A
new method for looking at how proteins fold inside mammal cells could
one day lead to better flu vaccines, among other practical applications,
say Cornell researchers.

The
method, described online in the Proceedings of the National Academy of
Sciences July 16, allows researchers to take snapshots of the cell’s
protein-making machinery—called ribosomes—in various stages of protein
production. The scientists then pieced together the snapshots to
reconstruct how proteins fold during their synthesis.

Proteins
are made up of long chains of amino acids called polypeptides, and
folding gives each protein its characteristic structure, which
determines its function. Though researchers have used synthetic and
purified proteins to study protein folding, this study looks at proteins
from their inception, providing a truer picture for how partially
synthesized polypeptides can fold in cells.

Proteins
fold so quickly—in microseconds—that it has been a longtime mystery
just how polypeptide chains fold to create the protein’s structure.

“The
speed is very fast, so it’s very hard to capture certain steps, but our
approach can look at protein folding at the same time as it is being
synthesized by the ribosomes,” said Shu-Bing Qian, assistant professor
of nutritional sciences and the corresponding author on the paper. Yan
Han, a postdoctoral associate in Qian’s lab, is the paper’s first
author.

In
a nutshell, messenger RNA (mRNA) carries the coding information for
proteins from the DNA to ribosomes, which translate those codes into
chains of amino acids that make up proteins. Previously, other
researchers had developed a technique to localize the exact position of
the ribosomes on the mRNA. Qian and colleagues further advanced this
technique to selectively enrich only a certain portion of the
protein-making machinery, basically taking snapshots of different stages
of the protein synthesis process.

“Like
a magnifier, we enrich a small pool from the bigger ocean and then
paint a picture from early to late stages of the process,” Qian said.

In
the paper, the researchers also describe applying this technique to
better understanding a protein called hemagglutinin (HA), located on the
surface of the influenza A virus; HA’s structure (folding) allows it to
infect the cell.

Flu
vaccines are based on antibodies that recognize such proteins as HA.
But viruses have high mutation rates to escape antibody detection.
Often, flu vaccines lose their effectiveness because surface proteins on
the virus mutate. HA, for example, has the highest mutation rate of the
flu virus’ surface proteins.

The researchers proved that their technique can identify how the folding process changes when HA mutates.

“If people know the folding picture of how a mutation changes, it will be helpful for designing a better vaccine,” Qian said.

“Folding
is a very fundamental issue in biology,” Qian added. “It’s been a
long-term mystery how the cell achieves this folding successfully, with
such speed and with such a great success rate.”

Monitoring cotranslational protein folding in mammalian cells at codon resolution

Source: Cornell University