Fuzzy Complex Formation between the Intrinsically Disordered Prothymosin α and the Kelch Domain of Keap1 Involved in the Oxidative Stress Response

Khan, Halema; Cino, Elio A.; Brickenden, Anne; Fan, Jing‐Song; Yang, Daiwen; Choy, Wing‐Yiu

doi:10.1016/j.jmb.2013.01.005

Cited by 38 publications

(59 citation statements)

References 105 publications

(181 reference statements)

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“…These residues were not directly involved in DNA or MSL1 binding, but rather their environment was altered upon addition of DNA. A similar behaviour (residues that disappear and others with variations in their chemical shifts) has also been observed in the complexes formed between several IDPs [39].…”

Section: Resultssupporting

confidence: 73%

“…These results suggest that the narrowing of the conformational states of both proteins, or, alternatively, the desolvation of the binding surface of Nupr1 induced by DNA binding was different to that occurring when the sole protein target was the isolated MSL1; this finding could be probably due to the different size of both proteins. Large and negative values of Δ S have been observed in binding involving IDPs leading to “fuzzy” complexes ([39] and references therein).…”

Section: Discussionmentioning

confidence: 99%

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Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity

et al. 2013

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The stress protein Nupr1 is a highly basic, multifunctional, intrinsically disordered protein (IDP). MSL1 is a histone acetyl transferase-associated protein, known to intervene in the dosage compensation complex (DCC). In this work, we show that both Nupr1 and MSL1 proteins were recruited and formed a complex into the nucleus in response to DNA-damage, which was essential for cell survival in reply to cisplatin damage. We studied the interaction of Nupr1 and MSL1, and their binding affinities to DNA by spectroscopic and biophysical methods. The MSL1 bound to Nupr1, with a moderate affinity (2.8 µM) in an entropically-driven process. MSL1 did not bind to non-damaged DNA, but it bound to chemically-damaged-DNA with a moderate affinity (1.2 µM) also in an entropically-driven process. The Nupr1 protein bound to chemically-damaged-DNA with a slightly larger affinity (0.4 µM), but in an enthalpically-driven process. Nupr1 showed different interacting regions in the formed complexes with Nupr1 or DNA; however, they were always disordered (“fuzzy”), as shown by NMR. These results underline a stochastic description of the functionality of the Nupr1 and its other interacting partners.

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Section: Resultssupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity

et al. 2013

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“…Such affinity is relatively small, but we believe that this low value is necessary to obtain a proper regulation of the several pathways where NUPR1 intervenes (32), achieving a high specificity despite a low affinity. Affinities with a similar order of magnitude (i.e., in the range 1-10 μM) have also been described in the formation of "fuzzy" complexes, involving at least an IDP, which remains disordered upon binding (49,50).…”

Section: Structural Determinants Of the C-ring1b/nupr1 Interaction Inmentioning

confidence: 85%

Intrinsically disordered chromatin protein NUPR1 binds to the C-terminal region of Polycomb RING1B

