# Dynamics of Translation

> **NIH NIH R01** · STANFORD UNIVERSITY · 2021 · $393,856

## Abstract

PROJECT SUMMARY
Protein synthesis by the ribosome is central to life and disease. We have developed single-
molecule approaches to provide a real-time dynamic perspective to the basic and unusual steps
of protein synthesis. Here we build on our methodological developments over the past funding
period to provide combined structural and dynamic view of how mRNA and nascent protein
sequence and structure modulate translation and affect its outcome. In Aim 1 we focus initiation
and termination. We will understand the conformational dynamics of the 30S subunit during
initiation and how the process is controlled by mRNA sequence and structure; we will study
termination regulation by RF3, and recoding in selenocysteine incorporation; finally, we will
watch how polysomes form. In Aim 2, we will study the role of mRNA sequence and structure in
controlling elongation. We will investigate how modified nucleotides in mRNA change
elongation, and study how ribosomes navigate secondary structures. We will determine the
basis for pausing and reading-frame changes that occur during elongation due to mRNA
sequence or structure, tracking pathways, branchpoints and mechanism. We will also determine
how two ribosomes translating on an RNA navigate secondary structures and possibly interact
during elongation. In Aim 3, we explore the interplay of nascent protein sequence and folding
with elongation kinetics. We will determine how antibiotic sensitivity or resistance is determined
by the nascent chain, and how translation is disrupted. We will determine how the folding of
well-characterized protein domains on the ribosome affect real time translation (pausing, stalling
acceleration). Finally, we will explore the directly the correlation of folding and translation in real
time. The proposed research is buttressed by strong collaborations on the various systems to
support biophysical and structural analysis, reagent preparation, and in vivo correlation. The
results of this proposal will provide a deeply textured view for how protein synthesis is regulated
and controlled.

## Key facts

- **NIH application ID:** 10247726
- **Project number:** 5R01GM051266-28
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** JOSEPH D PUGLISI
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $393,856
- **Award type:** 5
- **Project period:** 1995-05-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10247726

## Citation

> US National Institutes of Health, RePORTER application 10247726, Dynamics of Translation (5R01GM051266-28). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10247726. Licensed CC0.

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