# SARS-CoV-2 N interactions with RNA and host cell cyclophilin-A

> **NIH NIH R21** · UNIVERSITY OF COLORADO DENVER · 2023 · $233,250

## Abstract

PROJECT SUMMARY
 Coronaviruses (CoVs) have emerged as formidable human pathogens since their detection within
human populations only 50 years ago, underlying the need to rapidly characterize their molecular mechanisms
in order to thwart their infections through therapeutics. Seven CoVs that infect humans are known with a range
of pathogenicity, which include the more recent virulent CoVs such as MERS, SARS-CoV-1 and SARS-CoV-2.
CoVs comprise four structural proteins that includes the envelope (E), membrane (M), spike (S), and
nucleocapsid (N) proteins. CoV N proteins perform numerous functions during the viral life-cycle that includes
both packaging genomic RNA and manipulating the host cell machinery, making the N protein the most
abundantly expressed viral protein during infection. However, the unique and diverse functions of CoV N
proteins have made standard structural methods that address its molecular interactions difficult. For example,
such difficulties include their promiscuity in RNA binding, engaging multiple binding sites simultaneously, and
the presence of inherently dynamic regions thought to be critical for engaging RNA and host proteins. NMR
offers a solution to such challenges, as multiple binding modes can be simultaneously characterized both
dynamically and structurally and we have previously shown that the inherently dynamic regions within a CoV N
protein (SARS-CoV-1) can be studied by NMR. Thus, the exploratory nature of this R21 proposal is to develop
strategies aimed at elucidating the molecular details that underlie the SARS-CoV-2 N protein interactions with
RNA (Aim 1) and host proteins (Aim 2).
 Based on our preliminary studies, we hypothesize that specific regions within the N protein have
preferred RNA binding sites (Aim 1) and host cell cyclophilin-A binding sites (Aim 2). We will address these
aims through the following:
Aim 1) Determine how the SARS-CoV-2 N protein targets RNA. Biochemical and biophysical approaches
that include NMR will be used to identify the high affinity binding sites of the N protein within sequences
derived from genomic RNA and identify the associated dynamic and structural changes that occur upon
complex formation.
Aim 2) Determine how the SARS-CoV-2 N protein targets host cell cyclophilin-A. NMR will be used to
determine whether the N protein targets the cyclophilin-A active site and whether the N protein is a substrate.

## Key facts

- **NIH application ID:** 10622478
- **Project number:** 5R21AI166292-02
- **Recipient organization:** UNIVERSITY OF COLORADO DENVER
- **Principal Investigator:** ELAN Z EISENMESSER
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $233,250
- **Award type:** 5
- **Project period:** 2022-05-16 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10622478

## Citation

> US National Institutes of Health, RePORTER application 10622478, SARS-CoV-2 N interactions with RNA and host cell cyclophilin-A (5R21AI166292-02). Retrieved via AI Analytics 2026-06-03 from https://api.ai-analytics.org/grant/nih/10622478. Licensed CC0.

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