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1. chinaXiv:201605.01492 [pdf]

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses

De Colibus, Luigi; Spyrou, John A. B.; Ren, Jingshan; Grimes, Jonathan M.; Stuart, David I.; Wang, Xiangxi; Rao, Zihe; Tijsma, Aloys; Neyts, Johan; Leyssen, Pieter; Grimes, Jonathan M.; Stuart, David I.; Puerstinger, Gerhard; Rao, Zihe
Subjects: Biology >> Biophysics

The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity.

submitted time 2016-05-12 Hits1999Downloads1170 Comment 0

2. chinaXiv:201605.01405 [pdf]

Structure of Ljungan virus provides insight into genome packaging of this picornavirus

Zhu, Ling; Ren, Jingshan; Porta, Claudine; Kotecha, Abhay; Siebert, C. Alistair; Fry, Elizabeth E.; Stuart, David I.; Zhu, Ling; Porta, Claudine; Wenham, Hannah; Panjwani, Anusha; Knowles, Nick J.; Tuthill, Tobias J.; Wang, Xiangxi; Rao, Zihe; Ekstrom, Jens-Ola; Lindberg, A. Michael; Rao, Zihe; Stuart, David I.
Subjects: Biology >> Biophysics

Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-angstrom resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.

submitted time 2016-05-12 Hits1714Downloads999 Comment 0

3. 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 Hits1951Downloads1198 Comment 0

4. chinaXiv:201605.01382 [pdf]

A Unique Human Norovirus Lineage with a Distinct HBGA Binding Interface

Liu, Wu; Chen, Yutao; Yang, Yang; Li, Xuemei; Rao, Zihe; Jiang, Xi; Xia, Ming; Tan, Ming; Jiang, Xi; Tan, Ming
Subjects: Biology >> Biophysics

Norovirus (NoV) causes epidemic acute gastroenteritis in humans, whereby histo-blood group antigens (HBGAs) play an important role in host susceptibility. Each of the two major genogroups (GI and GII) of human NoVs recognizes a unique set of HBGAs through a distinct binding interface that is conserved within a genogroup, indicating a distinct evolutionary path for each genogroup. Here, we characterize a Lewis a (Le(a)) antigen binding strain (OIF virus) in the GII. 21 genotype that does not share the conserved GII binding interface, revealing a new evolution lineage with a distinct HBGA binding interface. Sequence alignment showed that the major residues contributing to the new HBGA binding interface are conserved among most members of the GII. 21, as well as a closely related GII. 13 genotype. In addition, we found that glycerol inhibits OIF binding to HBGAs, potentially allowing production of cheap antivirals against human NoVs. Taken together, our results reveal a new evolutionary lineage of NoVs selected by HBGAs, a finding that is important for understanding the diversity and widespread nature of NoVs.

submitted time 2016-05-12 Hits2386Downloads1321 Comment 0

5. 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 Hits1852Downloads1053 Comment 0

6. 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 Hits2011Downloads1180 Comment 0

7. chinaXiv:201605.01313 [pdf]

Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope

Hao, Ning; Chen, Yutao; Liu, Wu; Guan, Xiaotao; Li, Xuemei; Rao, Zihe; Hao, Ning; Xia, Ming; Tan, Ming; Jiang, Xi; Xia, Ming; Jiang, Xi
Subjects: Biology >> Biophysics >> Cell Biology

Human noroviruses (huNoVs) recognize histo-blood group antigens (HBGAs) as attachment factors, in which genogroup (G) I and GII huNoVs use distinct binding interfaces. The genetic and evolutionary relationships of GII huNoVs under selection by the host HBGAs have been well elucidated via a number of structural studies; however, such relationships among GI NoVs remain less clear due to the fact that the structures of HBGA-binding interfaces of only three GI NoVs with similar binding profiles are known. In this study the crystal structures of the P dimers of a Lewis-binding strain, the GI.8 Boxer virus (BV) that does not bind the A and H antigens, in complex with the Lewis b (Le(b)) and Le(y) antigens, respectively, were determined and compared with those of the three previously known GI huNoVs, i.e. GI.1 Norwalk virus (NV), GI.2 FUV258 (FUV) and GI.7 TCH060 (TCH) that bind the A/H/Le antigens. The HBGA binding interface of BV is composed of a conserved central binding pocket (CBP) that interacts with the beta-galactose of the precursor, and a well-developed Le epitope-binding site formed by five amino acids, including three consecutive residues from the long P-loop and one from the S-loop of the P1 subdomain, a feature that was not seen in the other GI NoVs. On the other hand, the H epitope/acetamido binding site observed in the other GI NoVs is greatly degenerated in BV. These data explain the evolutionary path of GI NoVs selected by the polymorphic human HBGAs. While the CBP is conserved, the regions surrounding the CBP are flexible, providing freedom for changes. The loss or degeneration of the H epitope/acetamido binding site and the reinforcement of the Le binding site of the GI.8 BV is a typical example of such change selected by the host Lewis epitope.

submitted time 2016-05-11 Hits1763Downloads976 Comment 0

8. 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 Hits4445Downloads1584 Comment 0

9. 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 Hits1812Downloads1115 Comment 0

10. chinaXiv:201605.01300 [pdf]

Hepatitis A virus and the origins of picornaviruses

Wang, Xiangxi; Gao, Qiang; Sun, Yao; Li, Xuemei; Rao, Zihe; Ren, Jingshan; Stuart, David I.; Fry, Elizabeth E.; Gao, Qiang; Yin, Weidong; Hu, Zhongyu; Wang, Junzhi; Rowlands, David J.; Rowlands, David J.; Stuart, David I.; Rao, Zihe; Rao, Zihe
Subjects: Biology >> Biophysics

Hepatitis A virus(HAV) remains enigmatic, despite 1.4 million cases worldwide annually(1). It differs radically from other picornaviruses, existing in an enveloped form(2) and being unusually stable, both genetically and physically(3), but has proved difficult to study. Here we report high-resolution X-ray structures for the mature virus and the empty particle. The structures of the two particles are indistinguishable, apart from some disorder on the inside of the empty particle. The full virus contains the small viral protein VP4, whereas the empty particle harbours only the uncleaved precursor, VP0. The smooth particle surface is devoid of depressions that might correspond to receptor-binding sites. Peptide scanning data extend the previously reported VP3 antigenic site4, while structure-based predictions(5) suggest further epitopes. HAV contains no pocket factor and can withstand remarkably high temperature and low pH, and empty particles are even more robust than full particles. The virus probably uncoats via a novel mechanism, being assembled differently to other picornaviruses. It utilizes a VP2 'domain swap' characteristic of insect picorna-like viruses(6,7), and structure-based phylogenetic analysis places HAV between typical picornaviruses and the insect viruses. The enigmatic properties of HAV may reflect its position as a link between 'modern' picornaviruses and the more 'primitive' precursor insect viruses; for instance, HAV retains the ability to move from cell-to-cell by transcytosis(8,9).

submitted time 2016-05-11 Hits1805Downloads1130 Comment 0

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