# Probing protein structure and aggregation in complex environments with 2D IR spectroscopy

> **NIH NIH R35** · VANDERBILT UNIVERSITY · 2024 · $395,943

## Abstract

The goal of our proposed research program is to develop new spectroscopic methods capable of
providing enhanced insight into protein structure and dynamics within complex environments that
impact human health. We will apply these methods to study structural changes induced by
protein-protein and protein-surface interactions under conditions that are not accessible by other
experimental approaches. Our first research direction focuses on advancing the use of unnatural
amino acids (UAAs) beyond probes of local environment by taking advantage of the unique
spectral features provided by two-dimensional infrared (2D IR) spectroscopy to measure
vibrational couplings between UAA labels. These couplings depend sensitively on the distance
and relative orientation between UAA vibrational modes and thus can be used to map protein
structure. We will select UAAs modified with functional groups that have vibrational modes within
a biologically transparent region of the infrared spectrum, allowing us to probe the structure of
protein complexes and aggregates in biological media. We will use the Alzheimer’s β-amyloid
(Aβ) protein, the most studied self-assembling protein, in cerebrospinal fluid as a prototypical
system to develop and refine our approach into a broadly applicable method that will enable the
study of dynamic protein interactions that result in formation of protein complexes and aggregates
involved in a range of diseases. The Aβ studies will also allow us to bridge the gap between in
vitro aggregation studies and ex vivo fibril structures and gain unprecedented new insight into
physiologically relevant self-assembly pathways in Alzheimer’s disease. Our second research
direction aims to understand, for the first time, the detailed residue-level changes to protein
structure that occur when proteins interact with nanoparticle (NP) surfaces. NPs are ubiquitous in
our lives and are increasingly being considered for biomedical applications. However, the effect
of nanomaterials on living systems remains unclear. One concern is that proteins readily adsorb
onto the surfaces of NPs, which can result in changes to protein structure and thus function. Our
initial studies will examine the differing effects of NPs on the secondary structure of model
peptides and lysozyme, first with metallic NPs as a model system to understand the effects of NP
size and concentration, and then with silica NPs to examine the role of surface chemistry in
affecting structural changes. Machine learning-based approaches to enhance the sensitivity of
2D IR spectroscopy to site-specific labels will be developed to further improve structural
resolution. Ultimately, these studies will be expanded to understand the interactions between a
broader range of both nanomaterials and proteins in biologically relevant media.

## Key facts

- **NIH application ID:** 10940937
- **Project number:** 1R35GM155058-01
- **Recipient organization:** VANDERBILT UNIVERSITY
- **Principal Investigator:** Lauren E Buchanan
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $395,943
- **Award type:** 1
- **Project period:** 2024-09-01 → 2029-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10940937

## Citation

> US National Institutes of Health, RePORTER application 10940937, Probing protein structure and aggregation in complex environments with 2D IR spectroscopy (1R35GM155058-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10940937. Licensed CC0.

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