Dr. Ryohei Yasuda: A Run of “Fortunate Bad Luck” Led Him from Physics to Biophysics and Into Imaging Single Protein Molecules
2003 - A glowing dot spinning like a dervish features in the movie Ryohei Yasuda made as a graduate student. Though by no means a Hollywood production, Dr. Yasuda’s film is an elegant sight to biologists.
Dr. Riyohei YasudaThe reason for the movie’s allure is that it vividly portrays the rotation of a single protein enzyme, which Dr. Yasuda cleverly tagged with a much larger protein complex and imaged the resulting motion through a microscope. In so doing, he revealed the detailed spinning mechanism of one of only two rotary engines known in nature—the other being the molecular motor that powers the spinning, whiplike flagella of bacteria.
Dr. Yasuda’s achievement in imaging the enzyme, called F1-ATPase, while he was still working on his Ph.D. at Keio University in Japan, illustrates the creativity that the young biophysicist has brought to his research. Now a postdoctoral researcher at Cold Spring Harbor Laboratory, he is a 2003 recipient of a Burroughs Wellcome Fund Career Award at the Scientific Interface.
Working in the laboratory of Dr. Karel Svoboda, Dr. Yasuda uses sophisticated imaging techniques to actually see the interactions of single protein molecules. His quarry are the proteins that form the machinery in “dendritic spines,” the infinitesimal bristles that stud the surface of nerve cell structures called dendrites.
These spines are the critical receiving and amplifying stations for chemical signals from neighboring neurons and are responsible for triggering the impulses that drive all nervous system function. Once triggered, the protein machinery in these spines opens porelike channels in the neuron’s surface membrane that enable cations (mainly sodium) to flow into the cell to generate the electrical signal. Calcium influx into the spines triggers a number of cascades of biochemical reactions between proteins, leading the reorganized protein machinery to regulate the efficiency and strength of the electrical signal transmissions. These signalings underlie network plasticity —and ultimately, learning and memory.
“These dendritic spines are really small, and they often contain only a few copies of a given protein,” Dr. Yasuda says. “So, it requires a single-molecule-level imaging technique to really figure out what these molecules are doing.”
Dr. Yasuda has his work cut out for him, because these tiny compartments, called the “postsynaptic density,” consist of hundreds of proteins. It is the chemical reactions that occur when these proteins grab and release one another that constitute the biochemical signaling pathways in the dendritic spine. And it is these pathways that underlie learning, memory, and perhaps other brain functions in animals, including humans.
The problem with understanding these pathways, says Dr. Yasuda, is that no other analytical technique can reveal interactions between proteins. “Many molecular biologists are trying to understand signaling in the postsynaptic density by knocking out a particular protein or activating a particular protein,” he says. “While this helps understand which proteins are involved in a pathway, it can’t tell you about how the protein works and how the protein interacts with other proteins. Also, the commonly used biochemical techniques of measuring the reactions between these proteins won’t work, because these compartments are so small. So, I think imaging is really the optimal way to study the postsynaptic density. We really need to see the interactions between each molecule in response to calcium influx.”
Dr. Yasuda uses a physical phenomenon that occurs between two fluorophores, called “fluorescence resonance energy transfer,” or FRET, to see such molecule-level interactions. By attaching different fluorophores to each of two proteins and measuring FRET between the fluorophores, he can study interactions of these proteins. To make sure the proteins are behaving as they naturally would in real tissue, Dr. Yasuda performs his experiments on slices of rat brain. Using a microscope that shoots a laser beam of a specific wavelength into the brain slice, he can excite just one of the two fluorophores to produce light and then measure precisely how that “donor” fluorophore transfers its energy to the “acceptor” fluorophore on the other protein.
The efficiency of FRET depends on the distance between the two fluorophores, Dr. Yasuda says. FRET is efficient only when two fluorophores are within nanometers—about the size of proteins. Therefore, by monitoring FRET efficiency, he can study whether two labeled proteins bind to each other. Also, it is possible to calibrate distance between two fluorophores to determine how they interact.
The process is like studying how one runner in a relay race hands off the baton to another: the hand-off process can reveal important information about how the two runners are performing. Similarly, by studying the efficiency of the hand-off process between the paired proteins, Dr. Yasuda can glean critical information about how the two proteins are interacting. So exacting are Dr. Yasuda’s techniques that he can now measure quantitatively FRET in the two proteins—a technique he calls “two-photon fluorescence lifetime imaging microscopy.”
These techniques promise to yield a far more detailed understanding of the protein machinery within the dendritic spine. And although his work is basic, Dr. Yasuda says such improved understanding could lead to development of drugs for mental disorders or drugs that could enhance memory or other neurological functions.
Dr. Yasuda emphasizes that BWF’s award has proven crucial in helping him launch his career. “First of all, it has given me confidence that I am able to do work in the United States,” he says. “I’m now seeking a faculty position, and this also gives me a credential that will help me in that search, as well as initial funding to set up my own laboratory.”
Dr. Yasuda was not always interested in biophysics, but it was a remarkable run of what he calls “fortunate bad luck” that led him into the field. “I was a physics student as an undergraduate and didn’t even think about biophysics,” he recalls. “Then, in my fourth year, we had to get into a lab to do our thesis. I had chosen particle theory, but there were too many applicants for that lab, so they held a lottery, as was the tradition. I lost. My second choice was a semiconductor lab, but I also lost that lottery. The biophysics lab was my tenth choice, and since there were only ten labs, I did get that one.”
However, in that laboratory he saw a sight that fascinated him—a movie of the action of a tiny molecular “superhighway” in the cell called an actin filament. Such actin filaments are not only the molecular paths along which cargoes of molecules are transported within the cell. They also are one of the basic structures of the muscles that power movement.
“In the biophysics lab, the professor showed a beautiful movement of actin filaments across a surface, like a worm crawling on a plate,” recalls Dr. Yasuda. “I became fascinated by this movement, because even though you couldn’t say these proteins were really ‘living,’ they were intermediate between living and nonliving stuff. So, I became a biophysicist because I wanted to know how these proteins work, in contrast to a biologist, who wants to know what proteins do.”
When he is not pondering the elegance of protein interactions, Dr. Yasuda is making elegant music. An accomplished harpsichordist and pianist who began his training at age five, he prefers to play the early Baroque music of Bach, Mozart, and Beethoven. He met his wife, a classical violinist, in an ensemble class and they play duets regularly. They have three children, ranging from five months to six years old, and Dr. Yasuda reports that they have thoroughly adapted to American schools and culture.
He has recently had to restrict his playing to the piano, because “when I came to the United States three years ago, I had to sell my harpsichord,” he says. “But if I get a faculty position, one of the first things I want to do is buy a good harpsichord.”