The frozen electron microscopic structure of meningitis doctor-worker cross-type IV fimbriae compounded with nano-antibody reveals the immune escape mechanism.

Type IV fimbriae (T4P) is a ubiquitous polymeric surface structure in pathogenic bacteria, which makes it an ideal target for effective vaccines. However, bacteria have evolved effective strategies to avoid the type IV fimbriae-directed antibody reaction. Neisseria meningitidis is a typical gram-negative bacterium with type IV pili expression, which can lead to life-threatening septicemia and meningitis. This species has evolved several genetic strategies to modify the surface of its type IV fimbriae and change the amino acid sequence, glycosylation and phosphorylation properties of fimbriae, but how these modifications affect antibody binding at the structural level is still unclear. Here, in order to explore this problem, we have determined the cryo-EM structures of different sequence types of fimbriae, which have high resolution enough to visualize post-translation modification. Then, we generate nano-antibodies against type IV fimbriae, which change the function of fimbriae in vitro and in vivo. Combined with molecular dynamics simulation of nano-antibody-fimbriae complex, Cyro-EM reveals how different types of fimbriae surface modification can change the binding of nano-antibody. Our results reveal the impressive complementarity between different strategies used by bacteria to avoid antibody binding. Importantly, we also show that structural information can be used to modify nano-antibodies in an informed way as a countermeasure to these immune escape mechanisms.

Innovations: 1. cryo-EM technology was used for the first time to accurately analyze the high-resolution structure of different sequence types of fimbriae, and the visualization of post-translation modification was realized; 2. The nano-antibody against type IV pili was developed, and its ability to change the function of pili was verified by in vitro and in vivo experiments. 3. Combined with molecular dynamics simulation, the complex influence mechanism of bacterial surface modification on nano-antibody binding was deeply revealed; 4. The molecular strategy of bacterial immune evasion was clarified from the structural level, and the fine regulation of antibody binding by sequence modification, glycosylation and phosphorylation was revealed.

 Scientific research inspiration: 1. Inspire researchers to pay attention to the dynamic changes of pathogen surface structure and its complex influence on immune response; 2. It provides a new research paradigm of structural biology for developing targeted vaccines and therapeutic strategies; 3. Emphasize the importance of multi-scale and interdisciplinary research methods in solving complex biological problems; 4. The ingenious mechanism of bacteria escaping from immune system monitoring through fine molecular modification is revealed. 

Extension of ideas: 1. Similar research methods can be extended to other pathogens with complex surface modifications, such as HIV and influenza virus; 2. Explore and develop smarter and more accurate nano-antibodies, which can overcome the immune escape mechanism of different bacteria; 3. Combining artificial intelligence and machine learning technology to predict and design more effective antibody structure; 4. Expand the research scope and discuss the dynamic change law of bacterial surface modification under different environmental conditions; 5. Develop personalized immunotherapy strategies based on structural information, aiming at specific bacterial strains; 6. Apply the research method to the in-depth analysis of the mechanism of antibiotic resistance; 7. Explore the possibility of designing new antibacterial drugs and vaccines using structural biology methods. 

Similar research ideas: 1. Analyze the complex structure of virus capsid protein and neutralizing antibody by high-resolution cryomicroscope, and reveal the structural basis of virus immune escape. 2. By analyzing the binding complex of bacterial flagellin and nano-antibody, the immune escape mechanism related to bacterial movement was clarified. 3. Molecular dynamics simulation and cryoelectron microscopy were used to study how the post-translation modification of bacterial outer membrane protein affects antibody recognition. 4. Structural characterization of cell wall-specific glycosylation modification of Mycobacterium tuberculosis was carried out, and more targeted antibody drugs were designed. 5. Based on the structural information of pathogen surface protein, the therapeutic antibody was rationally reformed to improve its recognition ability and therapeutic effect.

10.1038/s41467-024-46677-y