Open-sided models, enzyme modeling

A model for operation of the Na+-K+ pump. The enzyme exists in two conformational states, E] and E2. In state E, the ion-binding site is open to the intracellular solution and preferentially binds Na+ ions in E2, the ion-binding site faces the extracellular solution and preferentially binds K+. ATP phosphorylates the enzyme in the Ei conformation to give a high-energy intermediate, Ej P. When the enzyme relaxes to the low-energy conformation E2—P, the Na+ ions dissociate on the extracellular side of the membrane and K+ ions are bound. Hydrolysis of E2—P releases P inside the cell. This returns the protein to the E, conformation so that the K+ ions are released inside the cell. 

Since the structure observed in the crystals represents an inactive form of the enzyme, several structural modifications were required to accommodate a substrate molecule in the active site. These modifications were performed such that the resulting model remained as similar as possible to the experimental structure. First, the loop covering the active site which is anchored at a disulfide bridge was shifted to an alternative strainless conformation opening up the active site. Second, the side-chain orientations of three aromatic residues near the active site had to be changed (Fig. 19). Third, the segment to the right of the active site had to be... 

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