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


CONCLUSIONS
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.
Yan
Dong
D
Shenyang Pharmaceutical University, Shenyang 110016, China.
Hu
Yuan-dong
YD
Li
Song
S
Cheng
Mao-sheng
MS
D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D015195:Drug Design; D017506:H(+)-K(+)-Exchanging ATPase / Q000737:chemistry*; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D017506:H(+)-K(+)-Exchanging ATPase