Week 1 HW: Final Project Ideas

Idea 1 — Glumen: a de novo gluten-binding protein

Framing questions

1. What do you want to make? →
2. What living system could make it? →
3. How could automation help you make it? →
4. What would it take to make it at a meaningful scale?

(1) What you would like to biomanufacture and why?

Describe the target product or output you would like to make. Why are you interested in making it? Your motivation might be utilitarian—for example, addressing a problem in health, sustainability, food, energy, or manufacturing—but it does not need to be. Your project might instead have a social, cultural, artistic, or personal motivation. Clearly articulate what you want to make, who or what it is for, and why you think it is interesting or important.

I’m interested in producing a gluten binding protein to be a key component in a gluten detector - Glumen.

The goal is to make a very reliable gluten detector for individuals with Celiac Disease - something that can be used remotely at resturants, that is compact, fast, and highly reliable for a broad range of foods.

My wife and 2 daughters have celiac disease and eating out is quite challenging. Even food that is nominally gluten free - free of wheat or obvious gluten containing ingredients is not always safe. Hidden ingredient in sauces, cross contamination, lack of knowledge within the kitchen, all contribute to such challenging circumstances.

The human digestive/immune system obviously reacts to even these small amounts of gluten - and we’d like to detect small amount of gluten directly in a non-lab/compact consumer device.

I think the total system for gluten detection will be complicated including some method (e.g. ethanol, heat, and mechnical agitation) to release the gluten from food and to detect and calibrate thea mount of gluten present. But the key piece would be this de novo protein binder that can be used to bind to gluten and provide opportunity for identification. Existing gluten detection systems have limitations across food types particularly for fermenetd and hydrolyzed foods (e.g soy sauce, fried rice, pho, etc).

(2) What living system would you use?

Propose at least one living-system manufacturing chassis that could produce your target—for example, a microbial, mammalian, or cell-free system. At a high level, describe how the system would make your target product. What goes into the system? What biological process or processes occur? What comes out? You do not need to design the complete biological system yet. Make reasonable assumptions where necessary and identify them.

The living system I unerstand could be an E. coli expression system.

We would introduce the DNA that encodes our protein binder into the E. coli cells. Grow those cells and then extract and purify out our protein.

(3) How would you use automation?

Identify at least one automation technology that you would combine with your living system. This could include a large-scale Cloud Lab, a desktop liquid-handling robot such as an Opentrons, a programmable microfluidics platform such as Nuclera’s, or another automation technology. Describe what part of the biomanufacturing workflow you would automate and why. For example, you might automate liquid handling, culturing, assembly, screening, sampling, measurement, optimization, or another step.

While we can design the protein in-silico - using RF Diffusion, Protein MPNN, and predict the structure with Boltz/Protenix or AlphaFold3 - we will not actually know if the protein folds properly, if it will bind to the gluten fragment as expected, and if it has the selectivity needed to not identify other confoudners. I believe an automated wet lab can help experimentally determine effectiveness.

I had been looking at Adaptyv as a potential vendor/CRO lab that could both express the protein and then test the protein folding, binding strength, binding time, selectivity, etc.

(4) How much would you need to make, and how long would it take?

Perform a back-of-the-envelope calculation estimating what it would take to manufacture your target at a meaningful scale.

(a) How much?

Define a scale relevant to your project and calculate approximately how much of your target product you would need to manufacture. For example, if you are producing a medicine, you might estimate the amount required to treat 1,000 people, everyone in Massachusetts, or everyone in the world. If you are producing a building material, you might calculate the amount required for one structure or an entire neighborhood. If you are producing an art or design artifact, define an appropriate scale yourself. Clearly show your calculation, including units, assumptions, and sources for important numbers.

While we dont know the exact amount of binder we’d need, for planning we can estiamte 250ug of binder per test. Lets say we are looking to equip a device with 20 tests to begin with.

And we want to get 500 trial devices x 20 ==> 10000 test x 250 ug = 2.5 g of binder

Lets assume some loss (20%) - round up to 3.0g.

This is for production.

For the automation run - I think we need small amount of samples to test binding affinity, binding time etc.

Assay volumes

Gluten Concentration

(b) How long?

Using your proposed living system and automation technology, estimate how long it would take to manufacture that amount. Consider quantities such as production rate, yield, volume, number of parallel experiments or reactors, automation throughput, or whatever parameters are most appropriate for your system. You may discover that the automation technology you would use to prototype your system is very different from what you would use to manufacture at scale. If so, describe both. Again, we are looking for a reasonable engineering estimate. Show your assumptions and calculations.

According to Adaptyv Bio - they can express the protein in about a week, run the measurements by week 2, and have the full data by week 3. 16-21 days in total.

https://www.adaptyvbio.com/services/binding

I believe the in-silico design can be done in a few days. So maybe the full loop is 3-4 weeks in total - from start of a design to getting results from wet-lab.

(5) What don’t you know yet?

After completing your analysis, identify the 2–3 biggest technical unknowns, bottlenecks, or assumptions in your proposed biomanufacturing system. What would you need to learn, measure, or experimentally determine to know whether your idea could actually work?

LOTS. There are a few classes of problem in general with this device.

1. can we separate enough signal of the gluten from the food - this is pure extraction or “gluten release”
2. can we get a binder that can bind to enough of the types of gluten but be selective enough to not bind to the other type of confounders (e.g. maize etc)
3. will the binder survive the diltuion liquid (e.g ethanol)
4. Will the binder provide enough signal - can we attaach a flouresence or something else - so that we can detect the amount of gluten that binds.

I think for this project - we should focus on step 2 - as that is the biomanufacturing part of making a de novo protein

The first test would be to see if we can make a binder that binds strong enough to these small fragments. And test folding, binding affinity etc.

I think the concern will then be is the binder will survive the gluten release step (ethanol, heat, etc.) and if its selective enough amongst the confoudners like maize and those that have similar amino acid seqeunces.

AI use

I’ve been using AI substantially over the past several weeks and months to learn the basics of AI protein design — RFdiffusion, ProteinMPNN, and structure prediction with Boltz/Protenix and AlphaFold3.

For this write-up specifically:

• The idea, motivation, chassis choice, and open questions are mine.
• AI assisted with the estimates in section 4(a) — the per-test binder quantity, the assay volumes, and the resulting ethanol concentrations.
• Claude Code handled formatting and publishing: it converted my plain-text draft into Markdown, built the two tables from my values, and committed and pushed to this repository. It was instructed not to change my wording, and did not. Although it did draft this note :)

Prompt to Claude Code: “can you put Idea 1.txt in very nice attractive markdown. Update the table. DO NOT change the text from my language. Just format nicely.”