When a protein is first produced in a cell, it consists of a long linear strand of amino acids. The vast majority of proteins do not gain a function until they fold into a particular shape. Learning how proteins fold is of major consequence for biophysics and medicine.
In a recent article from the Journal of Biological Chemistry, graduate student Nancy Burgess and biophysics professor Karen Fleming demonstrated new ways to understand how proteins fold in the cell membrane, the part of the cell that isolates and protects it from the outisde environment.
Since the early 1950s, when Christian Anfinsen of the Hopkins biology department showed that the 3D structure of proteins is determined by its amino acid code, researchers have been trying to figure out what rules proteins use to fold themselves into their complicated structures.
There are 20 different amino acids - the chemical groups that create a protein - that can be found in proteins. It is the assorted combinations of these groups that determine how a protein looks in 3D.
The easy part is figuring out what amino acids make up a protein, but the tough part that has stymied researchers is how the amino acid sequence determines the 3D structure.
Understanding how this process works will open up interesting avenues for medicine. If we can know how to create our own proteins, then we can design a protein to do any job in the human body that we want. We can also create drugs that stop a particular protein from working.
Burgess asked, "How do these [amino acid] sequences encode biological function?" She sought to determine this by looking at membrane proteins in the bacterium E. coli. Imagine that your room is like a cell found in your body.
Now take a wine-barrel, or an oil-barrel, and put it through a wall in your room. (Don't try this in your dorm!)
This is analogous to the proteins that Burgess studied. "How water-soluble proteins fold has been studied for over 50 years," Burgess said. However, there exists another class of proteins about which far less is known.
"About 25 percent of proteins reside in lipid membranes, where water is excluded," Burgess said. Interestingly, the folding patterns of these proteins have not been studied nearly as much.
Burgess looked at nine different membrane proteins, all with this barrel shape, and studied how they responded to different environmental factors such as the acidity of the water, the thickness of the cell wall and the curvature of the cell wall.
Using biophysical methods, the researchers could monitor how the proteins were folding into the cell wall.
A few initial trends were observed: These proteins fold more efficiently in a less acidic environment, a thinner cell wall and a more rounded cell wall. They also noticed that the proteins did not respond the same to changes in temperature.
Burgess next studied the efficiency of folding by actually looking at how the proteins unfold. This gives clues as to how stable the protein is in the folded state.
Their results indicate novel ways for proteins to fold that have never been studied before. "By observing the folding behavior of nine outer membrane proteins in identical environments, our study represents the largest set of E. coli outer membrane proteins whose folding behavior has been studied in tandem," Burgess said. "We have presented the strongest evidence of general folding principles to date."
To continue further investigation into membrane-protein folding, Burgess will next look more at the intrinsic properties - the specific amino acid sequence - of the proteins that help to determine how proteins fold.
In the future, understanding how proteins fold will aid in uncovering how certain diseases are caused and how we can treat them.
"Many diseases have been linked to protein misfolding, including Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, cystic fibrosis, night blindness and deafness," Burgess said.
