Title:	Computational design of protein cages
DNr:	NAISS 2024/22-525
Project Type:	NAISS Small Compute
Principal Investigator:	Mads Jeppesen <mads.jeppesen@biochemistry.lu.se>
Affiliation:	Lunds universitet
Duration:	2024-04-08 – 2025-05-01
Classification:	10603
Homepage:	https://andrelab.lu.se
Keywords:

Abstract

Protein cages are an exciting class of nanomaterials that can be used to trap or scaffold other molecules. It is highly desirable to be able to design the overall 3-dimensional structure of these materials, encompassing factors such as shape, porosity, and size, as it is essential for their many promising applications in areas that ranges from drug delivery, vaccine design, imaging, and molecular synthesis. In our lab we have developed a method to design the structure of protein cages. It incorporates existing state-of-the-art computational protein sequence design methods (such as ProteinMPNN), an evolutionary molecular docking software called EvoDOCK, and energy-function guided conformational search and screening based on the Rosetta macromolecular software. Through the resources provided by the facility we aim to computationally design thousands of protein cages with different 3-dimonsonal structures and then experimentally verify promising leads in the laboratory. We expect the methodology and resulting protein cages to be useful in many areas of science and medicine, in particular for small molecule drug delivery and as nanoparticle scaffolds for vaccines.