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Conditionally Essential and Promiscuous Functions
of De Novo Designed Proteins in Escherichia coli

Adviser: Michael H. Hecht

Kara L. McKinley

Molecular Biology

“The thesis you write barely resembles the thesis you set out to write, because if you know the outcome of an experiment before you do it, it is not worth doing.”

mckinley-kara-lavidge

What comes to mind when you imagine a Princeton student writing a thesis? Maybe a boy at his laptop in a carrel in Firestone Library; maybe a girl making notes in a book in one of the comfy chairs in East Pyne Hall. Probably not two students playing with crayons. But there I was, one summer night before my senior year, sitting opposite a lab mate, drawing with crayons. On the tablecloth. In a restaurant. 

Like many students in the experimental sciences, I was spending the summer doing research in my thesis lab. In these departments, “senior” thesis work formally begins in the spring of junior year and continues over the summer and through senior year. This extra time is designed to accommodate the fact that the amount of time spent in lab very rarely correlates with the amount of data generated that is worth putting on fancy archival paper. Some experiments do not work and need to be altered and repeated, others simply generate data that are uninteresting. Perhaps most often, a question needs to be approached from an entirely new direction. I had come across such a question. So I was drawing on the table. 

On the most basic level, that moment was emblematic of my thesis experience as a whole because I spent most of my senior year finding new ways to approach that same question. Professor Michael Hecht, my thesis adviser, had long worked on designing large libraries of artificial proteins that had never been observed in nature but “look” like natural proteins. Some of these artificial proteins also do things that natural proteins do in a test tube, like facilitate chemical reactions. I joined a project that looked at whether some of these proteins might do things that natural proteins do in living bacterial cells. Amazingly, we found that several of these designed, entirely novel proteins in fact were sufficient to replace natural proteins and so keep alive a cell that would otherwise die. The question was how they were keeping the cell alive. 

Questions like that were, for me, one of the greatest aspects of working in a lab for my thesis, because they meant that I was venturing into new territory. The nature of the lab thesis is such that you are constantly finding out new things, and not just things that are new to you—things that are new to the field as a whole. The thesis you write barely resembles the thesis you set out to write, because if you know the outcome of an experiment before you do it, it is not worth doing. Even an experiment that does not give the result you were looking for may lead you in a new and interesting direction. In conducting an experiment that I expected to give very predictable (read: boring) results, I found that some of “my” proteins could actually do more than one thing, a discovery that added an entire chapter to my thesis (and led to the inclusion of the word “promiscuous” in my title). 

The dynamic nature of the lab thesis leads me to my first piece of advice: Choose your adviser very carefully. You are likely to meet with your adviser frequently, much more so than your library-thesis friends. This is in part because you will be spending most of your time next door to his or her office, as opposed to holed up in Firestone. In addition, coming across these new problems, questions, and directions will be the rule rather than the exception, and it is a huge help to have someone much more experienced to guide your inquiry (crayons can only get you so far). It is therefore important that you not only like the work done in a lab, but also that you get along well with your adviser, and that you like the way that he or she thinks. As important as it is to be excited about the project they originally propose, it is equally—if not more—important to have an adviser who will guide you in a direction that continues to excite you when ultimately the project veers away from the proposal. 

Your adviser will not be the only important person in your thesis life. In a lab, you add in all the other members, with whom you will share space, lab meetings, ideas, and occasionally fresh baked goods. So in spite of the often-discussed independence of the thesis, in the experimental sciences, the thesis is most certainly a team sport. The independence allowed me to ask questions that interested me, to look for the answer in my own way, and to decide how my results would affect the direction of my project. But in order to actually do anything, I needed people to show me the techniques, share materials, and talk through my ideas for asking, looking, and deciding. Case in point: I wasn’t the only one drawing on that table; another senior, working on a completely different project, was drawing with me, bringing an outside perspective to my question. 

My crayon friend was one of several new and close friends I made entirely as a result of my thesis. Some were members of the lab; others were fellow seniors I had known through classes but with whom I grew close because we were both in lab late at night. I have many great memories during thesis period when I was working at night, and a lab mate or friend would come to work or visit, and we would crank up the volume on a playlist more appropriate for an eating club tap room, and dance around the lab between experiments.

Which leads me to my final piece of advice: Make it fun. The thesis period is long and difficult at times, especially when experiments are not working. Find a project and an adviser that you think will continue to motivate you in those challenging times, and maybe a few friends who will dance around the lab with you. This summer, I had the great pleasure of going to a scientific conference (another reason it is great to have a supportive adviser!). One of the speakers was Oliver Smithies, who won the Nobel Prize in Medicine for work completed in his 60s and who still, at 85 years old, was in lab on a Saturday two days before the conference. Someone asked him how he found balance between work and play. He answered that students should not work hard; we should play hard. He meant that if we could find something about which we were truly passionate and excited, it would mean we would never have to work, only play. So try to find a project where you can play hard. Try to find something that makes you want to draw on the table at dinner.

