Good Luck Green

These glowing crystals generated by Tania Darnton, a Caltech graduate student in the lab of chemist Harry Gray, are composed of the tetraphenylphosphonium (Ph4P+) salt of the compound tetrakis(diphosphonato) diplatinate(II), commonly known as Pt(POP) due to its phosphorus-oxygenphosphorus bridges. This compound is a precursor to another molecule Darnton is studying for her thesis, which is a highly luminescent derivative of Pt(POP) with possible applications in oxygen sensing thin films and catalytic electron-transfer reactions. According to Darnton, the crystals were created via the slow evaporation of a methanol solution of the compound—quite by accident, in fact. She hadn’t synthesized the Ph4P+ salt before, and after several frustrating hours of trying unsuccessfully to isolate the compound she decided to just leave the solution out and try again in the morning. When she returned the following day, she was greeted with bright green crystals, which she called a “wonderful reward” after the disappointment of the night before. Such compounds could be used in building detectors for laboratories to ensure proper atmospheric conditions for sensitive chemical reactions.


Photo: Courtesy of Tania Darnton

Unlocking the Chemistry of Life

Scientists can easily sequence an entire genome in just a day or two, but sequencing a proteome—all of the proteins encoded by a genome—is a much greater challenge says Ray Deshaies, protein biologist and founder of the PEL.

“One challenge is the amount of protein. If you want to sequence a person’s DNA from a few of their cheek cells, you first amplify—or make copies of—the DNA so that you’ll have a lot of it to analyze. However, there is no such thing as protein amplification,” Deshaies says.

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Take it to the Crowd

When you have a question about your health or your finances, you go to a doctor or an accountant for advice; you figure they have the knowledge you need to get the answers you’re looking for. But what about when you’re wondering where to go for dinner in a new city? Rather than hiring an expert chef to individually rate each restaurant—a pricey and time-consuming endeavor—you’d probably find it far more practical and efficient to trust the recommendations of the thousands of local diners who’ve already voluntarily rated the restaurants online.

Today, crowdsourcing—in which many individuals work toward the collective goal of narrowing down a large amount of information—has indeed made it easier to choose a good restaurant or pick a movie you’ll likely enjoy. But the concept has also found an application in areas of research where numerous scientists have collected far more data than they could ever analyze on their own.

By taking this data to the crowd, researchers at Caltech have found a way to engage the public while also allowing so-called citizen scientists to investigate a variety of research topics—from very tiny cells on Earth to massive star clusters in our galaxy.

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Good Vibrations

For their 1966 song, “Good Vibrations,” the Beach Boys assembled an unusual mix of instruments—including a jaw harp, a cello, and an Electro-Theremin—to produce one of their biggest hits. By arranging sound waves in a unique and particular way, they were able to elicit a positive response.

Many doctors and researchers have the same goal. After all, the same “excitations” that helped the Beach Boys usher in an era of feel-good pop—the sound waves that propagate through air and water, bringing notes of music to our ears—are also noninvasively able to explore body tissues, helping to visualize babies in the womb, heal back pain, or even deliver chemotherapeutics to targeted tumors.

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The Quiet Man Who Helped Make the Noyes (+)

A painting and plaque honoring Arthur Amos Noyes hangs in the entrance of the building that bears his name.
A painting and plaque honoring Arthur Amos Noyes hang in the entrance of the building that bears his name.

 

Our Summer 2015 issue’s examination of all things noise omitted one homophonic subject also of interest to the Institute—the Arthur Amos Noyes Laboratory for Chemical Physics, built in honor of and named for the chair of the Division of Chemistry and Chemical Engineering from 1926 to 1936.

Although named for Noyes, the building was actually built with funds provided by Caltech alum Chester F. Carlson. Carlson graduated in 1930 with a degree in physics and went on to invent an electrophotographic process that came to be called “xerography”—Greek for “dry writing.” (Carlson described the xerographic process in a 1940 issue of E&S.)

