I have a production problem to solve. Normally this surrounds “how can I scale up this reaction”? But this week it surrounds producing more protein. I finally hit a major milestone in my project last week of doing initial binding studies. Like most milestones in research you take a second to appreciate all the hard work it took to get there, you bask in the pride/joy of reaching that point, then you look to the next problem you have to solve and the next and the next. Pretty soon that accomplishment seems pretty darn small compared to where you are trying to go. And if you aren’t careful it will lead to you feeling like Linus:

impending doom

Credit: https://www.tumblr.com/search/linus%20shops

I had the reality check that if I wanted to screen my whole library the way I was currently doing screening I would need over 10 mg of protein. For those who can buy their protein this is only a matter of money. But for me it takes about 1-1.5 weeks to produce 100 ug pure protein with my current method. Yeah. I’d like to graduate at some point and producing protein isn’t what I want my PhD to be about. I have some many interesting questions to answer that span from basic immunological all the way to medical chemistry and new aspects to drug discovery. My project can at least highlight these questions and attempt to answer some of them…but I need enough protein to do that.

So, fortunately our lab, and my project in particular, has funding and we can purchase new equipment to address this issue. But, before doing that I have 3 or 4 crucial experiments to do in order to address a few inherent bottlenecks in the purification process. Remember that pesky polymer issue I had? Well, it hasn’t fully gone away and is probably limiting how much protein I can purify. After this week though I should have the figured out and be able to order what I need to scale up my production between 2-12 fold. Depending on which end of the spectrum I want to be on this could mean spending $1k or +$12k. I’m hoping it falls on the higher side so I can spend less time producing protein going forward. Besides this protein I have 2 others we will likely need to make using the same methods, so this is an investment.

Meanwhile, on the synthesis side of things, I have a new functional group to try to add to each of my library backbones. Why? Well, this functional group use to be hard to access and recently some new methods were developed. Even more important is that this functional group has many desirable med chem properties that are important for what I’m trying to accomplish. Sorry to be vague, but you know how it goes. Someday when this paper is published I will give a huge back story on all the components and the process that lead to them, plus the things you don’t see in the paper (like what failed miserably).

End log.


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