Browsing by Subject "Protein Interaction Domains and Motifs"

Now showing 1 - 6 of 6
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    A Sweet Embrace: Control of Protein-Protein Interactions by O-Linked β-N-Acetylglucosamine.
    (Biochemistry, 2018-01) Tarbet, Heather J; Toleman, Clifford A; Boyce, Michael
    O-Linked β-N-acetylglucosamine (O-GlcNAc) is a critical post-translational modification (PTM) of thousands of intracellular proteins. Reversible O-GlcNAcylation governs many aspects of cell physiology and is dysregulated in numerous human diseases. Despite this broad pathophysiological significance, major aspects of O-GlcNAc signaling remain poorly understood, including the biochemical mechanisms through which O-GlcNAc transduces information. Recent work from many laboratories, including our own, has revealed that O-GlcNAc, like other intracellular PTMs, can control its substrates' functions by inhibiting or inducing protein-protein interactions. This dynamic regulation of multiprotein complexes exerts diverse downstream signaling effects in a range of processes, cell types, and organisms. Here, we review the literature about O-GlcNAc-regulated protein-protein interactions and suggest important questions for future studies in the field.
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    Calmodulin dissociation regulates Myo5 recruitment and function at endocytic sites.
    (EMBO J, 2010-09-01) Grötsch, Helga; Giblin, Jonathan P; Idrissi, Fatima-Zahra; Fernández-Golbano, Isabel-María; Collette, John R; Newpher, Thomas M; Robles, Virginia; Lemmon, Sandra K; Geli, María-Isabel
    Myosins-I are conserved proteins that bear an N-terminal motor head followed by a Tail Homology 1 (TH1) lipid-binding domain. Some myosins-I have an additional C-terminal extension (C(ext)) that promotes Arp2/3 complex-dependent actin polymerization. The head and the tail are separated by a neck that binds calmodulin or calmodulin-related light chains. Myosins-I are known to participate in actin-dependent membrane remodelling. However, the molecular mechanisms controlling their recruitment and their biochemical activities in vivo are far from being understood. In this study, we provided evidence suggesting the existence of an inhibitory interaction between the TH1 domain of the yeast myosin-I Myo5 and its C(ext). The TH1 domain prevented binding of the Myo5 C(ext) to the yeast WIP homologue Vrp1, Myo5 C(ext)-induced actin polymerization and recruitment of the Myo5 C(ext) to endocytic sites. Our data also indicated that calmodulin dissociation from Myo5 weakened the interaction between the neck and TH1 domains and the C(ext). Concomitantly, calmodulin dissociation triggered Myo5 binding to Vrp1, extended the myosin-I lifespan at endocytic sites and activated Myo5-induced actin polymerization.
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    Domain-oriented edge-based alignment of protein interaction networks.
    (Bioinformatics, 2009-06-15) Guo, Xin; Hartemink, Alexander J
    MOTIVATION: Recent advances in high-throughput experimental techniques have yielded a large amount of data on protein-protein interactions (PPIs). Since these interactions can be organized into networks, and since separate PPI networks can be constructed for different species, a natural research direction is the comparative analysis of such networks across species in order to detect conserved functional modules. This is the task of network alignment. RESULTS: Most conventional network alignment algorithms adopt a node-then-edge-alignment paradigm: they first identify homologous proteins across networks and then consider interactions among them to construct network alignments. In this study, we propose an alternative direct-edge-alignment paradigm. Specifically, instead of explicit identification of homologous proteins, we directly infer plausibly alignable PPIs across species by comparing conservation of their constituent domain interactions. We apply our approach to detect conserved protein complexes in yeast-fly and yeast-worm PPI networks, and show that our approach outperforms two recent approaches in most alignment performance metrics. AVAILABILITY: Supplementary material and source code can be found at http://www.cs.duke.edu/ approximately amink/.
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    DOMINE: a comprehensive collection of known and predicted domain-domain interactions.
