Research offers magic carpet ride to the atomic level
Imagine you’re a scientist transported to an alien planet. Here exists a tiny device miraculously able to organize and command the cells in any animal. Scrape your hand and the device rushes new skin cells to cover the wound. Conceive a child and it establishes construction sites for embryonic development. Suffer a tumor and it tells new blood vessels to stay away so the cancer can’t grow. Wouldn’t you want to know how the device is built and how it works? Wouldn’t you want to be able to make one yourself?
Welcome to the laboratory of UM structural biologist Klára Briknarová.
No, Briknarová, though born abroad in the Czech Republic, is not a space traveler. But she does study an alien environment replete with mysterious, miraculous machines: the human body. Inside the nucleus of every cell of a human being are the 23 pairs of chromosomes that make up our DNA, itself divisible into some 20,000 to 35,000 genes. Genetic information is copied into RNA, which then serves as a template to make proteins, Briknarová’s research subject, biological molecules not to be confused with their collective products – steak, say – in our diet.
This model depicts negatively and positively charged areas on the protein’s surface.
“There are lots of types of proteins in any living creature, be it a virus, bacteria, plant or animal,” Briknarová says. “They make up and maintain much of the body and tell all our cells what they’re supposed to do.”
An example of a specific protein with a specialized function is hemoglobin, which carries oxygen from head to toe. Less well-known but no less important is our imagined “alien” device, the protein fibronectin, which forms a kind of “carpet” outside cells where they may gather and organize into tissues or blood vessels.
“Functional fibronectin sends signals inside cells that may indicate to them that they should stay put, move, divide or evolve into a different type,” Briknarová says. Without it, then, wounds may heal slower and less completely, if at all; embryos die in the womb; and experimental anti-cancer therapies are less effective.
So important is fibronectin, in fact, that last year the National Science Foundation awarded Briknarová a $788,000 Early Career Development Program grant for her study of the protein. The question they and she want answered: What is in this carpet?
For starters, like all proteins, fibronectin is made of a combination of the 20 kinds of simple organic compounds called amino acids. “Imagine a 20-letter alphabet with very long words,” Briknarová says. “In this alphabet, fibronectin is 2,400 letters long.”
Her lab studies only a tiny fragment – about 100 linked amino acids, a couple thousand atoms in space – of the larger tongue twister.
“Separate parts of proteins adopt unique three-dimensional structures,” Briknarová says. “We try to figure out how this piece of the protein looks at the atomic level. How are its atoms arranged? How do those atoms interact with other atoms when two different proteins encounter each other? How do the proteins rearrange upon such encounters?”
The lab answers these questions using a technique called nuclear magnetic resonance spectroscopy, which can identify distinct chemical entities in a molecule by their respective magnetic properties. Because such entities are literally atomic in size – 100 billion billion of them still weigh less than a gram – seeing and separating signals requires a magnetic field as much as 500,000 times that of Earth.
UM chemistry graduate student Jessica Glicken analyzes data from UM’s 600 MHz spectrometer. Each dot in the data spectrum on the right computer screen represents a different amino acid in the protein. This information is used to generate 3-D computer models of the fibronectin protein, such as the one on the left computer monitor.
Enter UM’s 600 MHz spectrometer, one of two purchased five years ago at a cost of $1.4 million. By appearance, it’s a large metal vat, roughly 9 feet tall, about the size and shape of a small water tower or stainless steel tank of a microbrewery.
“That’s the magnet,” Briknarová says, explaining the vat contains a coil through which current passes without resistance. Called superconductivity, this effect necessitates regular additions of liquid nitrogen and liquid helium around the coil to maintain a temperature lower than 5 degrees Kelvin (negative 451 degrees Fahrenheit).
Briknarová and her students lower ultra-thin glass tubes, each holding 0.6 milliliters of the protein sample, into the middle of the machine, where the magnetic field is strongest. Then a wide cabinet of accompanying electronics – picture an advanced phone-switching station – allows Briknarová and her team to send electromagnetic impulses through the entire setup and measure the samples’ telltale magnetic oscillations.
“Protein fragments contain many different atoms, and each atom will give a distinct signal,” Briknarová says. “We look at signals and gather information from every separate atom in our fragment. From these results, we can determine the protein’s structure and dynamics.”
Call it a full-body scanner for molecules. “The technology is quite similar to an MRI,” Briknarová says. “We’re trying to generate three-dimensional models.”
The hope is to move from knowing the carpet’s constituent elements to how it’s arranged – and rearranged – inside us. “Most molecules aren’t rigid,” Briknarová says. “They can do all sorts of gymnastics. Very often those motions” – for example, opening a lid – “are important for their function.”
The fragment of fibronectin the lab works with is called anastellin. It’s important because fibronectin actually takes two forms: soluble and insoluble. The former travels fluidly – it’s present in our blood – rather than staying put and taking charge. “To make ‘real’ insoluble fibronectin – our carpet – you need cells, and what they do is complex and unclear,” Briknarová says. “But when you add this fragment of fibronectin – anastellin – to soluble fibronectin molecules, it can produce insoluble fibrils. Using anastellin, we can make a similar reaction without cells in a test tube.”
As anastellin is considered for use in clinical trials, the UM lab’s work will help scientists better understand how it and fibronectin operate at the atomic level. Regardless of other research, Briknarová’s experiments should illuminate proteins’ hidden inner workings.
“In biochemistry textbooks, proteins are depicted as one structure,” Briknarová says. “But the structures move, breathe and partially open. Our work should provide some insight into how these molecules move – and how that affects their lives.”
Lives? Briknarová backtracks. “I don’t think of them as living creatures, but there are lots of dynamics,” she says. “They can have complicated and intriguing structures. They move and interact, stick to each other and change how they look. They’re made and they’re eliminated, so you could say they die.”
Philosophies of existence aside, Briknarová most enjoys the puzzle-solving aspect of her work, common to a field combining math, physics, biology, chemistry, computer science and engineering.
“The techniques we use are themselves very physical, and you also need quite a bit of analytical thinking,” she says. “Think of my data as a jigsaw puzzle. From which atom is each signal?”
To illustrate the point, Briknarová points to the gray and black tile-patterned carpeting covering her office floor.
“I’m studying little fuzz balls,” she laughs. “Some pieces may look exactly the same, some pieces are missing and you’re trying to put it all together so that it fits and you have a picture of a small piece of the fibronectin carpet.”
— By Jeremy Smith
|(Above) UM chemistry Assistant Professor Klára Briknarová works with a 600 MHz spectrometer, which helps her laboratory visualize the structure of the fibronectin protein. Ropes secure the device in the unlikely event of an earthquake.