The self-effacing inventor and philanthropist, who gave away more than $100 million to foundations and universities, requested that his contribution to the building remain anonymous until after his death.

Some 21 years after his 1968 death, Carlson was remembered by the U.S. Postal Service by a stamp issued in his honor to commemorate the 50th anniversary of his invention. (See third page of the linked PDF.)

The 92,000-square-foot Noyes Laboratory, opened in 1967, bears plaques honoring Carlson and Noyes.

Carlson2
The Noyes building honors Chester F. Carlson, who was instrumental in its creation, with this plaque bearing his likeness.

Caltech Biochemist Sheds Light on Structure of Key Cellular ‘Gatekeeper’ (+)

Credit: Lance Hayashida/Caltech Office of Strategic Communications and the Hoelz Laboratory/Caltech
Click image to enlarge
Credit: Lance Hayashida/Caltech Office of Strategic Communications and the Hoelz Laboratory/Caltech

Facing a challenge akin to solving a 1,000-piece jigsaw puzzle while blindfolded—and without touching the pieces—many structural biochemists thought it would be impossible to determine the atomic structure of a massive cellular machine called the nuclear pore complex (NPC), which is vital for cell survival.

But after 10 years of attacking the problem, a team led by André Hoelz, assistant professor of chemistry, recently solved almost a third of the puzzle. The approach his team developed to do so also promises to speed completion of the remainder.

In an article published online February 12 by Science Express, Hoelz and his colleagues describe the structure of a significant portion of the NPC, which is made up of many copies of about 34 different proteins, perhaps 1,000 proteins in all and a total of 10 million atoms. In eukaryotic cells (those with a membrane-bound nucleus), the NPC forms a transport channel in the nuclear membrane. The NPC serves as a gatekeeper, essentially deciding which proteins and other molecules are permitted to pass into and out of the nucleus. The survival of cells is dependent upon the accuracy of these decisions.

Understanding the structure of the NPC could lead to new classes of cancer drugs as well as antiviral medicines. “The NPC is a huge target of viruses,” Hoelz says. Indeed, pathogens such as HIV and Ebola subvert the NPC as a way to take control of cells, rendering them incapable of functioning normally. Figuring out just how the NPC works might enable the design of new drugs to block such intruders.

“This is an incredibly important structure to study,” he says, “but because it is so large and complex, people thought it was crazy to work on it. But 10 years ago, we hypothesized that we could solve the atomic structure with a divide-and-conquer approach—basically breaking the task into manageable parts—and we’ve shown that for a major section of the NPC, this actually worked.”

To map the structure of the NPC, Hoelz relied primarily on X-ray crystallography, which involves shining X-rays on a crystallized sample and using detectors to analyze the pattern of rays reflected off the atoms in the crystal.

It is particularly challenging to obtain X-ray diffraction images of the intact NPC for several reasons, including that the NPC is both enormous (about 30 times larger than the ribosome, a large cellular component whose structure wasn’t solved until the year 2000) and complex (with as many as 1,000 individual pieces, each composed of several smaller sections). In addition, the NPC is flexible, with many moving parts, making it difficult to capture in individual snapshots at the atomic level, as X-ray crystallography aims to do. Finally, despite being enormous compared to other cellular components, the NPC is still vanishingly small (only 120 nanometers wide, or about 1/900th the thickness of a dollar bill), and its highly flexible nature prohibits structure determination with current X-ray crystallography methods.

To overcome those obstacles, Hoelz and his team chose to determine the structure of the coat nucleoporin complex (CNC)—one of the two main complexes that make up the NPC—rather than tackling the whole structure at once (in total the NPC is composed of six subcomplexes, two major ones and four smaller ones, see illustration). He enlisted the support of study coauthor Anthony Kossiakoff of the University of Chicago, who helped to develop the engineered antibodies needed to essentially “superglue” the samples into place to form an ordered crystalline lattice so they could be properly imaged. The X-ray diffraction data used for structure determination was collected at the General Medical Sciences and National Cancer Institutes Structural Biology Beamline at the Argonne National Laboratory.

