Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions

Cohen, Ariel; Rosenthal, Eran; Shifman, Julia M.

doi:10.1016/j.jmb.2017.09.003

Cited by 8 publications

(11 citation statements)

References 46 publications

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“…All of these except His68 displayed considerable signal loss at 10°C with increasing DSS1 concentrations, therefore only His68 was used to estimate the binding affinity. Fitting the CSPs of His68 gave a K D of 430 ± 152 μM (Figure 3f, right panel); an affinity similar to many other ubiquitin binding domains 8,59–61 …”

Section: Resultsmentioning

confidence: 79%

“…The apparent affinities of the UBSs in human DSS1 were lower compared to S . pombe DSS1, 43 but in a similar range as other ubiquitin binding motifs 59–61 . In the case of UBS2, the affinity was too low to be accurately determined 58 .…”

Section: Discussionmentioning

confidence: 96%

“…The apparent affinities of the UBSs in human DSS1 were lower compared to S. pombe DSS1, 43 but in a similar range as other ubiquitin binding motifs. [59][60][61] In the case of UBS2, the affinity was too low to be accurately determined. 58 Because the UBS1 of DSS1 shares sequence similarities with the conserved C-terminus of CSNAP, this was expected to interact with ubiquitin.…”

Section: Discussionmentioning

confidence: 99%

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The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

et al. 2021

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Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.

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Section: Resultsmentioning

confidence: 79%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

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The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

et al. 2021

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“…We next used METRIS to investigate interactions with the protein post-translational modification ubiquitin. Ubiquitin has an expansive cellular regulatory role that is controlled by weaker interactions with effectors [7, 30] including non-covalent interactions with E2s and E3 ligases [5, 53]. Ubiquitin binding is wide-spread, and there are hundreds of UBLs in the human genome for these readers to discriminate amongst [20].…”

Section: Resultsmentioning

confidence: 99%

Mechanically Transduced Immunosorbent Assay To Measure Protein-Protein Interactions

Petell¹,

Randene

Pappas

et al. 2021

Preprint

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Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that indicates binding. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. Here we use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.

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“…A wide range of proteins with “Ubiquitin‐Binding Domains” (UBDs) recognize diverse ubiquitination types on specific substrate sites, thereby forming distinct signaling complexes (Fig. A–D) . Thus far, over 20 different families of UBDs have been identified .…”

Section: Ubiquitin‐binding Domains (Ubds)mentioning

confidence: 99%

Linear ubiquitin chain‐binding domains

2018

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Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitinbinding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs -specific for linear ubiquitin chains -have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.

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Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions

Cited by 8 publications

References 46 publications

The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

Mechanically Transduced Immunosorbent Assay To Measure Protein-Protein Interactions

Linear ubiquitin chain‐binding domains

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