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1. chinaXiv:201605.01398 [pdf]

Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus

Kong, Lingying; Yan, Lingming; Lou, Zhiyong; Rao, Zihe; Shaw, Neil; Rao, Zihe; Shaw, Neil; Rao, Zihe
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Papain-like protease (PLpro) of coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses. Avian infectious bronchitis virus (IBV), the causative agent of bronchitis in chicken that results in huge economic losses every year in the poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade Lys(48)- and Lys(63)-linked polyubiquitin chains to monoubiquitin but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15-angstrom resolution. The overall structure is reminiscent of the structure of severe acute respiratory syndrome CoV PLpro. However, unlike the severe acute respiratory syndrome CoV PLpro that lacks blocking loop (BL) 1 of deubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys(101), His(264), and Asp(275) is regulated by the flexible BL2. A model of ubiquitin-bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 subsites as well as residues interacting with the beta-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-7-amino-4-methylcoumarin and LRGG-7-amino-4-methylcoumarin with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.

submitted time 2016-05-12 Hits1805Downloads1114 Comment 0

2. chinaXiv:201605.01380 [pdf]

Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex

Ma, Yuanyuan; Gao, Yan; Lou, Zhiyong; Yan, Liming; Rao, Zihe; Wu, Lijie; Zhang, Rongguang; Rao, Zihe; Shaw, Neil; Sun, Yuna; Zhang, Rongguang; Rao, Zihe; Wang, Jin; Rao, Zihe; Wang, Jin; Rao, Zihe; Wang, Jin; Rao, Zihe
Subjects: Biology >> Biophysics

Nonstructural protein 14 (nsp14) of coronaviruses (CoV) is important for viral replication and transcription. The N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping. The molecular basis of both these functions is unknown. Here, we describe crystal structures of severe acute respiratory syndrome (SARS)-CoV nsp14 in complex with its activator nonstructural protein10 (nsp10) and functional ligands. One molecule of nsp10 interacts with ExoN of nsp14 to stabilize it and stimulate its activity. Although the catalytic core of nsp14 ExoN is reminiscent of proofreading exonucleases, the presence of two zinc fingers sets it apart from homologs. Mutagenesis studies indicate that both these zinc fingers are essential for the function of nsp14. We show that a DEEDh (the five catalytic amino acids) motif drives nucleotide excision. The N7-MTase domain exhibits a noncanonical MTase fold with a rare beta-sheet insertion and a peripheral zinc finger. The cap-precursor guanosine-P3-adenosine-5', 5'-triphosphate and S-adenosyl methionine bind in proximity in a highly constricted pocket between two beta-sheets to accomplish methyl transfer. Our studies provide the first glimpses, to our knowledge, into the architecture of the nsp14-nsp10 complex involved in RNA viral proofreading.

submitted time 2016-05-12 Hits1687Downloads944 Comment 0

3. chinaXiv:201605.01322 [pdf]

Studies on Inhibition of Proliferation of Enterovirus-71 by Compound YZ-LY-0

Yang, Qingzhan; Shaw, Neil; Rao, Zihe; Lou, Zhiyong; Jie, Qing; Shaw, Neil; Rao, Zihe; Yin, Zheng; Yin, Zheng; Yin, Zheng; Li, Lei; Rao, Zihe; Lou, Zhiyong; Li, Lei; Rao, Zihe; Lou, Zhiyong; Li, Lei; Rao, Zihe; Lou, Zhiyong
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

