# HDX and NMR Core

> **NIH NIH U54** · SEATTLE CHILDREN'S HOSPITAL · 2021 · $1,045,733

## Abstract

Abstract
 Proteins are dynamic molecules that undergo constant flexing and motion. Changes in protein conformation
and dynamics are important to molecular recognition and these changes occur during many key biological
processes including activation and inhibition of enzymes, ligand binding to receptors, posttranslational
modifications, and allosteric communication across protein-protein interfaces. All of these processes are
regulated through the structure and dynamics of the proteins within the functional complex. Thus, techniques to
study protein structure and dynamics are critical to the understanding of biological processes and to aid in
developing strategies to target proteins for therapeutic intervention in disease. The HDX-NMR Core will address
central goals of the HIVE Center that include characterization of HIV protein interactions among themselves,
with host molecules, or with small molecule probes. A key focus of HDX efforts will be the structure and dynamics
of the HIV-1 reverse transcriptase (RT) initiation complex, or RTIC, a large protein-nucleic acid complex
comprising RT (p66/p51 heterodimer), the primer-binding site region of the 5’ untranslated viral RNA (vRNA) and
a human tRNA (Project 3: Arnold, Musier-Forsyth, Griffin, Lyumkis, and Sarafianos). We will also investigate
the interactions of HIV-1 RT with members of the APOBEC3 (A3) family of restriction factors (most notably A3G),
which have been reported to suppress the polymerase activity of RT and will also be studied in Project 3. In
addition to the RTIC from lentivirus HIV-1, we will also investigate the RTIC of spumavirus prototype foamy virus
(PFV). We are taking a multifaceted approach towards understanding these important virus-host complex
interactions, using cryo-EM, X-ray crystallography, HDX, SAXS, and pre-steady state kinetic analyses. Among
the main questions addressable by HDX are: How does the vRNA/tRNA interact with RT compared to DNA/DNA
and DNA/RNA substrates (cryo-EM, X-ray, HDX, kinetics)? What is the role of RNA structure in this complex
and how does it interact with RT (cryo-EM, X-ray, HDX)? What are the dynamic properties of the initiation
complex (cryo-EM, SAXS, HDX, kinetics)? How do interactions in the HIV-1 and PFV RTICs differ? How does
HIV-1 RT interact with A3 proteins to contribute to HIV-1 restriction? HDX has been instrumental for studying
quinoline-based allosteric integrase (IN) inhibitor (ALLINIs) induced aberrant multimerization of full-length wild
type (WT) IN and its application will now be extended to examine how recently discovered (Core 4) thiophene-
based inhibitors alter the IN structure (Project 1). HDX-MS will also be used to probe inter-protein interactions
among HIV-1 Gag and Gag-Pol proteins (Project 2), the effect of resistance mutations or inter-clade differences
in inter-protein interactions in HIV-1 proteins (Project 5), and interactions between HIV-1 proteins and SuFEx or
other small molecule probes (Project 6). NMR will ...

## Key facts

- **NIH application ID:** 10242903
- **Project number:** 5U54AI150472-11
- **Recipient organization:** SEATTLE CHILDREN'S HOSPITAL
- **Principal Investigator:** Patrick Robert Griffin
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,045,733
- **Award type:** 5
- **Project period:** 2012-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10242903

## Citation

> US National Institutes of Health, RePORTER application 10242903, HDX and NMR Core (5U54AI150472-11). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10242903. Licensed CC0.

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