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Tuesday, December 18, 2007

How Cells Make ATP: ATP Synthase

In our previous posting we saw how cells can make ATP from ADP + Pi by substrate-level phosphorylation [How Cells Make ATP: Substrate-Level Phosphorylation].

This is not the most important route to ATP synthesis. Most of the ATP inside a cell is made by a membrane-bound enzyme called ATP synthase.

ATP synthase is found embedded in the inner membranes of mitochondria and chloroplasts and the inner membrane of bacterial cells. In all three cases, a membrane-associated electron transport system pumps protons (H+) across the membrane from the inside to the outside. In this case "outside" is actually the space between the inner and outer membranes. Protons accumulate in this space creating a protonmotive force. You can think of this "force" as the "pressure" of protons to move back into the cells because of the high concentration that has been created in the intermembrane space.

The protonmotive force is what drives synthesis of ATP. As protons move back into the cell they pass through a channel in the a subunit of ATP synthase. This subunit acts like a small motor driving the rotation of the c subunits (rotor) in the membrane. For every three protons that cross the membrane enough energy is given up to move the rotor through 120°. It takes 9 protons for one complete rotation.

The rotor (c subunits) is connected to a rod made up mostly of the γ subunit of ATP synthase. The rod rotates inside the head, which is a hexamer composed of three α and three β subunits. The head of ATP synthase doesn't rotate. It is fixed to the motor through the b subunits.

The γ rod is asymmetric as shown in the figure by depicting it with a kink. As it rotates inside the head it alters the conformation of the α and β subunits. The active site of the ATP synthase is located on the outside surface between an α and a β subunit. The spinning rod shifts the conformation of the active site between three states.

The first state is called the "open" state. In the "open" state ADP and Pi can bind to the active site. In the second state, called the "loose" state, ADP and Pi are locked in place and cannot be released. In the third state (the "tight" state") ATP is formed as ADP and Pi are squeezed together.

Since there are three active sites in each head, the effect of rotating the γ rod is to sequentially change each of the three sites from "open" to "loose" to "tight" for each 360° rotation of the rotor. Nine protons are used up in one rotation and three ATP's are synthesized. This works out to one ATP molecule for every three protons.

This mechanism of ATP synthesis is called the binding change mechanism. It was first worked out by Paul Boyer. The mechanism was confirmed by X-ray crystallographic studied done by John Walker. Boyer and Walker received the Nobel Prize in 1997.

[Image Credits: The images are from Horton et al. Principles of Biochemistry 4th edition ©Pearson/Prentice Hall]

[The animated gif is from Wikipedia]


paul01 said...

I know you're probably very busy, but is there any relation between this and the famous flagellum?

Larry Moran said...

The bacterial flagellum also has a molecular motor that's driven by protonmotive force.

The biggest difference is that the flagellar rotor is bigger and has a hole in the middle. Stuff passes trough the hole to be secreted outside the cell or to form the flagellum.

NickM said...

There is also common ancestry between the two structures -- not a common ancestor with rotary abilities (probably), but instead an ancestral secretion-ish system.

See this really, really cool new article:

Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV. "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases." Nat Rev Microbiol. 5(11):892-9.

The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. Based on this pattern of homology, we propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer.

wallace.b.s.88 said...

It's obvious that such molecular motor completely obliterates evolutionary theory.. It's a clear case for ID

prof prem raj pushpakaran said...

prof premraj pushpakaran writes -- 2018 marks the 100th birth year of Paul Delos Boyer!!!