October 9, 2015

Analyzing protein structures in their native environment

Antiparallel beta-sheet structure of the enzyme catalase: The antiparallel hydrogen bonds
(dotted) are between peptide NH and CO groups on adjacent strands. Arrows indicate
the chain direction, and electron density contours outline the non-H atoms.
Image: Wikimedia Commons (edited by MIT News)

Enhanced-sensitivity NMR could reveal new clues to how proteins fold.

(October 9, 2015)  Proteins can fold in different ways depending on their environment. These different configurations change the function of the protein; misfolding is frequently associated with diseases such as Alzheimer’s and Parkinson’s.

Until now, it has been difficult to fully characterize the different structures that proteins can take on in their natural environments. However, using a new technique known as sensitivity-enhanced nuclear magnetic resonance (NMR), MIT researchers have shown that they can analyze the structure that a yeast protein forms as it interacts with other proteins in a cell.

Using this type of NMR, which is based on a technique known as dynamic nuclear polarization (DNP), scientists can gain much more insight into protein structure and function than is possible with current NMR technology, which requires large quantities of purified proteins, isolated from their usual environment.

“Dynamic nuclear polarization has a capacity to transform our understanding of biological structures in their native contexts,” says Susan Lindquist, a professor of biology at MIT, member of the Whitehead Institute, and one of the senior authors of the paper, which appears in the Oct. 8 issue of Cell.

MIT researchers used this gyrotron to generate the microwaves used to transfer polarization
from unpaired electrons to protons. This allowed them to increase the sensitivity
of nuclear magnetic resonance enough to study protein structures in their natural environment.
Photo: Ta-Chung Ong

Robert Griffin, an MIT professor of chemistry and director of the Francis Bitter Magnet Laboratory, is also a senior author of the paper. Kendra Frederick, a former Whitehead postdoc who is now an assistant professor at the University of Texas Southwestern, is the paper’s lead author.

DNP-enhanced sensitivity

Traditional NMR uses the magnetic properties of atomic nuclei to reveal the structures of the molecules containing those nuclei. By using a strong magnetic field that interacts with the nuclear spins of carbon atoms in the proteins, NMR measures a trait known as chemical shift for some of the individual atoms in the sample, which can reveal how those atoms are connected.

“You look at changes in chemical shift and that tells you, for example, if there is an alpha helix or a beta sheet, which are two different conformations that a protein backbone often takes,” Frederick says.

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