According to a news release posted on UI's website on Tuesday, the researchers used a membrane channel naturally made by bacteria, called aerolysin, as their nanopore. In both computer modeling and experimental work, they chopped up proteins and used a chemical carrier to drive the amino acids into the nanopore. The carrier molecule kept the amino acids inside the pore long enough for it to register a measurable difference in the electrical signature of each amino acid, even leucine and isoleucine, the near-identical twins.
The researchers found they could further differentiate modified forms of amino acids by using a more sensitive measurement apparatus or by treating the protein with a chemical to improve differentiation. The measurements are precise enough to potentially identify hundreds of modifications, said UI physics professor Aleksei Aksimentiev, a co-leader of the study, and even more may be recognized by tweaking the pore.
"This is a proof-of-concept study showing that we can identify the different amino acids," he said. "The current method for protein characterization is mass spectrometry, but that does not determine the sequence; it compares a sample to what's already in the database. Its ability to characterize new variations or mutations is limited. With nanopores, we finally could look at those modifications which have not yet been studied."
The aerolysin nanopore could be integrated into standard nanopore setups, Aksimentiev said. The researchers are now exploring approaches to read the amino acids in sequential order as they are cut from the protein. They also are considering other applications for the system.
"One potential application would be to combine this with immunoassays to fish out proteins of interest and then sequence them. Sequencing them will tell us whether they're modified or not, and that could lead to a clinical diagnostic tool," Aksimentiev said.
The study has been published in the journal Nature Biotechnology.