Structural bioinformatics of six human integral membrane ion‑transport proteins and their AlphaFold3‑predicted water‑soluble QTY analogues

The claudins and the two-pore-domain (K2P/KCNK) potassium channels are human integral membrane proteins that seal the paracellular pathway and carry the transcellular leak pathway of epithelial ion homeostasis, and both families are high-value drug targets. However, their intrinsic hydrophobicity and membrane association have created longstanding challenges for extensive research. In this study, we applied the QTY code – a simple protein design strategy that replaces hydrophobic residues leucine (L), isoleucine (I), valine (V), and phenylalanine (F) with hydrophilic yet structurally compatible residues glutamine (Q), threonine (T) and tyrosine (Y) – to generate QTY analogs of Claudin-4, Claudin-9, TASK-1, TASK-3, TREK-2 and TRAAK with reduced hydrophobicity. Using AlphaFold3, we predicted and superposed the structures of native and QTY-engineered analog proteins. Our results show strong structural resemblance between each pair, with root mean square deviation (RMSD) values of 0.51–0.91 Å for four of the six proteins, and 1.28 and 1.42 Å for TREK-2 and TRAAK, which fall to 0.52 and 0.62 Å across the transmembrane core that the QTY code modifies. In addition, QTY substitution significantly reduced surface hydrophobicity, indicating improved water-solubility while preserving 3D structural fold integrity and the K⁺ selectivity-filter and claudin barrier signatures. Our findings demonstrate the potential of QTY-designed claudin and K2P variants with reduced hydrophobicity as candidate soluble antigens and screening reagents for high-value permeability targets. They serve as water-soluble surrogates in structural biology, drug discovery, and any application limited by the experimental properties of the native membrane protein.