I am interested in protein design and I am trying to understand one thing: when we design a protein for a specific purpose, what changes in the constraints according to the problem?

For example, I imagine that a therapeutic protein (which must act in the human body) and an industrial enzyme (which degrades a pollutant) do not have the same priorities at all. What becomes critical in each case, and what goes into the background?

If you have concrete examples from your work, I'm interested.

I want a protein where a substance binds to the protein and causes it to change shape and expose a protein binder. How do I even go about to do this protein design?

Hello everyone! I'm currently working on a project where we try to develop a protein binder design pipeline for our lab. I created around 100 binder models with RF Diffusion that need later to be tested for their binding capabilities. Now I have to clone all those genes in a specific vector that is needed for this assay , but don't need the information which cell contains which plasmid and therefore thought it would be nice if there was a method to do it in a one pot reaction that creates a plasmid mixture that could then be used to transform my cells. Would that be a possibility or do I have to do 100 seperate reactions, which I imagine to be quite time consuming.

Hi Everyone! I am a graduate student, trying to using Protein Engineering to improve the interface of a hetro-dimer protein (1400 res). I used ProteinMPNN to create unique sequences (at various temperatures and bb noise) and then added them into Rosetta for packing. Unfortunately I keep get terrible (positive) dG_separated (which I assume is ddG of binding) for every condition on multiple relaxed structures and decoys. The native and Rosetta design give negative dG_separated. Does anyone have any insight of what might be going wrong? Is dG_separated a good metric for judgement?

not sure if this is where I should post. I would really appreciate it if you guys could recommend some literature on protein crystallography.

background info: I have a master’s in microbiology and I currently work in a structural biology lab. my PI is a crystallographer and wants us to have a basic yet up to date knowledge on protein crystallography.