Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes

Abstract

The human SLC22A6/OAT1 plays an important role in the elimination of a broad range of endogenous substances and xenobiotics thus attracting attention from the pharmacological community. Furthermore, OAT1 is also involved in key physiological events such as the remote inter-organ communication. Despite its significance, the knowledge about hOAT1 structure and the transport mechanism at the atomic level remains fragmented owing to the lack of resolved structures. By means of protein-threading modeling refined by μs-scaled Molecular Dynamics simulations, the present study provides the first robust model of hOAT1 in outward-facing conformation. Taking advantage of the AlphaFold 2 predicted structure of hOAT1 in inward-facing conformation, we here provide the essential structural and functional features comparing both states. The intracellular motifs conserved among Major Facilitator Superfamily members create a so-called “charge-relay system” that works as molecular switches modulating the conformation. The principal element of the event points at interactions of charged residues that appear crucial for the transporter dynamics and function. Moreover, hOAT1 model was embedded in different lipid bilayer membranes highlighting the crucial structural dependence on lipid-protein interactions. MD simulations supported the pivotal role of phosphatidylethanolamine components to the protein conformation stability. The present model is made available to decipher the impact of any observed polymorphism and mutation on drug transport as well as to understand substrate binding modes.

Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale

“…The definition of the co-substrate and substrate required a parametrization using GAFF2 and DNA.OL15 forcefield's parameters, considering the latter being a purine derivative. MD simulations were performed using a similar setup as previously established [15]. The simulations were carried out with using the CPU and GPU codes of the Amber18 package [40], [41].…”

“…The comparison of the intracellular structural arrangement between OF and IF apo hOAT1 models revealed that the charge-relay system must be disrupted along transport cycle. This might ultimately unlock the IC gating required for substrate release [15]. Conformational changes are expected to be triggered upon substrate and/or co-substrate binding, suggesting the existence of a distant communication between substrate binding pockets and MFS conserved intracellular motifs.…”

“…Besides, it is important to note that MFS protein functions have been experimentally shown to strongly depend on the membrane composition [26,27,55]. Likewise, PE lipids were shown to non-covalently bind with the residues standing at the interface between N-and C bundles in apo hOAT1 structure [15]. Therefore, out of the structural interplay between surrounding lipid bilayer and hOAT1 protein, the active role of lipid bilayer membrane in the communication between extracellular and intracellular regions was also investigated.…”

“…Structural patterns of hOAT1 might provide insights into its roles regarding drug efficacy, toxicity, and elimination [13,14]. We recently proposed a structural and dynamic model of hOAT1 embedded in lipid bilayers [15]. hOAT1 is expected to adopt the Major Facilitator Superfamily (MFS) fold for which substrate translocation follows the alternating access model.…”

“…The so-called A-, E[X6]R and PETL motifs are repeated in both N-and Cbundles. The interactions between these motifs differ between IF and OF conformations [15]. Knowledge about binding modes of hOAT1 substrates remain fragmented while they are of particular importance for the understanding and prediction of transporter-mediated drug-drug interactions (DDIs) [21][22][23].…”