In recent years, hand-foot-and-mouth disease (HFMD), which is caused by Enteroviruses, has emerged as a serious illness. It affects mainly children under the age of five and results in high fatality rates. Enterovirus 71 (EV71) is the main causative agent of HFMD in China and currently there are no effective anti-viral drugs available to treat HFMD. In the present study, we screened compounds for inhibition of proliferation of EV71. Compound YZ-LY-0 stalled the life cycle of EV71. The inhibitor exhibited EC50 value of 0.29 mu m against SK-EV006 strain of EV71. Notably, YZ-LY-0 had low cytotoxicity (CC50 > 100 mu M) and a high selectivity index (over 300) in Vero and RD cells. YZ-LY-0 in combination with an EV71 RdRp inhibitor or an entry inhibitor showed an antagonistic effect at very low concentrations. However, at higher concentrations the inhibitors exhibited a synergistic effect in inhibiting viral replication. Preliminary results on investigation of the mechanism of inhibition indicate that YZ-LY-0 does not block the entry of the virus in the host cell, but instead inhibits an early stage of EV71 replication. Our studies provide a potential clinical therapeutic option against EV71 infections and suggest that a combined application of YZ-LY-0 with other inhibitors could be more effective in the treatment of HFMD.

submitted time 2016-05-11 Hits1851Downloads1082 Comment 0

4. chinaXiv:201605.01310 [pdf]

Molecular architecture of the ErbB2 extracellular domain homodimer

Hu, Shi; Guo, Huaizu; Qian, Weizhu; Hou, Sheng; Li, Bohua; Guo, Yajun; Hu, Shi; Guo, Huaizu; Qian, Weizhu; Hou, Sheng; Li, Bohua; Guo, Yajun; Hu, Shi; Sun, Yuna; Rao, Zihe; Hu, Shi; Sun, Yuna; Rao, Zihe; Lou, Zhiyong; Hu, Shi
Subjects: Biology >> Biophysics >> Oncology

Human epidermal growth factor receptors (HERs or ErbBs) play crucial roles in numerous cellular processes. ErbB2 is a key member of ErbB family, and its overexpression is recognized as a frequent molecular abnormality. In cancer, this overexpression correlates with aggressive disease and poor patient outcomes. Dimer-dependent phosphorylation is a key event for the signal transduction of ErbBs. However, the molecular mechanism of the dimerization of ErbB2 remains elusive. In the present work, we report the homodimer architecture of the ErbB2 extracellular domain (ECD) which is unique compared with other dimer-models of ErbBs. The structure of the ErbB2 ECD homodimer represents a "back to head" interaction, in which a protruding beta-hairpin arm in domain II of one ErbB2 protomer is inserted into a C-shaped pocket created by domains I-III of the adjacent ErbB2 protomer. This dimerized architecture and its impact on the phosphorylation of ErbB2 intracellular domain were further verified by a mutagenesis study. We also elucidated the different impacts of two clinically administered therapeutic antibodies, trastuzumab and pertuzumab, on ErbB2 dimerization. This information not only provides an understanding of the molecular mechanism of ErbBs dimerization but also elucidates ErbB2-targeted therapy at the molecular level.

submitted time 2016-05-11 Hits4252Downloads1480 Comment 0

5. chinaXiv:201605.01306 [pdf]

Structures of the yeast dynamin-like GTPase Sey1p provide insight into homotypic ER fusion

Yan, Liming; Wang, Wei; Rao, Zihe; Lou, Zhiyong; Sun, Sha; Shi, Juanming; Hu, Xiaoyu; Hu, Junjie; Sun, Sha; Shi, Juanming; Hu, Xiaoyu; Hu, Junjie; Rao, Zihe; Hu, Junjie; Wang, Wei; Wang, Shiyan; Su, Dan; Su, Dan; Rao, Zihe; Lou, Zhiyong
Subjects: Biology >> Biophysics >> Cell Biology

Homotypic membrane fusion of the endoplasmic reticulum is mediated by dynamin-like guanosine triphosphatases (GTPases), which include atlastin (ATL) in metazoans and Sey1p in yeast. In this paper, we determined the crystal structures of the cytosolic domain of Sey1p derived from Candida albicans. The structures reveal a stalk-like, helical bundle domain following the GTPase, which represents a previously unidentified configuration of the dynamin superfamily. This domain is significantly longer than that of ATL and critical for fusion. Sey1p forms a side-by-side dimer in complex with GMP-PNP or GDP/AlF4- but is monomeric with GDP. Surprisingly, Sey1p could mediate fusion without GTP hydrolysis, even though fusion was much more efficient with GTP. Sey1p was able to replace ATL in mammalian cells, and the punctate localization of Sey1p was dependent on its GTPase activity. Despite the common function of fusogenic GTPases, our results reveal unique features of Sey1p.

