Study protein folds

Study of protein folds

2:20 AM, 30th December 2011
Study of protein folds
Feng Gai, Professor, Department of Chemistry, University of Pennsylvania.

 

PHILADELPHIA, US: A protein’s function depends on the chains of molecules it is made of and the way those chains are folded. While figuring out the former is relatively easy, the latter represents a huge challenge with serious implications because many diseases are the result of misfolded proteins. Now, a team of chemists at the University of Pennsylvania has devised a way to watch proteins fold in ‘real-time’, which could lead to a better understanding of protein folding and misfolding.

The research was conducted by Feng Gai, Professor, Department of Chemistry, University of Pennsylvania, along with Arnaldo Serrano, graduate student, Chemistry, Penn’s Perelman School of Medicine and Robert Culik, graduate student, Department of Biochemistry and Molecular Biophysics, Penn’s Perelman School of Medicine. They collaborated with Michelle R. Bunagan, Department of Chemistry, College of New Jersey. The research was published in the international edition of the journal Angewandte Chemie.

“One of the reasons that figures out when protein fold is difficult is that we don’t have the equivalent of a high-speed camera that can capture the process. If the process were slow, we could take multiple ‘pictures’ over time and see the mechanism at work. Unfortunately, no one has this capability; the folding occurs faster than the blink of an eye,” said Gai.   

Gai’s team used infrared spectroscopy; a technique that measures how much light different parts of a molecule absorbs, to analyze proteins’ structure and how this changes. In this case, the researchers looked at a model protein known as Trp-cage with an infrared laser setup. In this experiment, Gai’s team used two lasers to study structural changes as a function of time. The first laser acts as the starting gun; by heating the molecule, it causes its structure to change. The second laser acts as the camera, following the motions of the protein’s constituent amino acids.

“Protein is made of different groups of atoms, and the different groups can be thought of as springs. Each spring has a different frequency with which it moves back and forth, which is based on the mass of the atom on either end. If the mass is bigger, the spring oscillates slower. Our ‘camera’ can detect the speed of that motion and we can relate it to the atoms it is made of and how that segment of the protein chain moves,” Gai said. With a single carbon atom of the Trp-cage slightly heavier than the others, the research team can use its signature to infer the position of the other atoms as they fold. The researchers could then ‘tune’ the frequency of their laser to match different parts of the protein, allowing them to isolate in their analyses. 

“We use an amino acid with a carbon isotope marker. If it’s incorporated into the protein correctly, we’ll know where it is,” said Culik.  “This technique enhances our structural resolution. It allows us to see which part is moving. That would allow us to see exactly how a protein is misfolding in a disease, for example,” Gai said.  

© University of Pennsylvania News

 

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