Nanopore Technology One Step Closer to Identifying Proteins and Peptides

Nanopore technology is generally used for DNA sequencing. It provides a portable, low-cost solution and works both in the jungle and in space. Now, this technology could potentially be used to identify proteins or peptides. Scientists from the University of Groningen have used a patented nanopore technology to detect the fingerprints of peptides and proteins.

This technology is also capable of detecting polypeptides that differ by just a single amino acid. The results of the study have been reported in the journal, Nature Communications.

The Researchers were able to detect several proteins and peptides passing through a funnel-shaped nanopore. In addition, they have successfully solved two major issues that have hindered efforts to inspect and sequence proteins with nanopores – first is getting the polypeptides into the pore, and second is detecting the variations in proteins through current recordings.

Nanopores usually carry a charge, and the amino acids that make up polypeptides are also charged. Getting the polypeptide inside the pore and to pass through nanopores is therefore a challenge.

Giovanni Maglia, Associate Professor of Chemical Biology, University of Groningen

Fingerprint

Maglia pulled the polypeptides into the pores by using an electro-osmotic flow. Within an applied potential across the nanopore, a flow of water and ions travel via the pore. By controlling the direction of the ion current, a fluid flow that is sufficiently strong to transport polypeptides can be produced.

We did this by tuning the charges inside the pore wall. By changing the pH of the medium, it was possible to fine-tune the balance between the electro-osmotic flow and the force of the electric field which was applied across the pore.

Giovanni Maglia, Associate Professor of Chemical Biology, University of Groningen

Maglia tested five different polypeptides that ranged from 1 to 25 kilodalton. "We used biomarker peptides linked to disease, with different charges and shapes," he says. As the polypeptides entered the pore, the current across the pore created a 'fingerprint' for each. Thus, Maglia was able to differentiate two versions of the 21 amino acid peptide endothelin, which vary by just a single amino acid (methionine or tryptophan).

Sequencing

It is difficult to obtain a good reading from a nanopore. Maglia employed a different kind of pore that he characterized and patented.

Pores used in the past are barrel-shaped, which means the shape and size of the pore has fundamental limitations. But our pore has an alpha helical funnel shape, and the size of the narrow end, which is where we do our measurements, means it should contain just one amino acid, so it is more easily tuned.

Giovanni Maglia, Associate Professor of Chemical Biology, University of Groningen

Presently, the polypeptides travel through the pore too quickly to detect the individual amino acids. This is required to sequence proteins at the single-molecule level. It would serve as a useful tool for research, explains Maglia, "Proteins can be chemically modified in many unique ways, and we have very little information on the exact composition of proteins in our body." This can only be observed at the single-molecule scale.

Maglia, "Molecular diagnostics and biomarker discovery should benefit particularly from the single-molecule characterization of proteomes." It is a significant advantage that nanopore technology has already been devised for DNA sequencing. This technology is robust, fast and economical: nanopore sequencing devices are employed in the field and one such device has even been delivered to the International Space Station. Using a similar method to detect proteins would need slight adaptations, predominantly in the pores, "In theory, we could build an application tomorrow."