With the help of Caltech’s Molecular Observatory—a facility, developed with support from the Gordon and Betty Moore Foundation, that includes a completely automated X-ray beamline at the Stanford Synchrotron Radiation Laboratory that can be controlled remotely from Caltech—Hoelz’s team refined the antibody adhesives required to generate the best crystalline samples. This process alone took two years to get exactly right.

Hoelz and his team were able to determine the precise size, shape, and the position of all atoms of the CNC, and also its location within the entire NPC.

The CNC is not the first component of the NPC to be fully characterized, but it is by far the largest. Hoelz says that once the other major component—known as the adaptor–channel nucleoporin complex—and the four smaller subcomplexes are mapped, the NPC’s structure will be fully understood.

The CNC that Hoelz and his team evaluated comes from baker’s yeast—a commonly used research organism—but the CNC structure is the right size and shape to dock with the NPC of a human cell. “It fits inside like a hand in a glove,” Hoelz says. “That’s significant because it is a very strong indication that the architecture of the NPC in both are probably the same and that the machinery is so important that evolution has not changed it in a billion years.”

Being able to successfully determine the structure of the CNC makes mapping the remainder of the NPC an easier proposition. “It’s like climbing Mount Everest. Knowing you can do it lowers the bar, so you know you can now climb K2 and all these other mountains,” says Hoelz, who is convinced that the entire NPC will be characterized soon. “It will happen. I don’t know if it will be in five or 10 or 20 years, but I’m sure it will happen in my lifetime. We will have an atomic model of the entire nuclear pore.”

Still, he adds, “My dream actually goes much farther. I don’t really want to have a static image of the pore. What I really would like—and this is where people look at me with a bit of a smile on their face, like they’re laughing a little bit—is to get an image of how the pore is moving, how the machine actually works. The pore is not a static hole, it can open up like the iris of a camera to let something through that’s much bigger. How does it do it?”

To understand that machine in motion, he adds, “you don’t just need one snapshot, you need multiple snapshots. But once you have one, you can infer the other ones much quicker, so that’s the ultimate goal. That’s the dream.”

Along with Hoelz, additional Caltech authors on the paper, “Architecture of the Nuclear Pore Complex Coat,” include postdoctoral scholars Tobias Stuwe and Ana R. Correia, and graduate student Daniel H. Lin. Coauthors from the University of Chicago Department of Biochemistry and Molecular Biology include Anthony Kossiakoff, Marcin Paduch and Vincent Lu. The work was supported by Caltech startup funds, the Albert Wyrick V Scholar Award of the V Foundation for Cancer Research, the 54th Mallinckrodt Scholar Award of the Edward Mallinckrodt, Jr. Foundation, and a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research.

Written by Jon Nalick

Snake-Bite Science

Snake-Bite Science

Steven Sogo (MS ’89) and Samantha Piszkiewicz (BS ’14)

Steven Sogo, a science teacher at Laguna Beach High School, had become frustrated by his chemistry curriculum. On paper, his students performed well in science placement exams, but still, he was troubled. “The type of students who scored high knew how to memorize facts and take tests, but they weren’t necessarily good scientists,” Sogo says. “I wanted to teach a class that rewarded curiosity, experimentation, and the risk of failure.”

So in 2007, Sogo partnered with Ken Shea, a professor of chemistry at nearby UC Irvine. Shea had developed new processes for molecular imprinting—a technique used to create nanoparticles capable of latching onto organic molecules. “We call them ‘plastic antibodies,’” Shea explains. One of the first applications was a synthetic antidote to bee venom.

