MOLECULAR MODELING AND IN SILICO ANALYSIS OF THE MOLYBDATE/TUNGSTATE TRANSPORTER WtpB IN THE HYPERTHERMOPHILIC ARCHAEON Thermococcus kodakarensis

Abstract

The WtpB permease from Thermococcus kodakarensis KOD1 is a membrane-integrated component of the WtpABC ATP-binding cassette (ABC) transporter system, mediating high-affinity uptake of tungstate (WO₄²⁻) and molybdate (MoO₄²⁻), essential metal oxoanions in hyperthermophilic archaea. Using comprehensive in silico approaches, we modeled the secondary and tertiary structure of WtpB, revealing nine α-helices with distinct functional domains, including putative periplasmic binding protein (PBP) interaction loops, a conserved gate region, dimer interface, and ABC-ATPase interaction site. Sequence alignment of 31 Thermococcus species demonstrated 44.5 % residue conservation, indicating evolutionary stability. Physicochemical profiling showed a high aliphatic index (131.94), isoelectric point of 9.69, and GRAVY score of 0.854, consistent with a thermally stable, hydrophobic transmembrane protein. Structural validation via Ramachandran plot indicated 95.5 % residues in favored regions, while ProQ and QMEAN scores (LG: 9.228; MaxSub: 0.407; QMEAN: 0.549) confirmed model accuracy. Interaction network analysis identified strong associations with WtpA and WtpC (confidence scores >0.99), predicting complex formation. Phylogenetic analysis resolved six clusters within Thermococcus, with WtpB sequence identities ranging from 72.6 % (Pyrococcus furiosus) to 97.1 % (closely related species), reflecting functional divergence aligned with ecological niches. This integrated structural and evolutionary characterization of WtpB advances understanding of archaeal metal oxoanion transport mechanisms, crucial for maintaining redox metabolism under extreme conditions, and provides a molecular basis for future functional and applied studies targeting hyperthermophilic ABC transport systems.