But seeing single protein molecules go through the motions is well beyond the capability of standard optical tools. That led the researchers to employ a unique combination of technologies. Vasanthi Jayaraman, an associate professor in UTHealth's Department of Biochemistry and Molecular Biology who studies chemical signaling, started the process when she used the binding domain of the AMPA receptor and attached fluorescent dyes to the points of the cleft in a way that would not affect their natural function.
Single-molecule FRET allowed Landes and her team to detect the photons emitted by the dyes. "These experiments had to be done in a box inside a box inside a box in a dark room," she said. "In a short period of measurement, we might be counting 10 photons."
The trick, she said, was to excite only one dye, which would in turn activate the other. "The amount of light that comes out of the dyes has a direct relationship to the distance between the dyes," Landes said. "You excite one, you measure both, and the relative amount of light that comes out of the one you're not exciting depends on how close they are."
Detecting very small changes in the distance between the two points over a period of time required calculations involving wavelets, a tool Rice mathematicians helped develop in the '70s and '80s. (Another recent paper by Landes and Taylor on their wavelet optimization method appears here.)
Wavelets allowed the researchers to increase the resolution of FRET results by reducing shot noise -- distortion at a particular frequency -- from the data. It also allowed them to limit measurements to a distinct time span -- say, 100 milliseconds -- during which the AMPA receptor would explore a range of conforma
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