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Journal of molecular biology 15건

  1. [해외논문]   Contents List   SCI SCIE


    Journal of molecular biology v.429 no.22 ,pp. iii - iv , 2017 , 0022-2836 ,

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  2. [해외논문]   Editorial Board   SCI SCIE


    Journal of molecular biology v.429 no.22 ,pp. IFC - IFC , 2017 , 0022-2836 ,

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  3. [해외논문]   Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions   SCI SCIE

    Cohen, Ariel (Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel ) , Rosenthal, Eran (The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel ) , Shifman, Julia M. (Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel)
    Journal of molecular biology v.429 no.22 ,pp. 3353 - 3362 , 2017 , 0022-2836 ,

    초록

    Abstract Ubiquitin is a small protein that enables one of the most common post-translational modifications, where the whole ubiquitin molecule is attached to various target proteins, forming mono- or polyubiquitin conjugations. As a prototypical multispecific protein, ubiquitin interacts non-covalently with a variety of proteins in the cell, including ubiquitin-modifying enzymes and ubiquitin receptors that recognize signals from ubiquitin-conjugated substrates. To enable recognition of multiple targets and to support fast dissociation from the ubiquitin modifying enzymes, ubiquitin/protein interactions are characterized with low affinities, frequently in the higher μM and lower mM range. To determine how structure encodes low binding affinity of ubiquitin/protein complexes, we analyzed structures of more than a hundred such complexes compiled in the Ubiquitin Structural Relational Database. We calculated various structure-based features of ubiquitin/protein binding interfaces and compared them to the same features of general protein–protein interactions (PPIs) with various functions and generally higher affinities. Our analysis shows that ubiquitin/protein binding interfaces on average do not differ in size and shape complementarity from interfaces of higher-affinity PPIs. However, they contain fewer favorable hydrogen bonds and more unfavorable hydrophobic/charge interactions. We further analyzed how binding interfaces change upon affinity maturation of ubiquitin toward its target proteins. We demonstrate that while different features are improved in different experiments, the majority of the evolved complexes exhibit better shape complementarity and hydrogen bond pattern compared to wild-type complexes. Our analysis helps to understand how low-affinity PPIs have evolved and how they could be converted into high-affinity PPIs. Highlights We compared structural features of Ub/target complexes to those of other PPIs. Ub/target binding interfaces display on average similar size to other PPIs. Ub/target interfaces contain fewer H bonds and more charge/hydrophobic interactions. Affinity maturation of Ub improves hydrogen bond pattern and surface complementarity. Our findings help to understand how low-affinity PPIs have evolved. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  4. [해외논문]   RING-Between-RING E3 Ligases: Emerging Themes amid the Variations   SCI SCIE

    Dove, Katja K. (Corresponding author.) , Klevit, Rachel E.
    Journal of molecular biology v.429 no.22 ,pp. 3363 - 3375 , 2017 , 0022-2836 ,

    초록

    Abstract Covalent, reversible, post-translational modification of cellular proteins with the small modifier, ubiquitin (Ub), regulates virtually every known cellular process in eukaryotes. The process is carried out by a trio of enzymes: a Ub-activating (E1) enzyme, a Ub-conjugating (E2) enzyme, and a Ub ligase (E3) enzyme. RING-in-Between-RING (RBR) E3s constitute one of three classes of E3 ligases and are defined by a RING-HECT-hybrid mechanism that utilizes a E2-binding RING domain and a second domain (called RING2) that contains an active site Cys required for the formation of an obligatory E3~Ub intermediate. Albeit a small class, RBR E3s in humans regulate diverse cellular process. This review focuses on non-Parkin members such as HOIP/HOIL-1L (the only E3s known to generate linear Ub chains), HHARI and TRIAD1, both of which have been recently demonstrated to work together with Cullin RING E3 ligases. We provide a brief historical background and highlight, summarize, and discuss recent developments in the young field of RBR E3s. Insights reviewed here include new understandings of the RBR Ub-transfer mechanism, specifically the role of RING1 and various Ub-binding sites, brief structural comparisons among members, and different modes of auto-inhibition and activation. Highlights Intramolecular contacts cause auto-inhibition of RBRs; release requires domain rearrangements. Mechanism of activation differs among RBR E3s. RBR RING1 domains bind an E2~Ub in an open conformation. Open E2~Ubs have low aminolysis activity ensuring transfer of Ub from E2~Ubs to the E3 active site. Contacts between the Ub of E2~Ub and RBR domains are required to generate the E3~Ub. RBR E3s (and not their E2s) dictate the type of Ub product made to the substrate. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  5. [해외논문]   SUMO in the DNA Double-Stranded Break Response: Similarities, Differences, and Cooperation with Ubiquitin   SCI SCIE

