In a striking demonstration of scientific ingenuity, an Oxford-based team of researchers has unveiled an innovative methodology for peering into the very fabric of life: proteins. By adapting nanopore technology—commonly used for DNA and RNA sequencing—these scientists from the University of Oxford's Department of Chemistry have developed a technique capable of decoding the convoluted lexicon of protein structures and their post-translation modifications (PTMs). This breakthrough was documented in an article published recently in Nature Nanotechnology.

A colossal proportion of the biological processes that constitute life are mediated by proteins. Despite there being roughly 20,000 protein-encoding genes, cells teem with over a million protein variants. These variants are birthed through a process called PTM, where a protein's structure is remodeled after its transcription from DNA, resulting in an astounding range of potential protein variants from a single chain. Akin to the sculptor chiseling a formless block of stone into an exquisite statue, PTM carefully tailors each protein into a distinctive configuration by appending chemical groups or carbohydrate chains to the protein's constituent amino acids.

These molecular masterpieces play an instrumental role in regulating an array of intricate biological operations within cells. Thus, creating a comprehensive inventory of protein variants would open a window into the enigmatic world of cellular functioning, which could revolutionize our comprehension of it. However, such an inventory remains one of the final frontiers in biology due in part to the labyrinthine complexity and the vast scope of protein diversity.

The Oxford team, in their quest for a resolution, combined their expertise with the innovative powers of nanopore technology. In their novel approach, the 3D structure of a protein is unfolded into a linear chain by a carefully directed water flow and is then threaded through infinitesimally small pores designed to only permit the passage of a single amino acid molecule at a time. This passage is monitored by an electrical current applied across the nanopore. As different molecules traverse the pore, they induce unique disruptions in the current—akin to distinct fingerprints for each type of molecule.

The researchers demonstrated the elegance and efficacy of their method by detecting three different PTM modifications (phosphorylation, glutathionylation, and glycosylation) on protein chains extending over 1,200 residues long. The method is designed to work without the need for labels, enzymes, or additional reagents, a significant advancement in the field of protein analysis.

“This simple yet powerful method opens up numerous possibilities. Initially, it allows for the examination of individual proteins, such as those involved in specific diseases. In the longer term, the method holds the potential to create extended inventories of protein variants within cells, unlocking deeper insights into cellular processes and disease mechanisms,” remarkd Professor Yujia Qing, contributing author of the study.

The approach is compatible with existing portable nanopore sequencing devices, paving the way for its deployment in a multitude of research settings. Its portability also opens up new possibilities for point-of-care diagnostics, offering personalized detection of protein variants associated with a broad array of diseases, from cancer to neurodegenerative disorders.

Professor Hagan Bayley, contributing author and co-founder of Oxford Nanopore Technologies, elaborated, stating that “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. It may also open new avenues for personalized medicine, diagnostics, and therapeutic interventions.”

This discovery marks a significant leap forward in our quest to unravel the enigma of protein structures, setting the stage for a new era in the exploration of biological complexity.