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Articles by Jun Qin
Total Records ( 6 ) for Jun Qin
  Bo Meng , Wei Huang and Jun Qin
  Soundness and coercion resistance are the important and intricate security requirements for remote voting protocols. In this study firstly the review of the formal methods of security protocols is introduced, then applied pi calculus and the automatic tool ProVerif are examined. Thirdly Meng et al. protocol recently proposed is modeled in applied pi calculus. Finally soundness and coercion resistance are verified with automatic tool ProVerif. The result we obtain is that Meng et al. protocol has coercion resistance. But it has not soundness because ProVerif found an attack on soundness. Finally the improvement of Meng et al. protocol is proposed and also modeled in applied pi calculus and automatically analyzed in ProVerif. The result we get is that the improvement of protocol has soundness. To our best knowledge, the first automated analysis of Meng et al. protocol for an unbounded number of honest and corrupted voters is finished.
  Panagiota Karagianni , Larbi Amazit , Jun Qin and Jiemin Wong
  Methylation of histone H3 on lysine 9 is critical for diverse biological processes including transcriptional repression, heterochromatin formation, and X inactivation. The biological effects of histone methylation are thought to be mediated by effector proteins that recognize and bind to specific patterns of methylation. Using an unbiased in vitro biochemical approach, we have identified ICBP90, a transcription and cell cycle regulator, as a novel methyl K9 H3-specific binding protein. ICBP90 and its murine homologue Np95 are enriched in pericentric heterochromatin of interphase nuclei, and this localization is dependent on H3K9 methylation. Specific binding of ICBP90 to methyl K9 H3 depends on two functional domains, a PHD (plant homeodomain) finger that defines the binding specificity and an SRA (SET- and RING-associated) domain that promotes binding activity. Furthermore, we present evidence that ICBP90 is required for proper heterochromatin formation in mammalian cells.
  Isao Kuraoka , Shinsuke Ito , Tadashi Wada , Mika Hayashida , Lily Lee , Masafumi Saijo , Yoshimichi Nakatsu , Megumi Matsumoto , Tsukasa Matsunaga , Hiroshi Handa , Jun Qin , Yoshihiro Nakatani and Kiyoji Tanaka
  Nucleotide excision repair is a versatile repair pathway that counteracts the deleterious effects of various DNA lesions. In nucleotide excision repair, there is a transcription-coupled repair (TCR) pathway that focuses on DNA damage that blocks RNA polymerase IIo in transcription elongation. XAB2 (XPA-binding protein 2), containing tetratricopeptide repeats, has been isolated by virtue of its ability to interact with xeroderma pigmentosum group A protein (XPA). Moreover, XAB2 has been shown to interact with Cockayne syndrome group A and B proteins (CSA and CSB) and RNA polymerase II, as well as XPA, and is involved in TCR and transcription. Here we purified XAB2 as a multimeric protein complex consisting of hAquarius, XAB2, hPRP19, CCDC16, hISY1, and PPIE, which are involved in pre-mRNA splicing. Knockdown of XAB2 with small interfering RNA in HeLa cells resulted in a hypersensitivity to killing by UV light and a decreased recovery of RNA synthesis after UV irradiation and regular RNA synthesis. Enhanced interaction of XAB2 with RNA polymerase IIo or XPA was observed in cells treated with DNA-damaging agents, indicating DNA damage-responsive activity of the XAB2 complex. These results indicated that the XAB2 complex is a multifunctional factor involved in pre-mRNA splicing, transcription, and TCR.

  Michael E. Greenberg , Xin-Min Li , Bogdan G. Gugiu , Xiaodong Gu , Jun Qin , Robert G. Salomon and Stanley L. Hazen
  An essential feature of the innate immune system is maintaining cellular homeostasis by identifying and removing senescent and apoptotic cells and modified lipoproteins. Identification is achieved through the recognition of molecular patterns, including structurally distinct oxidized phospholipids, on target cells by macrophage receptors. Both the structural nature of the molecular patterns recognized and their orientation within membranes has remained elusive. We recently described the membrane conformation of an endogenous oxidized phospholipid ligand for macrophage scavenger receptor CD36, where the truncated oxidized sn-2 fatty acid moiety protrudes into the aqueous phase, rendering it accessible for recognition. Herein we examine the generality of this conformational motif for peroxidized glycerophospholipids within membranes. Our data reveal that the addition of a polar oxygen atom on numerous peroxidized fatty acids reorients the acyl chain, whereby it no longer remains buried within the membrane interior but rather protrudes into the aqueous compartment. Moreover, we show that neither a conformational change in the head group relative to the membrane surface nor the presence of a polar head group is essential for CD36 recognition of free oxidized phospholipid ligands within membranes. Rather, our results suggest the following global phenomenon. As cellular membranes undergo lipid peroxidation, such as during senescence or apoptosis, previously hydrophobic portions of fatty acids will move from the interior of the lipid bilayer to the aqueous exterior. This enables physical contact between pattern recognition receptor and molecular pattern ligand. Cell membranes thus "grow whiskers" as phospholipids undergo peroxidation, and many of their oxidized fatty acids protrude at the surface.
  Hao Luo , Yehua Li , Jung- Jung Mu , Jinglan Zhang , Toru Tonaka , Yasuo Hamamori , Sung Yun Jung , Yi Wang and Jun Qin
  Structure maintenance of chromosome 1 (SMC1) is phosphorylated by ataxia telangiectasia-mutated (ATM) in response to ionizing radiation (IR) to activate intra-S phase checkpoint. A role of CK2 in DNA damage response has been implicated in many previous works, but the molecular mechanism for its activation is not clear. In the present work, we report that SMC3 is phosphorylated at Ser-1067 and Ser-1083 in vivo. Ser-1083 phosphorylation is IR-inducible, depends on ATM and Nijmegen breakage syndrome 1 (NBS1), and is required for intra-S phase checkpoint. Interestingly, Ser-1067 phosphorylation is constitutive and is not induced by IR but also affects intra-S phase checkpoint. Phosphorylation of Ser-1083 is weakened in cells expressing S1067A mutant, suggesting interplay between Ser-1067 and Ser-1083 phosphorylation in DNA damage response. Consistently, small interfering RNA knockdown of CK2 leads to attenuated phosphorylation of Ser-1067 as well as intra-S phase checkpoint defect. Our data provide evidence that phosphorylation of a core cohesin subunit SMC3 by ATM plays an important role in DNA damage response and suggest that a constitutive phosphorylation by CK2 may affect intra-S phase checkpoint by modulating SMC3 phosphorylation by ATM.
  Xiaoxia Wang , Koichi Fukuda , In-Ja Byeon , Algirdas Velyvis , Chuanyue Wu , Angela Gronenborn and Jun Qin
  α-Parvin is an essential component of focal adhesions (FAs), which are large multiprotein complexes that link the plasma membrane and actin cytoskeleton. α-Parvin contains two calponin homology (CH) domains and its C-terminal CH2 domain binds multiple targets including paxillin LD motifs for regulating the FA network and signaling. Here we describe the solution structure of α-parvin CH2 bound to paxillin LD1. We show that although CH2 contains the canonical CH-fold, a previously defined N-terminal linker forms an α-helix that packs unexpectedly with the C-terminal helix of CH2, resulting in a novel variant of the CH domain. Importantly, such packing generates a hydrophobic surface that recognizes the Leu-rich face of paxillin-LD1, and the binding pattern differs drastically from the classical paxillin-LD binding to four-helix bundle proteins such as focal adhesion kinase. These results define a novel modular recognition mode and reveal how α-parvin associates with paxillin to mediate the FA assembly and signaling.
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