Project Computational design of microprotein binders functional modulation; Danny Sahtoe

Microproteins are small proteins translated from short stretches of the genome called small open reading frames (smORFs), which standard protein catalogs long overlooked. Many are now being discovered, but their biological roles remain largely unknown, and there are few tools to probe or control what they do. To study a microprotein's function, or to target it therapeutically, researchers need molecules that bind it selectively and switch its activity on or off, yet many microproteins are small and structurally disordered, so ready-made binders rarely exist.

This project will use AI-based protein design tools and folding models (AlphaFold3, RoseTTAFold) to create synthetic proteins that bind and modulate selected microproteins. You will express and characterize a consortium-prioritized set of around 20 target microproteins, design high-affinity binders for them, and refine those designs iteratively using structural and biophysical feedback. The work sits at the heart of ORFeus Work Package 2, which moves from discovery to function: it turns microproteins found by other projects into design targets and delivers the resulting binders as tools for functional and therapeutic studies across the network.

It connects closely to partner projects on thermal proteome profiling, secreted and host-pathogen microproteins, and AI-driven prediction, which supply targets, prioritize the target list, and provide the structural and functional data that guide each design cycle.

• Express a consortium-prioritized set of around 20 target microproteins in
  
  E. coli, purify them, and characterize them biophysically using SEC-MALS and thermal stability assays.
• Design high-affinity synthetic binders using AI protein design tools and folding models (AlphaFold3, RoseTTAFold), refined iteratively through a feedback loop with structural and biophysical data from the project of another doctoral candidate (DC) in the network, here DC10 (thermal proteome profiling).
• Validate binder activity using biolayer interferometry and, in collaboration with DC5, functionally confirm that the binders modulate target activity in cellular assays.
• Contribute the binder library, structural models, and characterization data to the shared ORFeome platform, collaborate across the ORFeus network, and produce the project's scientific report.

Methods and platforms
: AI-based computational protein design, recombinant protein expression in

E. coli and purification, biophysical characterization (SEC-MALS, thermal stability assays, biolayer interferometry), directed evolution with yeast surface display, and cell-based functional assays, contributing designs and data to the ORFeome platform.

Secondment
: you will spend around three months at an ORFeus industry partner, designing and optimizing synthetic protein binders for therapeutic targeting of microproteins. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

You must meet all of the following on your recruitment date:

• You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.
• Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in the Netherlands for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.
• You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate,…