In this structural diagram of the protein ubiquitin, alpha helices are highlighted in red and beta sheets highlighted in blue. Image: Carlos Baiz
can take many different shapes, and those shapes help determine each protein’s
function. Analyzing those structures can tell scientists a great deal about how
a protein behaves, but many of the methods now used to study structure require
proteins to be crystallized or otherwise altered from their natural state.
Massachusetts Institute of Technology (MIT) researchers have developed a way to
analyze proteins that doesn’t require any pretreatment. The technique is also
extremely fast, allowing scientists to see, for the first time, how a protein
changes its shape over picoseconds.
researchers, led by chemistry professor Andrei Tokmakoff and postdoctoral
researcher Carlos Baiz, describe their new technique in the Analyst.
Their approach builds on a technology known as 2D infrared spectroscopy, which
works by shining pulses of infrared light on a molecule and measuring the
resulting molecular vibrations. In the new paper, the researchers came up with
a way to analyze that data and correlate it with common structural elements
found in proteins.
assembled, proteins tend to fold into one of two secondary structures, known as
alpha helices and beta pleated sheets. In this study, the researchers
distinguished between those two structures by examining how bonds between
carbon and oxygen—found in each of the amino acids that make up proteins—vibrate
when exposed to infrared light.
an alpha helix, the carbon-oxygen bonds run parallel to the protein’s backbone;
in a beta sheet, those bonds are perpendicular to the sheet. Because of that
difference, the bonds vibrate at different frequencies when struck with
infrared light. This allows the researchers to calculate the percentage of the
amino acids that belong to a helical structure and the percentage that form a
researchers confirmed the accuracy of their calculations by analyzing a set of
proteins whose structures are already known. Their method does not currently
reveal the exact structure of a protein, but the researchers are working on
ways to determine the arrangements of the sheets and helices from the spectroscopic
principle, the full structure of the protein is represented in the spectrum.
The trick is how to get out the information,” says Baiz, lead author of the
way to do that is to analyze data from a broader range of infrared wavelengths.
The researchers are also developing methods to get information about other
bonds within the amino acids.
the new method can be performed over millionths of a second, it can be used to
study how proteins fold and unfold when denatured by heat. After hitting a
protein with a laser blast to heat it up, the researchers can capture a series
of snapshots of how the protein unfolds over this very short time period.
is the first method that will allow us to take snapshots of the structure of
the protein as it’s denatured,” Baiz says. “Usually the way people look at
proteins is they start with the unfolded state and they end up with the folded
state, so you have two static structures. What we can do now is look at all the
structures along the pathway.”
Khalil, an assistant professor of chemistry at the University of Washington,
says the ability to track structural changes over time is the technique’s
biggest strength. “One big question is how do proteins fold—at what point does
it go from a completely disordered structure to an ordered structure?” says
Khalil, who was not involved in this research.
would be particularly useful for studying proteins that cause disease when
misfolded, such as the tau protein found in patients with Alzheimer’s disease
and the prion that causes Creutzfeldt-Jakob disease.
method can also measure the structural changes that occur as proteins bind to each
other. “If the protein is like a rock, and doesn’t change, then it’s never
really going to bind its target or do anything. Those are the types of
processes we can look at—the conformational changes that drive biological
function,” Baiz says.