An amino acid chain folding into a three-dimensional protein. Credit: Benjamin Schuler

An
international team of researchers has reported a new understanding of a
little-known process that happens in virtually every cell of our
bodies.

   

Protein
folding is the process by which not-yet folded chains of amino acids
assume their specific shapes, hence taking on their specific functions.
These functions vary widely: In the human body, proteins fold to become
muscles, hormones, enzymes, and various other components.

   

“This
protein folding process is still a big mystery,” said UC Santa Barbara
physicist Everett Lipman, one of several authors of a paper,
“Quantifying internal friction in unfolded and intrinsically disordered
proteins with single-molecule spectroscopy.” The paper was published in
the Proceedings of the National Academy of Sciences.

   

A
protein’s final shape, said Lipman, is primarily determined by the
sequence of amino acid components in the unfolded chain. In the process,
the components bump up against each other, and when the right
configuration is achieved, the chain passes through its “transition
state” and snaps into place.

“What
we would like to understand eventually is how the chemical sequence of a
protein determines what it is going to become and how fast it is going
to get there,” Lipman said.

   

Using
a microfluidic mixing technique pioneered in the UCSB physics
department by former graduate student Shawn Pfeil, the research team,
including collaborators from the University of Zurich and the University
of Texas, was able to monitor extremely rapid reconfiguration of
individual protein molecules as they folded.

The microfluidic mount devised to monitor a denatured protein as it folds. Credit: Shawn Pfeil

In
the microfluidic mixer, a “denaturant” chemical used to unravel the
proteins was quickly diluted, enabling observation of folding under
previously inaccessible natural conditions. The measurements
demonstrated that internal friction plays a more significant role in the
folding process than could be seen in prior experiments, especially
when the protein starts in the more compact unfolded configuration it
would have in a denaturant-free living cell.

   

“At
those size scales, everything is dominated by friction,” said Lipman,
comparing the environment of a protein molecule in water to a human body
in molasses. Friction between the molecule and its liquid environment
is an issue, as well as the “dry” friction that is independent of the
surrounding solvent.

   

Internal
friction slows down the folding process by reducing the rate at which
the amino acid chain explores different configurations that may lead to
the transition state. The longer it takes to find its native state—its
final form—the higher the likelihood it could get stuck in an unfolded
state.

   

“When
it is unfolded, it is more vulnerable to being trapped in a misfolded
state, or to aggregation with other unfolded protein molecules,” said
Lipman. Aggregation of misfolded proteins is thought to be a contributor
to many types of diseases, such as the amyloid plaques that are
associated with Alzheimer’s disease. Alternatively, the unfolded and not
usable protein could be broken back up into its component amino acids
by the cell.

   

While
there is no confirmed link between internal friction and aggregation,
or any pattern of friction for one protein that affects others in the
same way, Lipman and his colleagues are getting closer to understanding
the degree to which internal friction affects the protein folding
process.

   

“These
measurements show that under realistic conditions, internal friction
plays a significant role in the dynamics of the unfolded state. If a
model of the protein folding process doesn’t account for this, it will
need to be reconsidered,” he said.

Source: University of California, Santa Barbara