, Eric Beitz
Sep 22, 2017·Scientific Reports·Kalina Atkovska, Jochen S Hub
Nov 11, 2020·Molecular Microbiology·Michelle KammelRobert Gary Sawers
Jan 23, 2020·Biophysical Journal·Mishtu MukherjeeRamasubbu Sankararamakrishnan
Mar 8, 2019·Journal of Chemical Information and Modeling·Meng WuSuwen Zhao
Mar 19, 2019·Journal of Chemical Information and Modeling·Tomasz Pieńko, Joanna Trylska

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