Molecular motors and pumps

A molecular machine is a protein complex that converts chemical energy into mechanical work or directed motion. An enzyme just speeds up a reaction; a machine couples that chemistry to a repeating cycle of shape changes and turns it into a step, a spin, or a pumped ion. They run on one of three fuels: ATP hydrolysis, a transmembrane ion gradient, or the chemical potential of a polymer. This lesson covers the mechanical ones — motors and pumps.

In each viewer, use the mode toggle (top-right) to switch between the smooth surface and atom-level ball-and-stick, and explode to pull the subunits apart. Several of these machines you can watch move, as a looping animation, in the interactive Machines section.

Motor proteins

Motors generate force and movement. Linear motors walk along filament tracks; rotary motors spin a shaft inside a stator.

Linear motors — walking along a track

Each takes discrete ATP-powered steps along a cytoskeletal filament.

Myosins walk along actin filaments — powering muscle contraction, cargo transport, and the pinch of cell division. Each ATP turnover swings a long lever-arm helix by ~10 nm.

The bulky motor head carries the ATP pocket and the actin-binding face; the long lever arm trailing off it (stiffened by two wrapped light chains) amplifies a few ångströms of internal motion into a nanometre stride.

Kinesins move along microtubules, usually toward the cell periphery, hauling vesicles and organelles. The structure below is a dimer — two heads, the two "feet" that step hand-over-hand.

Dyneins also run on microtubules but travel the other way, toward the cell centre — and they power the beating of cilia and flagella. Unlike myosin and kinesin, dynein is built on a ring of six AAA+ modules.

Look for the ring of AAA+ subunits with a long stalk projecting off it; the tip of that stalk grips the microtubule, while ATP cycling in the ring drives the power stroke through a lever-like linker.

Rotary motors — spinning a shaft in a stator

ATP synthase is the most famous machine in biology — a molecular turbine. Proton flow down a gradient spins a membrane rotor whose asymmetric central shaft cranks the three catalytic sites of the F₁ head through a fixed sequence of shapes that forge ATP. It is fully reversible: burn ATP and it pumps protons.

Six subunits (three α, three β) ring the central γ shaft. The shaft is asymmetric — that is the trick: as it turns it presses on each β differently, so the three identical sites sit in three different states (open, loose, tight) at once. Watch the F₁ head turn, or see it inside the whole membrane enzyme.

The bacterial flagellar motor is the other great rotary engine — and the only true wheel-and-axle in biology. It burns no ATP: ions flowing across the membrane through ring-shaped stators apply torque to the rotor, spinning the corkscrew flagellum at up to ~1000 revolutions per second, and reversing to let the cell tumble and change direction.

This cryo-EM structure resolves the load-bearing core: the MS-ring in the inner membrane, the rod drive-shaft, and the flexible hook — a universal joint that passes the spin on to the filament. At 335,000 atoms it is far too large for the old PDB file format (it exists only as mmCIF) and too large for atom-by-atom modes, so it is drawn as a surface. See the whole thing spin in place.

Pumps and transporters

Membrane machines that move substances against their gradient, at the cost of ATP.

P-type ATPases phosphorylate themselves on an aspartate to drive a big rocking motion. SERCA, the calcium pump, drags two Ca²⁺ out of the cytoplasm per ATP; the Na⁺/K⁺-ATPase uses the identical mechanism to set the resting voltage of every nerve and muscle cell.

Note the mushroom shape: a stalk of ten membrane helices (calcium binds buried inside it) and a three-domain cytoplasmic head that moves like a pump handle between inward- and outward-facing states. Watch the pump cycle through its states.

ABC transporters are a vast family that shuttle everything from ions to lipids to drugs. They are clinically notorious: pumps like P-glycoprotein eject chemotherapy drugs from cancer cells, a major cause of multidrug resistance.

Two transmembrane domains form the export pathway; two cytoplasmic nucleotide-binding domains clamp together when they bind ATP, flipping the transporter from inward- to outward-facing and ejecting the cargo.

Every machine here follows the same blueprint: an energy source, a conformational cycle that returns to its start, and a direction — each loop biased forward by tying the mechanical step to an irreversible chemical event. The next lesson turns to machines that act on polymers instead of force: the ones that read, copy, and recycle the cell's information and proteins.