# Higher Order Protein Structure

> **NIH NIH P41** · UNIVERSITY OF WASHINGTON · 2021 · $457,244

## Abstract

Project Summary
Most essential proteins perform their function as part of a protein complex. Many such complexes are large,
multi-subunit entities whose structures are well beyond the capabilities of traditional methods of structural
determination. This TR&D builds upon previous pioneering achievements by the YRC in developing novel
techniques to determine the structure of proteins and protein complexes. We will develop an arsenal of new
techniques that will complement current methods of structural determination, empowering the scientific
community to address structural questions that were previously out of reach. In Specific Aim 1, we will develop
our already highly successful protein cross-linking/mass spectrometry (XL-MS) technology to: (1) Facilitate its
adoption throughout the scientific community through development of a quality control toolkit; (2) Increase its
sensitivity through improved fragmentation of cross-linked peptides; (3) Incorporate quantitative capabilities
allowing XL-MS to be used to study dynamic populations of protein complex conformations and; (4) Develop a
comprehensive set of computational tools to identify cross-linked peptides and statistically validate those
identifications. In Specific Aim 2, we will develop a complementary method, molecular painting, which will allow
the determination of surface-surface interactions in protein complexes – even in vivo where current techniques
such as HD exchange cannot be applied. In our third and final specific aim we will use co-evolution data to
model protein structures and interfaces based on covariation of pairs of residues. We will develop technology
to apply deep mutational scanning data (a technology developed in the YRC) to model protein interfaces if
sufficient sequences are not available for co-evolution methods to be used. We will integrate these predictions
with data generated by cross-linking and molecular painting. Through these aims we will drive the field of
higher order protein structure determination into the future.

## Key facts

- **NIH application ID:** 10141252
- **Project number:** 5P41GM103533-25
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Trisha Davis Muller
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $457,244
- **Award type:** 5
- **Project period:** 1997-09-30 → 2022-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10141252

## Citation

> US National Institutes of Health, RePORTER application 10141252, Higher Order Protein Structure (5P41GM103533-25). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10141252. Licensed CC0.

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