A case study in applying docking predictions: Modelling the tentoxin binding sites of chloroplast F1-ATPase

Vladimir Sobolev*, Alidin Niztaev, Uri Pick, Adi Avni, Marvin Edelman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The study presents an ab initio approach for locating a ligand-binding site and demonstrates that relevant conclusions can be deduced from multiple, predicted ligand positions. Tentoxin is a specific inhibitor of plastid CF1-ATPase, its interaction with the α- and β-subunits of the enzyme resulting in complex interference with ATPase activity. The uniquely different conformations of the β-subunits in the quasisymmetrical structure of the F1-ATPase from bovine mitochondria offer an opportunity to model tentoxin binding at multiple sites in plastid CF1-ATPase. Using software for molecular docking, we located and analysed three putative binding sites with approximately equally high complementarity to tentoxin. Complementarity at these sites is sensitive to the nucleotide occupancy state of the β-subunit. The main interactions stabilizing the putative complexes were determined, and homology models for the tentoxin-binding sites of Chlamydomonas plastid CF1-ATPase were created. The predicted binding pocket residues for Site I are at the αTPTP interface and include residue Glu-67βTP (codon 83β in plastid CF1-ATPase), previously identified as a molecular-genetic determinant for the high affinity, inhibitory response to tentoxin in Chlamydomonas. This site overlaps with that suggested by others, but ∼ 50% of residues differ. Sites II and III, possibly related to low-affinity binding of tentoxin, are located in functionally active regions: one entirely within the αTP-subunit and sharing a residue with the αTP nucleotide-binding site; the other at the αTPE/γ interface and sharing a residue with the conserved DELSEED sequence. Non-catalytic residues in these putative pockets represent potential targets for mutational analysis.

Original languageEnglish
Pages (from-to)857-867
Number of pages11
JournalCurrent Science
Issue number7
StatePublished - 10 Oct 2002


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