Sogo enlisted Shea’s help to establish a similar lab at Laguna High, but the high schoolers needed a target. One of Sogo’s students, Samantha Piszkiewicz, voiced her fascination with the Mozambique spitting cobra, which (as its name suggests) spits its venom, a noxious cocktail of protein toxins that break down the lining of cell walls. Starting in the fall of 2008, Sogo led Piszkiewicz and her fellow students in adapting and applying Shea’s techniques for molecular imprinting to the snake venom. The following spring, they had successfully synthesized an antibody. “The first test result we got was so beautiful and encouraging,” Piszkiewicz said. “We saw 85 to 95 percent inhibition of cell destruction.”

In 2009, the students presented their research at a science competition held at Caltech. “That felt like a home- coming of sorts,” Sogo says. “It was a chance to show off the research, and also to introduce my students to a place that made such an impression on me.”
It also made an impression on Piszkiewicz—who went on to enroll at Caltech, graduating this past spring with a bachelor’s degree in chemistry.

Sogo, meanwhile, continued to work on the snake venom project. New classes of Laguna students carefully refined and documented their procedures, and in 2013 their work was published in Chemical Communications, considered one of the field’s leading journals.
“They weren’t published just because they were high school students,” Shea says. “They made a valuable contribution and their work serves as a model for other high schools.”

“It’s hard to imagine that my first published project is for work I did when I was 16,” says Piszkiewicz, who was listed as lead author. Now pursuing her PhD in biophysics at the University of North Carolina, Chapel Hill, she dreams one day of leading her own research lab. “I wouldn’t be the researcher—or the person—that I am today without that class.” And perhaps that’s where Sogo’s real success lies. In addition to creating an antivenom, he is helping scientists like Piszkiewicz to discover themselves.

Alumni stories provided by the Caltech Alumni Association. For more about these stories and to read about other alumni in the news, visit alumni.caltech.edu.

Agents of Change

In the lab of chemist Jim Heath, Caltech’s Elizabeth W. Gilloon Professor and professor of chemistry, researchers are working to develop new capture agents for cancer—chemicals that could bind to a particular cancer biomarker, allowing the protein to be identified and studied more easily. The goal is to replace antibodies, the current gold standard for capture agents, with something cheaper and more stable.

The biomarkers that the researchers want to target are hundreds of amino acids long. Yet it is often the case that a single mutation within that sequence is enough to cause cancer. So graduate student Kaycie Butler Deyle (PhD ’14) and her colleagues have been trying to zoom in on just the chunk of protein where a mutation is known to occur. For example, Deyle focused on a point mutation on the protein AKT1, where the amino acid E at position 17 is known to change to amino acid K, allowing the protein to stay attached to a cell membrane four times longer than usual—a signal that tells the cell to continue to grow, triggering cancer. In the lab, she first synthesized the chunk of AKT1 that holds the mutation. Then she needed to come up with a chemical that could grab and hold onto that five-amino-acid-long chunk.

To figure out what that chemical might be, she used something called click chemistry, which relies on the ability of two types of molecules, or click handles, to click together when near one another. Typically this requires the incorporation of a copper catalyst, but the Heath lab came up with a new approach. Deyle first inserted one of the click handles two amino acids away from the mutation in her synthesized chunk of AKT1. Then she screened a million-member library to find a short sequence of amino acids with the other click handle attached that would bind to the AKT1 and click together with the first handle. That sequence of amino acids makes up a new capture agent for AKT1. “Essentially, we use the cancer protein to catalyze the formation of its own capture agent,” Deyle says.

Next, Deyle attached a cell- penetrating peptide to her capture agent, and she used a dye to spy on its progress, making sure that the agent was getting through. It was. “Even in cells, our capture agent is still really selective for the mutation,” Deyle notes. With that work in hand, the researchers began trying to block the action of the mutant protein completely. What they’ve found is that an expanded version of their capture agent can successfully stop the mutant protein from binding to the cell membrane. Thus far, the work has only been done on the benchtop. The next step will be to try it in cells. “We hope this is a route to a unique therapeutic for cancer,” Deyle says.

—Kimm Fesenmaier