Uncovering hidden protein modifications with native top-down mass spectrometry

Uncovering hidden protein modification with native top-down spectrometry 

In Nature Methods this week Kavli Oxford researchers, Jack Bennett and colleagues describe open-source software for use in native top-down mass spectrometry  

This tool reveals hidden protein modifications within their native structural context and helps resolve density in cryo-EM maps, a step forward for structural biology & drug discovery.  

Proteins rarely exist in a plain state. Rather, they are decorated with sugars, lipids, phosphates, and countless other chemical modifications that fine-tune their functions. These modifications are essential for processes from cell signalling to enzymatic activity, but their incredible diversity and instability makes them notoriously difficult to study. In their publication Bennett et al introduce precisION, a new computational workflow that unlocks hidden layers of modification complexity using native top-down mass spectrometry.

By fragmenting intact protein complexes and applying new spectrum-centric analyses, precisION can identify, localize, and even quantify elusive modifications that evade standard methods. We applied this approach to a range of biologically important systems including signalling proteins, viral targets, and neurotransmitter transporters. Most strikingly, we uncovered new lipid modifications on the human GABA transporter, a protein central to controlling brain activity and implicated in epilepsy. Integrating our mass spectrometry findings with cryoEM structures revealed how these lipid tags reshape the transporter’s interactions with its surrounding membrane.

Jack Bennett, Doctoral student said,

We believe precisION will enable the community to explore protein modifications in their full structural and functional context. By revealing the hidden chemical diversity of human proteins, it opens the door to deeper understanding of the molecular drivers of health and disease.

The paper, Uncovering hidden protein modifications with native top-down mass spectrometry is published in nature methods

Since April 2021, Oxford University's KAVLI Institute for Nanoscience Discovery is proudly serving as a hub for research groups from seven different departments spanning both the medical and physical sciences, including the Robinson Group from the Department of Chemistry.