Partnership Opportunities

Tools for Studying the Dynamic Interactome for Neurodegenerative and Infectious Diseases

Developing compact, high-affinity antibodies for research and clinical applications

Technology overview

John Aitchison        Dr. John Aitchison

The National Center for Dynamic Interactome Research (NCDIR) is advancing technologies to study the interactome – the interactions of proteins, nucleic acids, and other cell components. Dr. John Aitchison leads one of the three sites of NCDIR, which is funded by the National Institutes of Health. There is a critical need to determine the molecular networks that establish cellular dynamics, the influence of disease and infection, and potential therapeutic intervention strategies – with predictable outcomes. The pipeline of NCDIR work has three stages: 1) isolating, preserving, and visualizing macromolecular complexes; 2) determining their composition, spatial relationships, and dynamics; 3) and integrating diverse data for modeling and accurately representing the interactome. Driving NCDIR technology development are 20 projects with translational potential, including work on degenerative conditions and dementia and infectious diseases such as tuberculosis, influenza, and HIV.

Among the NCDIR tools are nanobodies – high-affinity, stable antibodies of about 400 amino acids that are easily produced in bacteria. These recombinant proteins are based on the unique small antigen-binding domains of llama single chain antibodies. NCDIR scientists collect these domains from immunized llamas, selecting for those with subnanomolar affinity. Mass spectrometry (MS) determines their amino acid sequence, which is matched to RNA-seq data from the donor llama. The sequences of the best antigen-binding domains are cloned for expression in E. coli.

Plasmids for generating nanobodies against the protein tags mCherry and green fluorescent protein (GFP) are publicly available. NCDIR scientists are producing other nanobodies for isolating and tagging cell complexes and their subunits. Nanobodies may also be used as reagents to detect biomarkers, as fusion domains for drugs and therapeutic proteins, and in humanized form, as passive immunotherapy.

Dr. Aitchison brings a broad spectrum of expertise to industry partnerships. In addition to experience with nanobodies and other reagents for tagging and purifying cellular complexes, his laboratory has advanced MS capabilities and develops sophisticated computational methods for integrating and analyzing data from multiple sources.

Stage of Development

  • Preclinical in vitro

Partnering Opportunities

  • Collaborative research opportunity
  • Sponsored research agreement
  • Consultation agreement


  1. Aitchison JD, Rout MP. The interactome challenge. J Cell Biol. 2015;211:729-732.
  2. Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA....Aitchison JD...Rapid, optimized interactomic screening. Nat Methods. 2015;12:553-560. 

Learn more

To learn more about partnering with Seattle Children’s Research Institute on this or other projects, email the Office of Science-Industry Partnerships