A model of 3D-structure of H+, K+-ATPase catalytic subunit derived by homology modeling.

AIM To build a model of 3D-structure of H(+), K(+)-ATPase catalytic subunit for theoretical study and anti-ulcer drug design. METHODS The model was built on the basis of structural data from the Ca(2+)-ATPase. Structurally conserved regions were defined by amino acid sequence comparisons, optimum interconnecting loops were selected from the protein databank, and amino (N)- and carboxyl (C)-terminal ends were generated as random coil structures. Applying molecular mechanics method then minimized the model energy. Molecular dynamics technique was used to do further structural optimization. RESULTS The model of 3D-structure of H(+), K(+)-ATPase was derived. The model is reasonable according to several validation criteria. There were ten transmembrane helices (TM1-TM10) in the model and inhibitor-binding site was identified on the TM5-8 riched negatively charged residues. CONCLUSION The 3D-structure model from our study is informative to guide future molecular biology study about H(+), K(+)-ATPase and drug design based on database searching.