Conformational Transition Pathways in Major Facilitator Superfamily Transporters

Abstract

Major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of MFS superfamily.We have performed a variety of equilibrium, non-equilibrium, biased, and unbiased allatom molecular dynamics (MD) simulations of bacterial proton-coupled oligopeptide transporter GkPOT, glucose transporter 1 (GluT1), and glycerol-3-phosphate transporter (GlpT) to compare the similarities and differences of the conformational dynamics of three different classes of transporters. Here we have simulated the apo protein in an explicit membrane environment. Our results suggest a very similar conformational transition involving interbundle salt-bridge formation/disruption coupled with the orientation changes of transmembrane (TM) helices, specifically H1/H7 and H5/H11, resulting in an alternation in the accessibility of water at the cyto-and periplasmic gates.

Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters

“…This is important because many antiporters use the proton-motive force (PMF) to drive their action of transporting substrates across the membrane. There are many antiporters that use the rocker-switch mechanism, including nitrate/nitrite transporters [28], glycerol-3-phosphate transporters [25,64,74], and oxolate/formate transporters [25] to name a few. One example of an antiporter in the MFS is the glycerol-3-phosphate (GlpT) antiporter that uses the rocker-switch mechanism to move its substrates across the cellular membrane [74].…”

“…This is important because many antiporters use the proton-motive force (PMF) to drive their action of transporting substrates across the membrane. There are many antiporters that use the rocker-switch mechanism, including nitrate/nitrite transporters [ 28 ], glycerol-3-phosphate transporters [ 25 , 64 , 74 ], and oxolate/formate transporters [ 25 ] to name a few.…”

“…As discussed previously, these domains are made up of helical bundles with helices 1–6 in the N-domain and helices 7–12 in the C-domain with the substrate binding site at the interface of the domains. The model states that the binding site is never open to both sides of the membrane at the same time [ 64 ]. Thus, once the rocking occurs, one side opens, while the other side closes, changing which side of the membrane the substrate binding site is open to allow substrates to move in and out of the cell ( Figure 3 ).…”

Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus

“…PepT St is the only POT symporter that has been crystallized in OCC, IF, and IF occ conformational states. ,,, Hence, in this study, we simulated all three available conformational states of PepT St via unbiased all-atom MD − with either E300 protonated or deprotonated. Additionally, we simulated IF occ Leu–Ala (LA) in all possible protonation combinations of E299, E300, and E400 residues, which resulted in a total of eight substrate-bound systems (see Methods for more details).…”

Mechanistic picture for chemo-mechanical couplings in a bacterial proton-coupled oligopeptide transporter from Streptococcus thermophilus

“…17,18,22,27 PepT St is the only POT symporter that has been crystallized in OCC, IF, and IF occ conformational states. 17,18,22,27 Hence, in this study we simulated all three available conformational states of PepT St via unbiased all-atom MD [30][31][32][33] with either E300 protonated or deprotonated. Additionally, we simulated the IF occ (LA) in all possible protonation combinations of E299, E300, and E400 residues, which resulted in a total of eight substrate bound systems (see methods for more details).…”