Abstract
The human SLC22A6/OAT1 plays an important role in the disposition of a broad range of endogenous substances and xenobiotics. This is particularly important from the pharmacological point of view since OAT1 is involved in drug elimination events. Furthermore, OAT1 is also involved in key physiological events such as the remote inter-organ communication. In spite of its significance, the knowledge about OAT1 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 charged residues that appear crucial for the transporter dynamics and function. Besides, 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 (PE) components on 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.
The models of hOAT1 in inward- (IF) and outward-facing (OF) conformation. The arrangement of intracellular motifs (intracellular view) in IF and OF state: A-motif (red), E[X6]R (blue), [P/X]ESXRW[L/X] or PETL (yellow) in N- and C-bundle, respectively. The importance of lipid bilayer membrane composition is mirrored in exhibited lipid-binding spots in POPC:POPE:Chol (2:1:1) membrane for PE (cyan), cholesterol (orange) with respect to their lacking in pure POPC (blue) membrane.
Graphical Abstract
Highlights
MD-refined protein threading techniques provide the first robust model of outward facing hOAT1
AlphaFold 2 prediction ensures the structural patterns of hOAT1
Intracellular motifs exhibit the pivotal role in conformation modulation
The lipid bilayer membrane composition is crucial for hOAT1 function
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- ABC
- ATP-Binding Cassette
- AF2
- AlphaFold 2
- aKG
- α-ketoglutarate
- Chol
- Cholesterol
- Cryo-EM
- Cryogenic Electron Microscopy
- EC
- ExtraCellular
- ECL
- ExtraCellular Loop
- GlpT
- Glycerol-3-phosphate Transporter
- GLUT
- Glucose Transporter
- H-bond
- Hydrogen bond
- IC
- IntraCellular
- ICH
- IntraCellular Helix
- ICLs
- IntraCellular Loops
- IF
- Inward-Facing
- IFocc
- Inward-Facing occluded
- LacY
- Lactose permease
- LeuT
- Leucine Transporter
- MD
- Molecular Dynamics
- MFS
- Major Facilitator Superfamily
- NaDC3
- Na+/dicarboxylate transporter
- NKT
- New Kidney Transporter
- OAT
- Organic Anion Transporter
- OF
- Outward-Facing
- OFocc
- Outward-Facing occluded
- PC
- PhosphatidylCholine
- PCA
- Principal Component Analysis
- PD
- PharmacoDynamics
- PE
- PhosphatidylEthanolamine
- PGx
- Pharmacogenetics
- PK
- PharmacoKinetics
- PME
- Particle Mesh Ewald
- POPC
- 1 -palmitoyl-2-oleoyl-sn-glycero-3 -phosphocholine
- POPE
- 1 -palmitoyl-2-oleoyl-sn-glycero-3 -phosphoethanolamine
- PTC
- Proximal Tubular Cells
- SLC
- SoLute Carrier
- SNP
- Single Nucleotide Polymorphisms
- TMH
- TransMembrane Helix
- XylE
- Xylose transporter
