1986-1988 – A Visitor From a Strange Land
Professor of Biochemical & Biophysical Science
William A. Brookshire Department of Chemical and Biomolecular Engineering
University of Houston
Sometime in 1986 I was standing in line at the Blue Goose pizza truck (“Some of the world’s smartest people eat here…”) talking with my friend David Wu about a problem which had recently become of interest to engineers, the practical refolding of recombinant proteins, especially pharmaceuticals, expressed as inclusion bodies in bacteria. We happened to be next to Greg Petsko and asked him a few questions about this, and he said: “Oh, you should talk to Jonathan King. He’s the only person on the campus who’s thought seriously about this”.
David and I wound up sitting in on Jon’s class, I believe it was a freshman seminar, on protein folding. We found the class interesting, but the most valuable part was the fact that Jon would patiently sit and answer additional questions for the two of us for as much as 45 minutes after the class was nominally over. I’m not sure I’ve ever encountered an instructor who was so generous with his time, right after class, for students who didn’t even really belong.
My official advisers were Robert Reid in physical chemistry and thermodynamics, and Charlie Cooney in biochemical engineering, and the chair of my thesis committee was Danny Wang. We had a lot of fermentation capacity, and we thought that, or at least I thought that the contributions of biology to emerging engineering problems were both fascinating and likely to be very practically important. At some point I started using my control of these means of production to increase the King lab’s capacity to generate experimental reagents. I also was quite fascinated with the purification processes that followed the fermentation, including density centrifugation and especially chromatography, which was then done by putting the source vessel on a higher shelf for gravity-driven flow. I mainly interacted with Peter and Dennis, with additional input from Cammie, Anna, Bertrand, and others.
The entire group, and especially Jon, were very welcoming to me. I think Jon even felt a certain professional obligation to share his group’s wealth of knowledge with this strange new creature, probably the first engineer to join the hallowed MIT department of Biology.
My engineering advisers were very tolerant of my spending a lot of time on things not directly related to my Ph.D. research. This may have been simple collegiality or lack of detailed knowledge of what I was doing, but it occurred to me later that the NSF Engineering Research Center in Biochemical Engineering, a very successful enterprise led by Danny Wang which generated many of the leaders in the industrial production of biopharmaceuticals, probably was not fully living up to its billing as a genuine close interaction between the engineers and the biologists because the cultures were so different, and everyone had their own projects and their own reward systems. It probably was fairly useful in the annual grant reporting to describe an actual ongoing and increasingly deep physical transfer of personnel between the two communities. But this is just speculation with the benefit of hindsight, now that I know more about how these things work.
As I approached the completion of my Ph.D. work, I was looking for academic jobs and having pretty good success. I remember a very short and pivotal conversation with Jon which was probably the best few minutes of my professional career, although I’m not sure it was actually a great investment on Jon’s part. Jon: “So, are you going to go off to Houston soon, then?” Me: “I was hoping I might stay here a bit and work for you”. Jon: “OK”.
My assigned task was to test the hypothesis that a certain messenger RNA might fold to form an assembly jig for the P22 portal vertex, and also to look at the possibility of in vitro assembly of the portal. I primarily reported to Peter and Dennis, occasionally being accurately referred to by Peter as “The technician’s technician”. They ran a bit of a boot camp for me, but were helpful and friendly and generous, and tolerant of my misadventures.
They teased me about my engineer’s machinophilia. I was convinced we could get higher resolution in purifying my precious few milligrams of almost-pure portal protein by using higher-resolution chromatography, and somehow we established diplomatic relations with people in Alex Rich’s lab to use their shiny new Pharmacia FPLC machine. They had a very expensive high-resolution Mono Q column onto which I dutifully loaded my precious sample, and then watched in horror as the UV280 signal went to maximum and stayed there. While I had carefully washed the column in advance, it was almost certainly saturated with leftover nucleic acids which were hard to elute but which could be displaced by the addition of protein. I collected my gp1, now much less pure than before, and repurified it.
Not all was misadventures, however. I made lots of hot mRNA, and I still remember the day my in vitro assembly experiments began to work, with clear evidence of dimers on the path to assembly of the dodecamer. I was quite happy with this, and Jon shared my joy and said: “You got peaks! Getting that first signal It’s always a very good sign.”
There are other notable things I’ve taken away from my time in the King lab. One is the centrality of the out-loud formal statement of hypotheses and the design of experiments to test them. This isn’t really part of the engineering culture in most settings, and perhaps isn’t now quite as rigorously pursued by most biologists as it might be.
Another is a certain opening of my eyes to societal and political issues that I really hadn’t thought very much about, being mostly cloistered in the laboratory and with my own young family.
Something I admired but have not done well at replicating is the feeling of a small group community pursuing closely-aligned investigations, over a long period of time. Engineers tend to work on the problem du jour, though often with tools they develop and reuse. Jon got an NIH MERIT award for a magisterial proposal addressing both head assembly and tail spike, in a single effort and with a budget “now large for this area”, as I recall he said it.
Another is a great respect for the contributions of other disciplines and perspectives. My own presence in the lab was a great testament to Jon’s belief here, but it was reflected in many other ways and I could see the benefits as well as the sheer fun of working in an interdisciplinary and International environment.
My time in the King Lab was enormously valuable to me, in several ways. Jon’s personal prestige gave me credibility with biologists in many settings. I interacted for a long with Wah Chiu in Houston, and collaborated with the Goldberg lab at the Pasteur (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373722/). I became familiar enough with phage to introduce to engineers the now-common idea of phage libraries as sources of purification ligands (https://pubmed.ncbi.nlm.nih.gov/7764430/) and to use phage in diagnostic assays (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666763/). Finally, I was able to follow to at least some degree Jon’s injunction to consider structural changes in assembly processes (https://pubmed.ncbi.nlm.nih.gov/18383102/).