Santofimia‐Castaño

Rizzuti

Pey

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often associated with diseases in humans. The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the development and progression of pancreatic cancer; however, the details of such functions are unknown. Polycomb proteins are involved in specific transcriptional cascades and gene silencing. One of the proteins of the Polycomb complex is the Ring finger protein 1 (RING1). RING1 is related to aggressive tumor features in multiple cancer types. In this work we characterized the interaction between NUPR1 and the paralogue RING1B in vitro, in silico, and in cellulo. The interaction occurred through the C-terminal region of RING1B (C-RING1B), with an affinity in the low micromolar range (∼10 μM). The binding region of NUPR1, mapped by NMR, was a hydrophobic polypeptide patch at the 30s region of its sequence, as pinpointed by computational results and site-directed mutagenesis at Ala33. The association between C-RING1B and wild-type NUPR1 also occurred in cellulo as tested by protein ligation assays; this interaction is inhibited by trifluoperazine, a drug known to hamper binding of wild-type NUPR1 with other proteins. Furthermore, the Thr68Gln and Ala33Gln/Thr68Gln mutants had a reduction in the binding toward C-RING1B as shown by in vitro, in silico, and in cellulo studies. This is an example of a well-folded partner of NUPR1, because its other interacting proteins are also unfolded. We hypothesize that NUPR1 plays an active role in chromatin remodeling and carcinogenesis, together with Polycomb proteins.G ene expression control occurs through the combined activities of transcription factors and chromatin regulators, considered as effectors of epigenetic mechanisms. Posttranslational modifications of nucleosomal histones, DNA methylation, local compaction, and long-range interactions determine a variety of chromatin structures that can affect the transcriptional output.A group of chromatin regulators are the Polycomb Repressive complexes (PRCs) (1, 2). These Polycomb group (PcG) proteins are encoded by genes initially discovered over 60 years ago as repressors of the Hox genes in Drosophila (3). The PcG proteins form two main silencing heteromeric complexes called PRC1 and PRC2; both are highly conserved in eukaryotes and either in isolation or synergistically can silence genes (4, 5). The catalytic functions of both complexes include ubiquitin-ligase (H3K119ub1) and methyltransferase activity (H3K27Me3), respectively. In mammals, the PRC2 core is formed by, at least, four heteromeric units, one of which is EZH2 (or its paralog, EZH1), the methyltransferase that catalyzes the trimethylation of histone H3 at Lys27 (5). This modification can act as an anchoring site of PRC1 complexes containing chromobox (CBX) proteins. These CBX proteins recruit PRC1 complex onto PRC2-enriched chromatin, facilitating the monoubiquitylation. The PRC1-dependent monoubiquitylation at Lys119 of histone H2A correlates with transc...

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“…Recently, two new PTMA variants (iso b and pseudogene 7) lack of nuclear localization signal (NLS) were isolated and identified from CD8 + T cells and cervicovaginal lavage with potent anti‐HIV‐1 activity, which were suggested to be innate immune mediators involved in immune surveillance . PTMA can induce the import of Kelch‐like ECH‐associated protein 1 (Keap1) into the nucleus to inhibit nuclear factor erythroid 2‐related factor 2 (Nrf2)‐mediated antioxidant response through Nrf2 degradation . From our previous studies, we found that not only PTMA could be detected in the nucleus of the tumor cell, but also in the cytoplasm.…”

Section: Introductionmentioning

confidence: 99%

Prothymosin‐α enhances phosphatase and tensin homolog expression and binds with tripartite motif‐containing protein 21 to regulate Kelch‐like ECH‐associated protein 1/nuclear factor erythroid 2‐related factor 2 signaling in human bladder cancer

et al. 2019

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Prothymosin‐α ( PTMA ) is a small, acidic protein that is usually transported into the nucleus and involves many cellular and immunological functions. Previous studies demonstrated that aberrant location of PTMA expression exists in human bladder cancer, but the role of PTMA protein expression remains elusive. In this study, we created ectopic nuclear or cytoplasmic PTMA expression in human bladder cancer cells by infecting lentiviruses carrying wild type or deleted nuclear localization signal of the PTMA gene. The in vivo tumorigenesis assay showed PTMA protein with deleted nuclear localization signal promotes J82 xenograft tumor growth in mice and shortens their survival more so than the wild type. Chromatin immunoprecipitation showed that wild‐type PTMA protein binds to the PTEN promoter and enhances phosphatase and tensin homolog ( PTEN ) expression. Through immunoblot proteomics and in vivo ubiquitination studies, PTMA protein can bind with tripartite motif‐containing protein 21 ( TRIM 21) and block its ubiquitination. Also, TRIM 21 can downregulate both forms of PTMA protein. In human bladder tumors, loss of nuclear PTMA expression was an unfavorable prognostic indicator for shorter disease‐free survival (hazard ratio, 1.54; P = 0.009). Our data support that nuclear PTMA protein serves as a tumor suppressor in bladder cancer through upregulating PTEN and orchestrating TRIM 21 for the regulation of Nrf2 signaling.

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Fuzzy Complex Formation between the Intrinsically Disordered Prothymosin α and the Kelch Domain of Keap1 Involved in the Oxidative Stress Response

Cited by 38 publications

References 105 publications

Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity

Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity

Intrinsically disordered chromatin protein NUPR1 binds to the C-terminal region of Polycomb RING1B

Prothymosin‐α enhances phosphatase and tensin homolog expression and binds with tripartite motif‐containing protein 21 to regulate Kelch‐like ECH‐associated protein 1/nuclear factor erythroid 2‐related factor 2 signaling in human bladder cancer

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