# Solution structure and dynamics of polyubiquitin chains

> **NIH NIH R01** · UNIV OF MARYLAND, COLLEGE PARK · 2024 · $350,028

## Abstract

Project Summary
This work will characterize the solution structure, dynamics, and interactions of polyubiquitin (polyUb) chains,
which function as signaling molecules in the regulation of a host of cellular processes, ranging from
progression through the cell cycle, to transcriptional activation, antigen processing and vesicular trafficking of
proteins. Conjugation of substrates to polyUb chains of different linkage types commits the target protein to
distinct fates in the cell. In particular, Lys48-linked polyUb acts as a universal signal in the ubiquitin-
proteasome proteolytic pathway, the principal regulatory mechanism for the turnover of short-lived proteins that
influences a variety of vital cellular events. Understanding how polyUb chains are recognized by the 26S
proteasome and other downstream effector molecules is central to our understanding of the mechanisms of
regulation. Despite an increasing wealth of information on the cellular processes regulated by
polyubiquitination and the identification of numerous ubiquitin-binding proteins that tie the polyUb signal to
downstream events, the molecular basis of diversity in ubiquitin-mediated signaling remains unclear. The
mechanisms underlying the ability of different polyUb chains to signal for distinct outcomes remain to be
elucidated before the origin of specificity in polyUb signaling is understood. Obtaining such information is
absolutely necessary in order to develop a molecular understanding of how different polyUb chains are able to
act as specific molecular signals. The objective of the proposed work is to characterize the structure and
recognition properties of various types of polyUb chains, in order to understand at a molecular level the
structural basis for ubiquitin's ability to serve as a versatile yet specific cellular signal. These studies will focus
on the so-called non-canonical ubiquitin chains: linked via lysines other than Lys48 or Lys63 (e.g., Lys6,
Lys27) and chains containing heterogeneous linkages (e.g., Lys11 & Lys48), branched and unbranched, and
the mechanisms of selective recognition of these chains by dedicated receptors from the DNA repair or
proteasomal degradation pathways. We will also determine the conformations of the canonical, Lys48-linked
tetraUb chains in solution in order to gain insights into the mechanisms of their recognition by cellular
receptors. Finally, these studies will characterize the interactions and determine the structures of polyUb
complexes with the recently designed macrocyclic peptides that bind polyUb chains with high affinity and
linkage specificity, in order to facilitate further development and optimization of this entirely novel class of
modulators and potential therapeutics for ubiquitin-mediated signaling pathways. We will use modern NMR
approaches in combination with small-angle X-ray and neutron scattering (SAXS, SANS) and other biophysical
techniques in order to determine the three-dimensional structures and conformationa...

## Key facts

- **NIH application ID:** 10879300
- **Project number:** 2R01GM065334-18
- **Recipient organization:** UNIV OF MARYLAND, COLLEGE PARK
- **Principal Investigator:** DAVID FUSHMAN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $350,028
- **Award type:** 2
- **Project period:** 2002-03-01 → 2028-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10879300

## Citation

> US National Institutes of Health, RePORTER application 10879300, Solution structure and dynamics of polyubiquitin chains (2R01GM065334-18). Retrieved via AI Analytics 2026-06-14 from https://api.ai-analytics.org/grant/nih/10879300. Licensed CC0.

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