submitted time 2016-05-11 Hits1641Downloads1006 Comment 0

6. chinaXiv:201605.01253 [pdf]

Cyanohydrin as an Anchoring Group for Potent and Selective Inhibitors of Enterovirus 71 3C Protease

Zhai, Yangyang; Zhao, Xiangshuai; Cui, Zhengjie; Wang, Man; Li, Linfeng; Yang, Xi; Zeng, Debin; Liu, Ying; Shang, Luqing; Yin, Zheng; Zhai, Yangyang; Zhao, Xiangshuai; Cui, Zhengjie; Wang, Man; Li, Linfeng; Yang, Xi; Zeng, Debin; Liu, Ying; Shang, Luqing; Yin, Zheng
Subjects: Biology >> Biophysics

Cyanohydrin derivatives as enterovirus 71 (EV71) 3C protease (3C(pro)) inhibitors have been synthesized and assayed for their biochemical and antiviral activities. Compared with the reported inhibitors, cyanohydrins (1S,2S,2'S,5S)-16 and (1R,2S,2'S,5S)-16 exhibited significantly improved activity and attractive selectivity profiles against other proteases, which were a result of the specific interactions between the cyanohydrin moiety and the catalytic site of 3C(pro). Cyanohydrin as an anchoring group with high selectivity and excellent inhibitory activity represents a useful choice for cysteine protease inhibitors.

submitted time 2016-05-11 Hits1740Downloads1038 Comment 0

7. chinaXiv:201605.00730 [pdf]

Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation

Guo, Yu; Ma, Chao; Wang, Xu; Wang, Xin; Liu, Pi; Lin, Jianping; Guo, Yu; Ma, Chao; Wang, Xu; Wang, Xin; Liu, Pi; Lin, Jianping; Lou, Zhiyong; Lou, Zhiyong; Sun, Yuna; Lou, Zhiyong; Shen, Shu; Deng, Fei; Wang, Hualin; Wang, Wenming
Subjects: Biology >> Biophysics

Hantaviruses, which belong to the genus Hantavirus in the family Bunyaviridae, infect mammals, including humans, causing either hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in humans with high mortality. Hantavirus encodes a nucleocapsid protein (NP) to encapsidate the genome and form a ribonucleoprotein complex (RNP) together with viral polymerase. Here, we report the crystal structure of the core domains of NP (NPcore) encoded by Sin Nombre virus (SNV) and Andes virus (ANDV), which are two representative members that cause HCPS in the New World. The constructs of SNV and ANDV NPcore exclude the N- and C-terminal portions of full polypeptide to obtain stable proteins for crystallographic study. The structure features an N lobe and a C lobe to clamp RNA-binding crevice and exhibits two protruding extensions in both lobes. The positively charged residues located in the RNA-binding crevice play a key role in RNA binding and virus replication. We further demonstrated that the C-terminal helix and the linker region connecting the N-terminal coiled-coil domain and NPcore are essential for hantavirus NP oligomerization through contacts made with two adjacent protomers. Moreover, electron microscopy (EM) visualization of native RNPs extracted from the virions revealed that a monomer-sized NP-RNA complex is the building block of viral RNP. This work provides insight into the formation of hantavirus RNP and provides an understanding of the evolutionary connections that exist among bunyaviruses. IMPORTANCE Hantaviruses are distributed across a wide and increasing range of host reservoirs throughout the world. In particular, hantaviruses can be transmitted via aerosols of rodent excreta to humans or from human to human and cause HFRS and HCPS, with mortalities of 15% and 50%, respectively. Hantavirus is therefore listed as a category C pathogen. Hantavirus encodes an NP that plays essential roles both in RNP formation and in multiple biological functions. NP is also the exclusiv

submitted time 2016-05-05 Hits1751Downloads974 Comment 0

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