Supervised learning model predicts protein adsorption to carbon nanotubes.

Abstract

Engineered nanoparticles are advantageous for biotechnology applications including biomolecular sensing and delivery. However, testing compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable protein corona formation prevents their effective implementation. We develop a random forest classifier trained with mass spectrometry data to identify proteins that adsorb to nanoparticles based solely on the protein sequence (78% accuracy, 70% precision). We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)–based nanosensor and study the relationship between the protein’s amino acid–based properties and binding capacity. Protein features associated with increased likelihood of SWCNT binding include high content of solvent-exposed glycines and nonsecondary structure–associated amino acids. To evaluate its predictive power, we apply the classifier to identify proteins with high binding affinity to SWCNTs, with experimental validation. The developed classifier provides a step toward undertaking the otherwise intractable problem of predicting protein-nanoparticle interactions.