Protein fingerprinting and sequencing with nanopores

Proteins are the major building blocks of life. The protein content of a cell or organism provides key information for the understanding of biological processes and disease.  Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences and these methods face limitations, for example in the sizeable sample volume needed. During the last few decades, nanopore technology has emerged as one of the most promising techniques to sequence DNA. Sequencing proteins at the single-molecule level is a clear next step. This however presents even greater challenges than DNA sequencing, due to the three-dimensional folded structure of proteins and the presence of 20 different amino acids to be identified.

Here, we propose a new scheme for protein sequencing in which we simplify the identification of proteins by using a fingerprinting method. We computationally show that the detection of two amino acids is sufficient for protein identification using an existing database, and we present our first experimental efforts in this direction using nanopore analysis.



This project is done in collaboration with the Chirlmin Joo Lab (Bionanoscience).