Making Life’s Rosetta Stone Crystal Clear

noeller-picture

by Meghan Sullivan

It would be easy to mistake the images in Harry Noller’s presentation last Thursday for shards of gemstones or modern art. “This part of the talk was influenced by our visit to the Art Institute,” he quipped, advancing through a gallery of slides that showed off a variety of crystals, ranging in color and shape. This was not, however, a geology talk. Noller, professor of molecular cell & developmental biology at the University of California, Santa Cruz, was this year’s invited speaker for the 6th annual Haselkorn Lecture, a seminar series named for UChicago molecular biologist Robert Haselkorn that invites leading researchers to the University for several days to interact with young scientists. His visit drew to a close with a lecture on the molecule he’s spent most of his life studying, the ribosome.

Every living thing possesses ribosomes. It makes sense, then, that ribosomes are fundamentally necessary for life, and may predate proteins and even DNA in the history of life on Earth. Since the identification of DNA, an overarching rule of life has emerged called the Central Dogma, which states that an organism’s DNA is transcribed into RNA, which is then translated into proteins. It’s as if you’re copying instructions from a cookbook. The cookbook – in this case, DNA – holds all the recipes, and you can copy out only the individual recipe you need – the RNA. The copied recipe can then be used as a reference to make the final product, proteins. But as with cooking, you can’t simply turn words on a page into chocolate chip cookies. Like a baker might hold a recipe with one hand and mix the ingredients together with the other, the ribosome is the stepping stone between RNA and proteins.

“Going from DNA to RNA is something like going from Spanish to Portuguese – they’re similar types of molecules,” Noller pointed out, “But going from RNA to protein is like going from Portuguese to Chinese – they’re two totally unrelated languages. In this case, the ribosome is the Rosetta stone.”

The ribosome, which can be found in the fossil record going back 3.5 billion years, is a molecular machine that reads RNA and assembles the protein it encodes. Unlike many of our enzymes, it is composed mostly of RNA, not proteins. Its unusual composition and the fact that it lies at the heart of a process fundamental to life has made it a frequent subject of research.

Noller’s laboratory focuses on the structure and function of the ribosome. This is where the gallery of crystals comes in. Ribosomes, while relatively large cellular structures, are small enough that microscopy can’t provide the kind of detail necessary to understand the nuances of their structure. To get around this, scientists use a method called X-ray crystallography. In essence, Noller’s lab tries a variety of conditions to coax ribosomes into forming microscopic crystals, made up of repeating units, which forces the ribosomes to form symmetrical, 3D structures. At low power on the microscope, researchers can see angular crystals. However, when placed in the path of a X-ray, the crystal breaks up the X-ray beam into a complex scatter, which is caught and recorded. Using a mathematical operation called a Fourier transformation, the scatter of dots, each of which represents a single atom in the molecule, is resolved into a 3D model.

The problem with crystallography is that it only gives us a snapshot of its target. By forcing the ribosomes into crystals, they lose all ability to move. It’s well established that ribosomes, which must deal with growing proteins and move along the RNA, are dynamic molecules, moving and changing conformation as they work. Thus, still images don’t tell the whole story, a limitation Noller described with the parable of the cavemen and the Ferrari.

“The caveman and his cave-buddies are having beers and telling stories and they come out of the cave and see this.” Noller showed an image of a vintage Ferrari.

“They open the door and get in and start messing around. They figure out how to start the engine, then they start driving it around and they develop a model for the structure and function of the Ferrari. You step on the gas it goes, you step on the brakes and it slows down. And they’re all ready to submit their manuscript to Nature and somebody opens the hood and says, oh my god, what’s all this?” The next slide was a close up of an incomprehensible tangle of tubes and steel of the engine. “That’s where the ribosome field is right now. We’ve opened the hood.”

For now, Noller’s lab is attempting to understand the complex molecular movements of ribosomes. Like a child using his finger to read underneath the words of a sentence, the ribosome translates the RNA message one word at a time, processing it and using that information to add to the protein. Then, by a process called translocation, the ribosome moves from the completed ‘word’ to the next. Given the size and complexity of the ribosome and all the factors interacting with it, this is a huge change in conformation, and the molecular mechanisms governing the movement are still poorly understood.

To get a better idea of what this change looks like, Noller’s lab uses crystallography in combination with computational modeling. Using two different crystals, one formed before the ribosome has moved and one formed afterwards, researchers in Noller’s lab use computers to predict the steps in between.

“It is all moving, writhing, rotating, counter-rotating,” Noller said of the simulation. Every atom in the ribosome moves in their prediction, shifting organically from one state to the other. Noller’s simulations are informative due to their exquisite detail, which will aid researchers in understanding the three-dimensional movements that underlie the formation of all proteins and the basis of life.

“This is obviously a living thing,” Noller said, watching the ribosome morph from one state to the next. “It makes sense that it is responsible for life.”

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