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Biochem Biophys Res Commun. 2005 Oct 28;336(3):961-6.

Proton binding sites and conformational analysis of H+K(+)-ATPase.

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Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad 500007, India.


It is proposed that the hydronium ion, H3O+, binds to the E1 conformation of the alpha-subunit of gastric proton pump. The H3O+ binding cavities are characterized parametrically based on valence, sequence, geometry, and size considerations from comparative modeling. The cavities have scope for accommodating monovalent cations of different ionic radii. The H3O+ transport is proposed to be aided by arenes which are arranged regularly along the pump starting from N-domain through the transmembrane region. Step-by-step structural changes accompanying H3O+ occlusion are studied in detail. The observations corroborate well with earlier experimental studies.

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