Protocol for preparing natural peptidoglycan nanoparticles and purifying plant-derived antigens

Purifying plant-derived proteins is challenging due to host contaminants and high downstream costs. Here, we present a protocol for the preparation of natural peptidoglycan nanoparticles (NPNs) from lactic acid bacteria (LAB) and their use to selectively capture SCpl7-tagged antigens from plant extracts. We describe steps for NPN preparation, plasmid construction and infiltration, and total soluble extraction. We then detail procedures for purifying target proteins. This protocol enables rapid protein capture, offering a cost-effective alternative to conventional Ni²⁺-NTA purification. For complete details on the use and execution of this protocol, please refer to Song et al.¹ and Song et al.².