# NMR Studies of Retroviral Nucleic Acid Binding Proteins

> **NIH NIH R01** · UNIVERSITY OF MARYLAND BALTIMORE COUNTY · 2022 · $701,302

## Abstract

7. Project Summary/Abstract
 Our goal is to understand how the HIV-1 5’-Leader RNA directs multiple, diverse functions during viral
replication, including selective packaging of the dimeric, unspliced viral genome during virus assembly.
Significant progress made during the current funding period includes: (1) We determined the 3D structure of
the HIV-1 packaging signal, a longstanding milestone. (2) We showed that transcriptional start site
heterogeneity affords RNA transcripts that contain one, two, or three 5’-guanosines and exhibit different
structures, functions, and fates; these findings established a new paradigm for controlling genome versus
mRNA fates. (3) We discovered that the intact 5’-leader rapidly adopts an extended dimer interface, even in
the absence of RNA chaperones. (4) We showed that packaging elements reside primarily in the 5’-leader and
do not extend into downstream regions of the gag gene, as previously proposed. (5) Several NMR methods
were developed that extend the size limit for RNA structural studies, including (i) a 2H-edited
NMR/mutagenesis approach for measuring RNA dimerization dynamics, (ii) a hybrid NMR/cryoEM approach
applicable to relatively small RNAs, including the HIV dimer initiation site, and (iii) a method that extends the
RNA size limit for residual dipolar coupling (RDC) measurement by more than an order of magnitude
compared to existing approaches. In addition, we now have preliminary evidence that transcriptional start site
heterogeneity modulates splicing, in addition to translation and packaging. We are now poised to determine the
5’-leader structures of the unspliced and spliced HIV RNAs generated by heterogeneous transcriptional start
site usage. These studies will explain how transcriptional inclusion of as few as one or two 5’-guanosines has
such a profound influence on RNA structure and function. Preliminary studies also reveal that truncated HIV
Gag protein constructs (comprising the capsid through the nucleocapsid domains of Gag) bind the cognate,
dimeric RNA packaging signal with high affinity and ~18:2 Gag:RNA stoichiometry. We are now also poised to
determine the 3D structure of this complex by hybrid NMR/EM, which will provide the first molecular views of
the Gag:RNA complex that nucleates virus assembly.
 NMR studies of large RNAs are technically challenging – the average size of NMR-derived RNA structures
in the RNA Structure Database is only 27 nucleotides – but the potential payoff is substantial and could
ultimately lead not only to a more detailed understanding of how HIV replicates, but also to the development of
new approaches for the treatment of AIDS and other virally-induced human diseases.

## Key facts

- **NIH application ID:** 10319933
- **Project number:** 5R01AI150498-33
- **Recipient organization:** UNIVERSITY OF MARYLAND BALTIMORE COUNTY
- **Principal Investigator:** MICHAEL FINLEY SUMMERS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $701,302
- **Award type:** 5
- **Project period:** 1989-07-01 → 2022-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10319933

## Citation

> US National Institutes of Health, RePORTER application 10319933, NMR Studies of Retroviral Nucleic Acid Binding Proteins (5R01AI150498-33). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10319933. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*