    Morris, Joanna R. (Corresponding author.) , Garvin, Alexander J.
    Journal of molecular biology v.429 no.22 ,pp. 3376 - 3387 , 2017 , 0022-2836 ,

    초록

    Abstract In recent years, our knowledge of the varied role that ubiquitination plays in promoting signal amplification, novel protein interactions, and protein turnover has progressed rapidly. This is particularly remarkable in the examination of how DNA double-stranded breaks (DSBs) are repaired, with many components of the ubiquitin (Ub) conjugation, de-conjugation, and recognition machinery now identified as key factors in DSB repair. In addition, a member of the Ub-like family, small Ub-like modifier (SUMO), has also been recognised as integral for efficient repair. Here, we summarise our emerging understanding of SUMOylation both as a distinct modification and as a cooperative modification with Ub, using the cellular response to DNA DSBs as the primary setting to compare these modifications. Highlights SUMO and Ub have both distinct and overlapping functions in DSB repair. Mixed SUMO~Ub polymers impart additional layers of complexity and specificity to DSB repair such as the dual recognition of mixed conjugates by “reader” proteins such as RAP80. SUMOylation cooperates with ubiquitination through promoting recruitment and regulating the activity of Ub ligases and de-ubiquitinating enzymes involved in DSB repair. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  6. [해외논문]   Advancing our Understanding of Ubiquitination Using the Ub-Toolkit   SCI SCIE

    Witting, Katharina F. (Corresponding author.) , Mulder, Monique P.C. , Ovaa, Huib
    Journal of molecular biology v.429 no.22 ,pp. 3388 - 3394 , 2017 , 0022-2836 ,

    초록

    Abstract Post-translational protein modification by ubiquitin (Ub) and Ub-like modifiers is orchestrated by the sequential action of Ub-activating, -conjugating, and -ligating enzymes to regulate a vast array of fundamental biological processes. Unsurprisingly, the dysregulation of the intricate interplay between ubiquitination and deubiquitination gives rise to numerous pathologies, most notably cancer and neurodegenerative diseases. While activity-based probes (ABPs) and assay reagents have been extensively developed and applied for deubiquitinating enzymes, similar tools for the Ub cascade have only recently emerged. Given the recent efforts to develop inhibitors for the Ub system, the urgency for developing ABPs and assay reagents is imminent. In this light, we comprehensively discuss the currently available ABPs with a focus on the newly developed reagents targeting the Ub cascade while illustrating their potential applications. Highlights Ubiquitination regulates nearly all cellular events, and deregulation contributes to disease. ABPs target the active site of enzymes allowing their identification, isolation, and characterization. Several ABPs specific for the Ub cascade have recently been reported. Novel tools for assaying E1, E2, and E3 enzyme activity are required for inhibitor development. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  7. [해외논문]   Regulation of USP7: A High Incidence of E3 Complexes   SCI SCIE

    Kim, Robbert Q. (Corresponding author.) , Sixma, Titia K.
    Journal of molecular biology v.429 no.22 ,pp. 3395 - 3408 , 2017 , 0022-2836 ,

    초록

    Abstract Ubiquitin (Ub) conjugation is a critical signalling process in eukaryotic cells. The precise regulation of deubiquitination is an important component of this signalling cascade. Here, we discuss how USP7 (or Herpes-Associated Ubiquitin-Specific Protease, HAUSP), one of the most abundant deubiquitinating enzymes, is regulated by complex formation with regulatory proteins and targets. Full activity of USP7 requires that its C-terminal Ub-like domains fold back onto the catalytic domain, to allow the remodelling of the active site to a catalytically competent state by the very C-terminal peptide. This regulatory mode can be modulated by complex formation with other proteins. USP7 is found in a large number of relatively stable complexes with different possible functions. Complex formation can provide recruitment of a target, bring in an E3 Ub ligase, or modulate the activation of the deubiquitinating enzyme activity. These complexes make up potential cellular “switches”, using their (de)ubiquitination ability to switch pathways on or off upon cellular signals. Here, we summarize what is known for USP7 complexes, focussing on the prevalence of E3 Ub ligases and how complex formation can affect Ub switches. Highlights USP7 activity is regulated by itself and interacting proteins. Many of the USP7 interacting proteins are E3 ubiquitin ligases. E3/USP7 complexes can form cellular switches. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  8. [해외논문]   Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics   SCI SCIE

    Lee, Brian L. (Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada ) , Singh, Anamika (Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada ) , Mark Glover, J.N. (Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada ) , Hendzel, Michael J. (Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada ) , Spyracopoulos, Leo (Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada)
    Journal of molecular biology v.429 no.22 ,pp. 3409 - 3429 , 2017 , 0022-2836 ,

