Protein sequencing is the latest cutting edge technique in our proteomics toolkit
Protein sequencing is the latest cutting edge technique in our proteomics toolkit. But when will it be ready for primetime?
Protein sequencing is the latest cutting edge technique in our proteomics toolkit. But when will it be ready for primetime?
The central dogma states that genetic information flows from DNA -> RNA -> Protein and that proteins don’t code for anything.
Organisms have evolved methods to make DNA from DNA and DNA from RNA (viruses!), but there are no enzymes that work backwards from proteins!
This makes the job of figuring out how to sequence proteins very hard because there aren’t any naturally occurring enzymes that we can co-opt to do our bidding like we can for DNA and RNA sequencing.
Luckily, we’re surrounded by creative scientists who are trying to defy nature and tackle this problem head on:
Fingerprinting (Nautilus Biotechnology) - Use a flowcell to bind and immobilize billions of full length proteins and expose them to different types of affinity reagents to sequentially probe their structures. The detection of 'features' at each position can be used to infer what protein is present and affinity reagents that can broadly recognize post-translational modifications (PTMs) are in development.
Edman Degradation (Erisyon) - A method where peptides are immobilized on a glass slide, cysteines are fluorescein labeled and then the slides are subjected to multiple cycles of chemical degradation. The fluorescence at each cycle is recorded and the position of the cysteines within each peptide can be inferred by the reduction of fluorescence every cycle. The sequence of the cysteines can then be used to infer which peptide was present.
Kinetic Sequencing (Quantum-Si) - Proteins are sequenced using fluorescent 'recognizers' that bind to the ends of peptides. Recombinant proteases are used to sequentially expose the next peptide in the chain for recognition and sequencing. The binding kinetics of the 'recognizers' can be used to both predict the terminal amino acid and whether it is modified with a PTM.
Nanopore Sequencing (ONT) - Oxford Nanopore and others are working on modifying nanopores to directly sequence proteins. This is similar to RNA and DNA applications where the molecules are linearized and pulled (or in the case of proteins, pushed) through the nanopore’s channel for detection. We’re still in the very early days on this one so it might be a minute before we see these in the hands of researchers!
Reverse Translation (Encodia) - Encodia are mostly a stealth mode company and have released very little information about how their technology works. But, they refer to it as reverse translation, (again, this doesn’t exist in nature), and their website describes using oligo-tagged ‘affinity reagents’ (Antibodies? Aptamers?) to sequence proteins.
Despite the fact that protein sequencing is still in its infancy, I’m excited to see what these and other companies are able to come up with to help reveal the secrets hidden in our proteomes!
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Brian Krueger