Conditionally Essential and Promiscuous Functions
of De Novo Designed Proteins in Escherichia coli

Kara L. McKinley

Michael H. Hecht

Professor of Chemistry

“... the novel genes and proteins that Kara studied did not exist until she discovered them in the lab.”

Shortly after I applied for a job at Princeton, I visited campus for an interview. My application was for a position as an assistant professor, and the interview process involved a day of one-on-one meetings with faculty. I asked each professor two questions: What is the best thing about your job at Princeton? And what is the worst? I don’t remember how they answered the second question (since they were recruiting, they didn’t say anything memorable). However, I vividly remember how several of them described the best part of their job at Princeton. One professor after another said the part he or she most enjoyed was working with Princeton undergraduates and guiding these students through their first experiences with research. In the years since those interviews, I have discovered time and again how much I agree with those initial statements: Mentoring undergraduate researchers like Kara McKinley is indeed one of the best parts of being a professor at Princeton.

Undergraduate students at other colleges and universities occasionally do research. At Princeton it is not an “occasional” thing. Everybody does research. Although the focus on undergraduate research may cause some applicants to shy away from Princeton, it also is one of the main reasons that some of the most talented college students in the world decline their other options and choose Princeton. 

Princeton endeavors to be two very different kinds of institutions: On one hand, Princeton tries (and succeeds) to be among the top research universities in the world. On the other hand, Princeton tries (and succeeds) to be a small and intimate undergraduate college where students can get to know their professors in a supportive and interactive environment. What makes Princeton unusual is that these two goals are not pursued separately; they are combined into one. This is accomplished by including undergraduate students into the research goals of the University.

Why is this important? Why is research so different from taking classes? A major difference between research and classes is that in research the professor doesn’t already know the answer before he or she asks the question. When students and faculty work together on a research problem, they can discover something novel that neither of them knew beforehand. 

Courses are where students absorb pre-existing knowledge; research is the opportunity to create new knowledge. At most universities, undergraduates study pre-existing knowledge, while the excitement of creating new knowledge is reserved for graduate students, postdoctoral researchers, and faculty. At Princeton, undergraduate students—through their senior thesis research—participate in this creative process.

Pursuing research in the experimental sciences can be particularly exciting. Not only does one have an opportunity to extend our understanding of the universe around us, but the daily activity of research is a collaborative and socially interactive process. This may be surprising to nonscientists, whose stereotypical image of a scientist is a solitary individual in a white lab coat working long hours in an obscure laboratory far from other people. Nothing could be further from the truth. Modern scientific research is rarely done by individuals working alone. Open any scientific journal and you will find that almost all articles have multiple authors. In my 20 years at Princeton, every one of my research projects was a collaborative undertaking with contributions from scientists with a range of experience and expertise. It is not unusual in our research for professors, graduate students, senior thesis students, and precocious sophomores and juniors to come together from the departments of chemistry, chemical and biological engineering, and molecular biology to bring a project to fruition. We design the experiments together; we discuss their progress at weekly (sometimes daily) meetings, and when the experiments are done, we write and publish the papers as coauthors. As a chemist I am intrigued by how molecules interact; as a teacher and mentor I am fascinated by the ways in which scientists of all ages and disciplines collaborate and interact.

Guiding Kara though her thesis research exemplified many of the themes I described above. Her project was multidisciplinary and involved scientists with various levels of experience. When Kara joined my lab in the middle of her junior year, she learned about the project from a graduate student in molecular biology. By the time she graduated a year and a half later, Kara was the lead person on the project, and she helped train a postdoctoral chemist to continue the work. 

In her research, Kara created new knowledge. But more than that, she also created new molecular parts that enable the growth of living cells. Just as the knowledge and understanding in Kara’s thesis did not exist until she wrote it, similarly the novel genes and proteins that Kara studied did not exist until she discovered them in the lab.

I was (and remain) fascinated by Kara’s results. Kara and her coworkers showed that it is possible to sustain the growth of a living organism using molecular parts that were designed “from scratch” in the laboratory. The experiments drew on chemistry and biology. However, the results have implications spanning from the molecular to the philosophical and even theological. Because we shared enormous enthusiasm for this project, Kara and I discussed it frequently, often daily. It became a true collaboration with student and teacher occasionally trading roles. 

Kara was the 49th undergraduate student to do senior thesis research in my lab. Along with her 48 predecessors, Kara reaffirmed what I heard when I first interviewed at Princeton: Guiding Princeton undergraduate students through their initial experiences with research is indeed one of the best parts of being a professor at Princeton.