Productive Nanosystems: The Ribosome Videos

While browsing the literature on the catalysis of bond formation in protein synthesis by ribosomes*, I came across a wonderful set of videos of the ribosomal protein manufacturing system at work, shown in recent-state-of-the-art molecular detail. These videos were presented in a Chemical & Engineering News article online, but I missed seeing them at the time. (This shows a shortcoming of my habit of reading only the paper bundles that the ACS sends by post.)

…but beware of
Ornithological Aeronautics

Ribosomes are productive nanosystems, that is, machines that combine small molecular building blocks under digital control to build complex structures. They’re programmable by means of genetic engineering, and extraordinarily useful in emerging molecular technologies. However, when watching how ribosomes work — in strange, messy, and subtle ways — it’s wise to keep in mind the usual relationship between biological examples (horses, birds) and engineered, mechanical systems (cars, aircraft) that serve similar functions. Biological examples show that functions can be performed (ground transport, air transport), but they don’t necessarily suggest the best approach to building machines for human purposes. If aeronautical engineering had been a branch of ornithology, there would be extensive research on artificial feathers and the ongoing challenge of artificial muscle, but no passenger aircraft.

There’s a much learn from ribosomes, but also much that needn’t be imitated.

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The first video (from the MRC Laboratory of Molecular Biology in Cambridge, UK) is based on structures determined by x-ray crystallography and electron microscopy; these are animated, and rendered at a fine, molecular level of detail. The video shows the entire process of protein manufacture, from initiation to release. The frantic pace of the middle part of the video shows action in approximately real time.

Note, however, that the actual motions of these biological molecular machines are far less purposeful — depicting realistic molecular trajectories would either show a blur, or be excruciatingly boring. (See “The videos lie because they must” in Molecular Machine Assembly: The Movie.)

 

The second video, produced by researchers at the Howard Hughes Medical Institute, focuses on the repeating cycle that extends the amino acid chain. It, too, is based on real structural data, but is presented at more diagrammatic level of detail.

 

The final video, showing detail at a molecular level, is shows the results of a targeted molecular dynamics simulation; targeting is another way to give an unnatural degree of direction to molecular motion, avoiding both excruciating boredom and (here) consumption of inordinate amounts of computer time.

The video shows a key step in tRNA binding, the “accommodation” process, the step where the appendage carrying the next amino acid (green) swings across from right to left. This step is central to kinetic proofreading in ribosomal translation, a process that keeps error rates tolerably low. A landmark paper on this process was co-authored by the new U.S. Secretary of Energy, physicist and Nobel laureate, Steven Chu.

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* Regarding catalysis: There’s none, in the usual chemical sense — ribosomes merely provide positional control that produces a high effective concentration of the right reactive molecules in the right place at the right time, thereby implementing the most straightforward kind of mechanosynthesis.

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See also these videos of molecular machines:

• Productive Nanosystems: The Movies
• Molecular Machine Assembly: The Movie
• Nanomachines: How the Videos Lie to Scientists

And of high-throughput manufacturing:

• High-Throughput Nanomanufacturing: Small Parts (with videos)
• High-Throughput Nanomanufacturing: Assembly (with videos)

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Tagged as: fabrication, mechanosynthesis, molecular biology, ribosomes