Scientists Close in on Elusive Goal of Adapting Nanopore Technology for Protein Sequencing
Technology could enable medical laboratories to deploy inexpensive protein sequencing with a handheld device at point of care and remote locations
Clinical laboratories engaged in protein testing will be interested in several recent studies that suggest scientists may be close to adapting nanopore-sensing technology for use in protein identification and sequencing. The new proteomics techniques could lead to new handheld devices capable of genetic sequencing of proteins at low cost and with a high degree of sensitivity, in contrast to current approaches based on mass spectrometry.
But there are challenges to overcome, not the least of which is getting the proteins to cooperate. Compact devices based on nanopore technology already exist that can sequence DNA and RNA. But “there are lots of challenges with proteins” that have made it difficult to adapt the technology, Aleksei Aksimentiev, PhD, Professor of Biological Physics at the University of Illinois at Urbana-Champaign, told ASBMB Today, a publication of the American Society for Biochemistry and Molecular Biology. “In particular, they’re not uniformly charged; they’re not linear, most of the time they’re folded; and there are 20 amino acids, plus a zoo of post-translational modifications,” he added.
The ASBMB story notes that nanopore technology depends on differences in charges on either side of the membrane to force DNA or RNA through the hole. This is one reason why proteins pose such a challenge.
Giovanni Maglia, PhD, a Full Professor at the University of Groningen in the Netherlands and researcher into the fundamental properties of membrane proteins and their applications in nanobiotechnology, says he has developed a technique that overcomes these challenges.
“Think of a cell as a miniature city, with proteins as its inhabitants. Each protein-resident has a unique identity, its own characteristics, and function. If there was a database cataloging the fingerprints, job profiles, and talents of the city’s inhabitants, such a database would undoubtedly be invaluable!” said Behzad Mehrafrooz, PhD (above), Graduate Research Assistant at University of Illinois at Urbana-Champaign in an article he penned for the university website. This research should be of interest to the many clinical laboratories that do protein testing. (Photo copyright: University of Illinois.)
How the Maglia Process Works
In a Groningen University news story, Maglia said protein is “like cooked spaghetti. These long strands want to be disorganized. They do not want to be pushed through this tiny hole.”
His technique, developed in collaboration with researchers at the University of Rome Tor Vergata, uses electrically charged ions to drag the protein through the hole.
“We didn’t know whether the flow would be strong enough,” Maglia stated in the news story. “Furthermore, these ions want to move both ways, but by attaching a lot of charge on the nanopore itself, we were able to make it directional.”
The researchers tested the technology on what Maglia described as a “difficult protein” with many negative charges that would tend to make it resistant to flow.
“Previously, only easy-to-thread proteins were analyzed,” he said in the news story. “But we gave ourselves one of the most difficult proteins as a test. And it worked!”
Maglia now says that he intends to commercialize the technology through a new startup called Portal Biotech.
The Groningen University scientists published their findings in the journal Nature Biotechnology, titled “Translocation of Linearized Full-Length Proteins through an Engineered Nanopore under Opposing Electrophoretic Force.”
Detecting Post-Translational Modifications in the UK
In another recent study, researchers at the University of Oxford reported that they have adapted nanopore technology to detect post-translational modifications (PTMs) in protein chains. The term refers to changes made to proteins after they have been transcribed from DNA, explained an Oxford news story.
“The ability to pinpoint and identify post-translational modifications and other protein variations at the single-molecule level holds immense promise for advancing our understanding of cellular functions and molecular interactions,” said contributing author Hagan Bayley, PhD, Professor of Chemical Biology at University of Oxford, in the news story. “It may also open new avenues for personalized medicine, diagnostics, and therapeutic interventions.”
Bayley is the founder of Oxford Nanopore Technologies, a genetic sequencing company in the UK that develops and markets nanopore sequencing products.
The news story notes that the new technique could be integrated into existing nanopore sequencing devices. “This could facilitate point-of-care diagnostics, enabling the personalized detection of specific protein variants associated with diseases including cancer and neurodegenerative disorders,” the story states.
The Oxford researchers published their study’s findings in the journal Nature Nanotechnology titled, “Enzyme-less Nanopore Detection of Post-Translational Modifications within Long Polypeptides.”
Promise of Nanopore Protein Sequencing Technology
In another recent study, researchers at the University of Washington reported that they have developed their own method for protein sequencing with nanopore technology.
“We hacked the [Oxford Nanopore] sequencer to read amino acids and PTMs along protein strands,” wrote Keisuke Motone, PhD, one of the study authors in a post on X (formerly Twitter) following the study’s publication on the preprint server bioRxiv titled, “Multi-Pass, Single-Molecule Nanopore Reading of Long Protein Strands with Single-Amino Acid Sensitivity.”
“This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification!” Motone wrote.
In a commentary they penned for Nature Methods titled, “Not If But When Nanopore Protein Sequencing Meets Single-Cell Proteomics,” Motone and colleague Jeff Nivala, PhD, Principal Investigator at University of Washington, pointed to the promise of the technology.
Single-cell proteomics, enabled by nanopore protein sequencing technology, “could provide higher sensitivity and wider throughput, digital quantification, and novel data modalities compared to the current gold standard of protein MS [mass spectrometry],” they wrote. “The accessibility of these tools to a broader range of researchers and clinicians is also expected to increase with simpler instrumentation, less expertise needed, and lower costs.”
There are approximately 20,000 human genes. However, there are many more proteins. Thus, there is strong interest in understanding the human proteome and the role it plays in health and disease.
Technology that makes protein testing faster, more accurate, and less costly—especially with a handheld analyzer—would be a boon to the study of proteomics. And it would give clinical laboratories new diagnostic tools and bring some of that testing to point-of-care settings like doctor’s offices.
—Stephen Beale
Related Information:
Nanopores as the Missing Link to Next Generation Protein Sequencing
Nanopore Technology Achieves Breakthrough in Protein Variant Detection
The Scramble for Protein Nanopore Sequencing
The Emerging Landscape of Single-Molecule Protein Sequencing Technologies
ASU Researcher Advances the Science of Protein Sequencing with NIH Innovator Award
The Missing Link to Make Easy Protein Sequencing Possible?
Engineered Nanopore Translocates Full Length Proteins
Not If But When Nanopore Protein Sequencing Meets Single-Cell Proteomics
Enzyme-Less Nanopore Detection of Post-Translational Modifications within Long Polypeptides
Unidirectional Single-File Transport of Full-Length Proteins through a Nanopore