    초록

    Abstract Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information and prevent development of disease. The most deleterious damage is a double-strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end-joining (NHEJ) and homologous recombination (HR), which are components of the DNA damage response system. NHEJ is an error-prone first line of defense, whereas HR invokes error-free repair and is the focus of this review. The functions of the protein components of HR-driven DNA repair are regulated by the coordinated action of post-translational modifications including lysine acetylation, phosphorylation, ubiquitination, and SUMOylation. The latter two mechanisms are fundamental for recognition of DSBs and reorganizing chromatin to facilitate repair. We focus on the structures and molecular mechanisms for the protein components underlying synthesis, recognition, and cleavage of K63-linked ubiquitin chains, which are abundant at damage sites and obligatory for DSB repair. The forward flux of the K63-linked ubiquitination cascade is driven by the combined activity of E1 enzyme, the heterodimeric E2 Mms2-Ubc13, and its cognate E3 ligases RNF8 and RNF168, which is balanced through the binding and cleavage of chains by the deubiquitinase BRCC36, and the proteasome, and through the binding of chains by recognition modules on repair proteins such as RAP80. We highlight a number of aspects regarding our current understanding for the role of kinetics and dynamics in determining the function of the enzymes and chain recognition modules that drive K63 ubiquitination. Highlights NHEJ or HR repairs DNA DSBs. HR repair is error-free and regulated by ubiquitination and SUMOylation. K63 ubiquitin chains are abundant at repair sites and obligatory for repair. The flux of the chain-building cascade reshapes the chromatin landscape and facilitates repair. The role of kinetics and dynamics in driving the flux of the chain-building machinery is emerging. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  9. [해외논문]   Regulation of E2s: A Role for Additional Ubiquitin Binding Sites?   SCI SCIE

    Middleton, Adam J. (Corresponding author.) , Wright, Joshua D. , Day, Catherine L.
    Journal of molecular biology v.429 no.22 ,pp. 3430 - 3440 , 2017 , 0022-2836 ,

    초록

    Abstract Attachment of ubiquitin to proteins relies on a sophisticated enzyme cascade that is tightly regulated. The machinery of ubiquitylation responds to a range of signals, which remarkably includes ubiquitin itself. Thus, ubiquitin is not only the central player in the ubiquitylation cascade but also a key regulator. The ubiquitin E3 ligases provide specificity to the cascade and often bind the substrate, while the ubiquitin-conjugating enzymes (E2s) have a pivotal role in determining chain linkage and length. Interaction of ubiquitin with the E2 is important for activity, but the weak nature of these contacts has made them hard to identify and study. By reviewing available crystal structures, we identify putative ubiquitin binding sites on E2s, which may enhance E2 processivity and the assembly of chains of a defined linkage. The implications of these new sites are discussed in the context of known E2–ubiquitin interactions. Highlights E2 enzymes have a critical role in the assembly of ubiquitin chains. E2s have well-established interactions with ubiquitin. Crystal contacts reveal common E2–ubiquitin interactions. New E2–ubiquitin interfaces are adjacent to well-established ubiquitin binding sites. These novel interactions may help regulate E2s. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  10. [해외논문]   Structure and Function of Viral Deubiquitinating Enzymes   SCI SCIE

    Bailey-Elkin, Ben A. (Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada ) , Knaap, Robert C.M. (Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands ) , Kikkert, Marjolein (Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands ) , Mark, Brian L. (Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada)
    Journal of molecular biology v.429 no.22 ,pp. 3441 - 3470 , 2017 , 0022-2836 ,

    초록

    Abstract Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including innate and adaptive immune responses. Ubiquitin-mediated control over these processes can be reversed by cellular deubiquitinating enzymes (DUBs), which remove ubiquitin from cellular targets and depolymerize polyubiquitin chains. The importance of protein ubiquitination to host immunity has been underscored by the discovery of viruses that encode proteases with deubiquitinating activity, many of which have been demonstrated to actively corrupt cellular ubiquitin-dependent processes to suppress innate antiviral responses and promote viral replication. DUBs have now been identified in diverse viral lineages, and their characterization is providing valuable insights into virus biology and the role of the ubiquitin system in host antiviral mechanisms. Here, we provide an overview of the structural biology of these fascinating viral enzymes and their role innate immune evasion and viral replication. Highlights Activation of host innate antiviral responses is largely ubiquitin-dependent. Virus-encoded DUBs can modulate innate immune signaling. Analysis of structurally diverse DUBs of DNA and RNA viruses. Viral DUBs are critical for virus replication and pathogenesis. Therapeutic strategies and vaccination approaches targeting viral DUBs. Graphical Abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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