When I was a little kid, my dad used to insist I help him work on our family car. I’m sure he saw it as a way to teach me how automobiles operate and at the same time for us to bond; but I hated it.
We lived near West Virginia Institute of Technology in off-campus faculty housing. Our home was located on a hillside. A long set of stairs was the only way to reach our house from the street, which meant we didn’t have a garage. Instead we parked the car next to the sidewalk, near the bottom of the stairs.
Every Saturday morning (or at least it seems to me like it was every Saturday), we worked on the car. To do this, we (and by “we,” I mean I) had to carry tools from the house to the street. Invariably, we (and by “we,” I mean my dad) needed a tool that we didn’t have with us, which meant another trip up and down the stairs for me. My sojourn to retrieve the required tools would usually be repeated many times before my dad finished whatever he was doing with the car.
As much as I hated this ordeal, one of the things I did find fascinating, however, was how complex our car’s engine was, and how my dad always seemed to know what part needed his attention. Even as a little kid, I knew just by looking under the hood that engineers—and pretty smart ones at that—were responsible for designing and assembling the engine.
One of the things I find intriguing as a biochemist is how much the inner workings of the cell have in common with an automobile engine. A number of protein complexes inside the cell operate as molecular-level machines. In fact, some of these machines bear a startling similarity to man-made machines. This similarity represents a potent argument for intelligent design.
I devoted an entire chapter to biomolecular motors in my book, The Cell’s Design and have written articles on these fascinating protein systems. (Go here, here, and here to access a few of these pieces.)
New work recently published by a team from Japan identifies yet another protein complex with machine-like properties: the HslU transporter. This motor translocates protein chains into a large barrel-shaped conglomerate of proteins (called the bacterial energy-dependent proteolytic complex, HslUV for short) found in certain bacteria. HslUV degrades specific types of proteins and, consequently, plays a role in regulating the cell’s activity.
HslUV consists of either one or two HslU motors that interact with the HslV complex. The HsLV ensemble is made up of twelve identical protein subunits arranged to form two rings (each ring is comprised of six subunits) stacked on each other. In this configuration, HslV forms a cylindrical structure with an internal cavity. Proteins are broken down within this cavity. HslU sits on top (or on the top and bottom if two HslU complexes are involved) of HslV, transporting protein chains into the HslV cavity.
Using a technique known as molecular dynamics simulation, the research team explored the molecular-scale processes involved when the HslU motor moves protein chains into the HslV digestion chamber. Each HslU complex consists of a ring of six identical protein subunits. Located centrally within the ring is a pore.
The simulations indicated that the HslU motor transports extended protein chains through this pore via a paddling mechanism. The paddles are made up of two tyrosine rings located across from each other within the interior of the pore. When provided with energy, the tyrosine rings/paddles move in a coordinated fashion, so that both rings circulate downward, away from each other, upward, and then toward each other.
When the tyrosine rings move toward each other they contact the protein chain; and as the rings move downward they drag the protein chain along. As the tyrosine paddles move away from each other, they disengage from the protein chain and re-engage it following their upward and inward movements. As this cycle repeats, the protein chain is transported in a step-wise manner into the HslV cavity as a result of the paddle-wheel motion.
The HslU motor is just one of a long list of molecular-level machines found inside the cell. The remarkable machine-like qualities of these biomolecular machines is provocative—even more so since these systems operate with a greater degree of efficiency than man-made machines. They suggest that perhaps a mind is responsible for their creation; the same conclusion that even a small child would draw when peering under the hood of an automobile.