    (Nucleic acids research, 2011-01) Yellaboina, Sailu; Tasneem, Asba; Zaykin, Dmitri V; Raghavachari, Balaji; Jothi, Raja
    DOMINE is a comprehensive collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. These additions bring the total number of unique DDIs in the updated version to 26,219 among 5140 unique Pfam domains, a 23% increase compared to 20,513 unique DDIs among 4346 unique domains in the previous version. The updated version now contains 6634 known DDIs, and features a new classification scheme to assign confidence levels to predicted DDIs. DOMINE will serve as a valuable resource to those studying protein and domain interactions. Most importantly, DOMINE will not only serve as an excellent reference to bench scientists testing for new interactions but also to bioinformaticans seeking to predict novel protein-protein interactions based on the DDIs. The contents of the DOMINE are available at http://domine.utdallas.edu.
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    SPOP Promotes Nanog Destruction to Suppress Stem Cell Traits and Prostate Cancer Progression.
    (Developmental cell, 2019-02) Zhang, Jinfang; Chen, Ming; Zhu, Yasheng; Dai, Xiangpeng; Dang, Fabin; Ren, Junming; Ren, Shancheng; Shulga, Yulia V; Beca, Francisco; Gan, Wenjian; Wu, Fei; Lin, Yu-Min; Zhou, Xiaobo; DeCaprio, James A; Beck, Andrew H; Lu, Kun Ping; Huang, Jiaoti; Zhao, Cheryl; Sun, Yinghao; Gao, Xu; Pandolfi, Pier Paolo; Wei, Wenyi
    Frequent SPOP mutation defines the molecular feature underlying one of seven sub-types of human prostate cancer (PrCa). However, it remains largely elusive how SPOP functions as a tumor suppressor in PrCa. Here, we report that SPOP suppresses stem cell traits of both embryonic stem cells and PrCa cells through promoting Nanog poly-ubiquitination and subsequent degradation. Mechanistically, Nanog, but not other pluripotency-determining factors including Oct4, Sox2, and Klf4, specifically interacts with SPOP via a conservative degron motif. Importantly, cancer-derived mutations in SPOP or at the Nanog-degron (S68Y) disrupt SPOP-mediated destruction of Nanog, leading to elevated cancer stem cell traits and PrCa progression. Notably, we identify the Pin1 oncoprotein as an upstream Nanog regulator that impairs its recognition by SPOP and thereby stabilizes Nanog. Thus, Pin1 inhibitors promote SPOP-mediated destruction of Nanog, which provides the molecular insight and rationale to use Pin1 inhibitor(s) for targeted therapies of PrCa patients with wild-type SPOP.
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    Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain.
    (Nucleic Acids Res, 2014-12-16) Wojtaszek, Jessica L; Wang, Su; Kim, Hyungjin; Wu, Qinglin; D'Andrea, Alan D; Zhou, Pei
    FAAP20 is an integral component of the Fanconi anemia core complex that mediates the repair of DNA interstrand crosslinks. The ubiquitin-binding capacity of the FAAP20 UBZ is required for recruitment of the Fanconi anemia complex to interstrand DNA crosslink sites and for interaction with the translesion synthesis machinery. Although the UBZ-ubiquitin interaction is thought to be exclusively encapsulated within the ββα module of UBZ, we show that the FAAP20-ubiquitin interaction extends beyond such a canonical zinc-finger motif. Instead, ubiquitin binding by FAAP20 is accompanied by transforming a disordered tail C-terminal to the UBZ of FAAP20 into a rigid, extended β-loop that latches onto the complex interface of the FAAP20 UBZ and ubiquitin, with the invariant C-terminal tryptophan emanating toward I44(Ub) for enhanced binding specificity and affinity. Substitution of the C-terminal tryptophan with alanine in FAAP20 not only abolishes FAAP20-ubiquitin binding in vitro, but also causes profound cellular hypersensitivity to DNA interstrand crosslink lesions in vivo, highlighting the indispensable role of the C-terminal tail of FAAP20, beyond the compact zinc finger module, toward ubiquitin recognition and Fanconi anemia complex-mediated DNA interstrand crosslink repair.