Unraveling the substrate preference of an uncharacterized phylogenetic subgroup in Formate/Nitrite Transporter (FNT) family: Computational studies of anion transport inEscherichia coliFNT homolog
Authors: Mukherjee Mishtu , Sankararamakrishnan Ramasubbu 
Published: May 2019

Formate/Nitrite Transporters (FNTs) selectively transport monovalent anions and are found in prokaryotes and lowers eukaryotes. They play significant role in bacterial growth and act against the defense mechanism of infected host. Since FNTs don’t occur in higher animals, they are attractive drug targets for many bacterial diseases. Phylogenetic analysis revealed that they can be classified into eight subgroups and two of which belong to the uncharacterized YfdC-α and YfdC-β groups. Experimentally determined structures of FNTs belonging to different phylogenetic groups adopt the unique aquaporin-like hourglass helical fold. We considered formate channel fromVibrio Cholerae(VcFocA), hydrosulphide channel fromClostridium difficile(CdHSC) and the uncharacterized channel fromEscherchia coli(EcYfdC) to investigate the mechanism of transport and selectivity. Using equilibrium molecular dynamics (MD) and umbrella sampling studies, we determined temporal channel radius profiles, permeation events and potential of mean force (PMF) profiles of different substrates with the conserved central histidine residue in protonated or neutral form. Unlike the VcFocA and CdHSC, MD studies showed that the formate substrate was unable to enter the vestibule region of EcYfdC. Absence of a conserved basic residue and presence of acidic residues in the vestibule regions, conserved only in YfdC-α, were found to be responsible for high energy barriers for the anions to enter EcYfdC. PMF profiles generated for ammonia and ammonium ion revealed that EcYfdC can transport neutral solutes and could possibly be involved in the transport of cations analogous to the mechanism proposed for ammonium transporters. Although YfdC members belong to the FNT family, our studies convincingly reveal that EcYfdC is not an anion channel. Absence/presence of specific charged residues at particular positions makes EcYfdC selective for neutral or possibly cationic substrates. This adds to the repertoire of membrane proteins that use the same fold but transport substrates with different chemical nature.

Author Summary

Channels and transporters are membrane proteins involved in the transport of solutes selectively across the cell membranes. Drugs for many diseases have been developed to inhibit ion channels. Formate/Nitrite Transporters (FNTs) are ion channels selective for monovalent anions and are present in bacteria and lower eukaryotes. Absence of FNTs in humans makes them as attractive drug targets against many pathogenic bacteria. To develop inhibitors for a protein, it is important to understand the mechanism of its function. Selectivity and transport mechanism of FNTs have been investigated for some members. One of the subgroups of FNTs, YfdC-α, is uncharacterized. In this study we used computer simulation approach to investigate the molecular mechanism of selectivity and transport of three FNTs including one from YfdC-α group fromEscherichia coli. Our studies show thatE. coliYfdC is not an anion channel although it belongs to FNT family. We hypothesize that the YfdC-α members could be involved in the transport of neutral or possibly cationic substrates. This is further supported by the conservation of specific acidic residues found only in YfdC-α in the vestibule regions. This finding has major implications in developing blockers for FNT members belonging to YfdC-α group.