Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities
Open accessAbstract
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
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Because SAXS data are low resolution and cannot precisely determine relative monomer orientation, MD-generated conformations differ somewhat from those fitted with the experimental structural library.
“It is noted that due to the low resolution nature of SAXS data which prevents a precise determination of relative orientation of the two monomers, the MD generated conformations differ somewhat from those fitted with the experimental structural library.232”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [232]
SAXS profiles for ubiquitin dimers connected by native and non-native linkages are similar.
“They found that SAXS profiles for the two types of dimers are similar.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [232]
MD results reveal similar conformational ensembles for native and non-native ubiquitin dimers.
“The MD results also reveal similar conformational ensembles for the native and non-native ubiquitin dimers.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [232]
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Flagged first, then by citations
Research works printed but not linked: 1
- Case D, Darden T, Cheatham T, III, Simmerling C, Wang J, Duke R, Luo R, Walker R, Zhang W, Merz K (2012) Amber 12. San Francisco: University of Califor- nia, Vol. 1, p 3.
Cited by
Sorted by citations
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works
- Authors
- Pham, G. H., Rana, A. S. J. B., Korkmaz, E. N., Trang, V. H., Cui, Q., & Strieter, E. R.
- Affiliations
- University of Wisconsin–Madison (US)
- Corresponding author
- Strieter, Eric R.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2016-01-12
- Volume
- 25
- Issue
- 2
- Pages
- 456-471
- ISSN
- 0961-8368 (ISSN-L)
- PMC
- PMC4815342
- OpenAlex
- W1881356601
- Cited by
- 21
- References
- 77
- Citations by year
- 2026: 1 · 2025: 4 · 2023: 3 · 2022: 1 · 2020: 3 · 2018: 2 · 2017: 3 · 2016: 4
- FWCI
- 1.30
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- General Motors Corporation
- University of Wisconsin-Madison
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- ubiquitin
- MeSH terms
- Animals, Humans, Hydrolysis, Models, Molecular, Protein Conformation, X-Ray Diffraction, Ubiquitin, Databases, Protein, Scattering, Small Angle, Protein Multimerization, Ubiquitin-Specific Proteases
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