Proteins Are Vastly More Complicated Than Previously Realized

This folding process is more complicated than previously realized, according to University of Washington researchers. Imagine trying to fold a delicate origami crane from silk paper — while you’re in a wind tunnel. In fact, imagine trying to fold the origami in a wind tunnel while countless other hands are also pulling at the paper. And yet, that’s comparable in complexity to what the hundreds of thousands of cells and proteins are doing in your body right now.

That’s because proteins and cells are locked together at numerous contact points. The movement of a cell stretches the proteins around it, and vice versa. A new UW study says scientists are going to have to study how protein structures change when stretched before they understand how the body functions.

"The function of a protein is tightly controlled by its structure, yet there is very little information about how mechanical forces may change the structure of proteins," says Dr. Viola Vogel, director of the University of Washington’s Center for Nanotechnology in the Department of Bioengineering. "Right now, it feels like we are only looking at part of the equation of how proteins work since we just know their equilibrium structures. If you do not know how mechanical forces change the function of cells and proteins, you will not understand different diseases that involve mechanical forces, such as hypertension."

Vogel is one of the authors of the first paper to show, at atomic resolution, how mechanical forces change the structure of a family of protein modules that fold into the same structures -- yet have less than 20 percent of their amino acids in common. "Comparison of the early stages of forced unfolding for fibronectin type III modules" appears in the May 1 Proceedings of the National Academy of Science, a journal of the National Academy of Sciences.

Fibronectin is a useful protein for studying the effects of mechanical force. Fibronectin is found in connective tissue, such as the skin. In the skin, cells are suspended in the extracellular matrix — consisting of thousands of protein fibers that attach to cells at numerous points. These proteins connect with other proteins and hold the mass together – a sort of super glue for cells. It is the movement of these fibers and the resulting pull and push on the cells attached to them, that transmits force to the cells.

Vogel and colleagues ask these questions: What does force do to the fiber? How is force transmitted from the fiber to the cell? And how is force used to determine how the cell regulates the expression of certain proteins? "We are very excited about this because we believe a new field is being born: non-equilibrium protein structure-function analysis. It’s very exciting to think about how nature regulates and controls function. We went from viewing the cell as a bag full of proteins a decade ago to a view of the cell as a dynamic place where proteins assemble and change under mechanical forces," Vogel says.

This new field became possible only in 1997, with the technology that allowed researchers to see what happens when you grab either end of a protein and stretch, using tools such as atomic-force microscopy. They found that proteins rupture as stretching forces overcome energy barriers that stabilize the protein structure.

"Computer simulations allow us to see what happens to the structure if the protein ruptures," Vogel says. The computer simulations were done in collaboration with Dr. Klaus Schulten at the Beckman Institute in Illinois and former UW graduate student Andre Krammer. "People tend to think of protein function as biochemical – chemicals binding to the protein, for example. Only recently have people realized that mechanical tension – cells pulling on the matrix – is important," says David Craig, a graduate bioengineering student and another of the paper’s authors.

Vogel’s lab is examining how mechanical force must be considered in the field of proteomics. "In proteomics, you go from the genome, then to the protein structure, and from that, make a prediction about the protein’s function. But is that enough? Is it sufficient to only know the function in the equilibrium state?," Vogel says. "We think there are a series of proteins that may have different structures, depending on how much force is applied and how it is applied. If that is so, then it adds additional dimension to the field of proteomics."