# Protein Footprinting Coupled to Mass Spectrometry for the Study of Protein Higher Order Structure in Complex Model Systems

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2022 · $571,502

## Abstract

Project Summary
The cellular environment is crowded with a concentration of macromolecules between
200-400 grams per liter. This crowding affects protein interactions, binding affinities, and
diffusion. These conditions are not replicated in the dilute solutions used for in vitro
studies. To have a full understanding of protein function, it is necessary to study
proteins in complex environments that mimic the in vivo environment. However, the high
concentration of macromolecules makes it difficult to perform structural studies in these
systems. Owing to this, it is necessary to develop new methods to study protein
structure in complex model systems. Here, we propose to further establish the protein
footprinting method fast photochemical oxidation of proteins (FPOP) for studying
complex model systems. FPOP utilizes hydroxyl radicals to oxidatively modify solvent
accessible amino acids in proteins. The in vitro method can identify protein-ligand and
protein-protein interaction sites as well as regions of protein conformation changes. My
group has further expanded FPOP for studies in cells (IC-FPOP) and in vivo (IV-FPOP)
in C. elegans, an animal model for human disease. We have demonstrated that IC- and
IV-FPOP can oxidatively modify hundreds to thousands of proteins in these complex
systems. The next step in method development is to establish their efficacy for
identifying protein interactions in these model systems by studying specific applications.
For the next 5 years, we plan to apply IC- and IV-FPOP to study protein folding and
aggregation. The identification of protein interactions involved in misfolding and
aggregation will help design new therapeutics. We also plan to extend the method into
another three-dimensional model system, ex vivo tissue. This will provide structural
information in a model system that more closely resembles the in vivo environment than
monolayer cell culture.

## Key facts

- **NIH application ID:** 10335397
- **Project number:** 1R35GM144324-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Lisa M Jones
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $571,502
- **Award type:** 1
- **Project period:** 2022-09-21 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10335397

## Citation

> US National Institutes of Health, RePORTER application 10335397, Protein Footprinting Coupled to Mass Spectrometry for the Study of Protein Higher Order Structure in Complex Model Systems (1R35GM144324-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10335397. Licensed CC0.

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