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Tuesday, May 20, 2014

The Giant De Novo Peptide Review: An Interview with Fangting Yu

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For researchers breaking into the field of protein design, life just got a whole lot easier.

In late March, a massive review of rational protein design ($) entitled "Protein Design: Towards Functional Metalloenzymes" hit the web. Scientists of all levels and disciplines use reviews to figure out where to start on new research projects or to gain a wider perspective of their field, so writing good review articles is an essential part of scientific research. The review was published in Chemical Reviews (ACS) as part of a specially-themed issue on enzymology and authored by Dr. Vince Pecoraro's group at the University of Michigan, along with collaborator Dr. Matteo Tegoni.

Enzymology, or the study of how enzymes do their jobs, is a diverse field of science that intersects chemistry, biochemistry, and biology (for example). Some enzymologists are interested in cataloguing existing functional proteins. Some take those proteins and, by changing their structure or the chemicals available for them to react with, learn the intimate mechanism of their function. Still others apply what is known about how the enzymes work in an attempt to create new enzymes or enzyme-like molecules that function even more efficiently than the natural structure.

The latter group of enzymologists most often utilize the two methods covered by the review: protein redesign/engineering, in which an existing protein is modified to enhance its function; and de novo protein synthesis, in which a functional protein that does not exist in nature is dreamt up and created in the lab.

Dr. Pecoraro's "Protein Design" review was a massive undertaking involving ten authors and over 1,000 cited papers. I sat down with Fangting Yu, the article's lead author and a 5th-year graduate student in Dr. Pecoraro's lab, to learn more about the process of putting the review together.

Fangting Yu, explaining how she uses a device in the lab to synthesize new proteins.
Image credit: Sung-Hei Yau; used with permission.
Getting into the Research
Fangting originally joined the Pecoraro group to work on making inorganic manganese complexes to model the reactivity of the oxygen-evolving complex in photosystem II (PSII). The calcium-manganese cluster in PSII is essential for the final step of photosynthesis in which water is oxidized to the oxygen that we breathe. The mechanism of its action has been debated since the structure of PSI and PSII began to become more clear in the late 1980's (see links).

Fangting got a publication ($) out of the project. However, the manganese project would soon run out of funding. Because of a broad interest in the reactivity of transition metal small molecule centers in proteins, she decided to take up a new project dealing with a more biologically relevant system. At the time, Dr. Matteo Tegoni, an Italian researcher currently at the University of Parma, Italy, and also an author on the review, was a visiting scholar in Dr. Pecoraro's lab. He made progress on a new aspect of de novo protein design involving copper reaction centers. Fangting took over the project as he left and devoted her interests to de novo protein synthesis, resulting in two papers thus far (1 and 2, $).

The All-Important First Draft
Writing a good review can be a huge undertaking, and most graduate students do not have the time to pursue it with hectic schedules and workloads. Fangting was no exception. "We got to write this because of [Dr. Pecoraro]," she said. In addition to de novo design, Dr. Pecoraro has worked on understanding the role of manganese and vanadium in biological systems for the bulk of his 30-year career at the University of Michigan. As one of the leading experts in the field, he was invited by Chemical Reviews to write the article.

Dr. Pecoraro left the first author position open to the student who made the best case for authorship. "I was debating whether or not to take it because that was my fourth year of grad school, and in that summer you can generate a lot of data," said Fangting. However, an instrument critical to moving her research forward broke down near the start of the summer, and she decided to make a bid for authorship.

The writing process began in earnest in May 2013. It took 3 months to put the first draft together for submission, which means it spent about 7 months in review before its publication online.

Collaboration, Here and Abroad
Reviewing a topic as deep and well-studied as protein design requires a ton of reading, and for one person to do it all would be an astronomical task. As such, the paper ended up with ten authors, nine of which are currently in the Pecoraro lab. However, Dr. Tegoni's appointment in Italy put the Atlantic Ocean between him and the rest of the authors.

When I asked if the international collaboration was difficult, Fangting waved the question off. "[Dr. Tegoni] is the person who started my thesis project. We're pretty close - we're both friends and collaborators." Electronic communication made the collaboration easy.

Fangting went on to say that managing multiple authors was not the hardest part of the process. Collaboration is essential for putting together a project of this scale. "One thing that I would advise on multi-author papers is, when you are the point person, you want to be as specific as possible when you give people assignments, and be firm about deadlines."

The Review Experience, In Review
The toughest part of the review for Fangting was deciding what to include. "There's so much out there," she said. "For example, say this protein design paper cites a few other papers that are kind of protein design, kind of engineering, kind of a directed evolution approach." The line of what is in the scope of a review and what is not is never black and white, and those papers fall into the grey area. "It takes time and energy to make a decision on what kind of material you want to include and how you want to connect them together."

Writing the review certainly brought benefits with it. First, in assembling all of the material, Fangting learned a great deal and feels more on top of her field than she did before.

Perhaps more tangibly, though, she feels like she has gotten a head start on her thesis. "Any Ph. D. student is going to have to go through writing a review chapter," she said, referring to the introduction of the final Ph. D. thesis. "It's just a matter of when. I personally think that the intro chapter is the most difficult to write. Deciding what context you want to put your thesis in is the most difficult."

Lessons Learned
Writing the review has certainly given Fangting a head start on her thesis, but has also taught her some valuable skills for tackling large writing projects in general. When I asked her what advice she would pass along to other students engaging their theses or similar publications, she paused and her face became much more serious. "Outline," she said.

"You need to think more than you need to write," she added. "At least for me. I would spend time just shutting down everything and thinking." She paused again. "And outline it."

To learn more about the other authors of the review, and for more specifics on what a rational protein design research project actually looks like, check out the Pecoraro group web page.

ACS - American Chemical Society
PSI/II - photosystem I/II


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