In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus

双链RNA病毒是病毒中最大的类群，其中轮状病毒作为双链RNA病毒家族最知名的病毒之一，每年引起接近百万的新生儿死亡，而单链RNA病毒虽然没有双链RNA病毒那么多，但是却包含了许多很有名的病毒：HIV，埃博拉病毒，小核糖核苷酸病毒（包括甲肝病毒HAV、肠道病毒、脊髓灰质炎病毒、口蹄疫病毒、感冒病毒等），SARS病毒，丙肝病毒HCV等等。而且与双链RNA病毒不同的是，单链RNA病毒不会把它们的基因组包裹到预制的外壳蛋白中，而是利用基因组共同装配壳体，关于这个共同组装的过程，科学家们了解的很少。最新研究中，研究人员获取了单链RNA病毒：大肠杆菌噬菌体MS2的冷冻电镜结构（分辨率为3.6Å），并追踪了80%病毒基因组结构，从而发现了这种病毒的壳体共同组装过程中的分子机制，这将为解析核蛋白复合物与病毒起源之间的联系提供了重要的信息。【Abstract】Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid1–3 , single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome4–7 ; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host ‘sex pilus’(F-pilus)8 ; it was the first fully sequenced organism9 and is a model system for studies of translational gene regulation10,11,RNA–protein interactions12–14 , and RNA virus assembly15–17 .Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T=3 icosahedral lattice18,19 . The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection8 ,but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryoelectron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome,built atomic models for 16 RNA stem–loops, and identified three conserved motifs of RNA–coat protein interactions among 15 of these stem–loops with diverse sequences. The stem–loop at the 3′end of the genome interacts extensively with the maturation protein,which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome–capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA–capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.This project was supported in part by grants from the National Institutes of Health (GM071940, DE025567, DE023591, CA177322 and AI094386) and National Science Foundation (DMR-1548924). We acknowledge the use of instruments at the Electron Imaging Center for Nanomachines (supported by UCLA and by instrumentation grants from the NIH (1S10OD018111, 1U24GM116792) and NSF (DBI-1338135))

Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10

9月20日，《科学》子刊《科学•进展》（Science Advances）刊出了我校夏宁邵教授团队发表的题为“Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10”的研究论文。该研究首次发现手足口病重要病原体柯萨奇病毒A组10型（CVA10）不同类型病毒颗粒共有的优势中和表位，揭示了病毒颗粒及其与优势中和抗体复合物的精确三维结构，阐明了中和抗体的功能与作用机制，为新型疫苗和治疗药物的研制提供了重要的理论基础。 该研究首次揭示并描绘了CVA10的病毒颗粒及其优势中和表位的精确特征，发现了具有良好应用潜能的治疗性中和抗体，为新型疫苗和特异性治疗药物的研究提供了关键基础。 我校夏宁邵教授、程通副教授和美国加州大学洛杉矶分校纳米系统研究所Z. Hong Zhou（周正洪）教授、美国加州大学圣地亚哥分校颜晓东博士为该论文的共同通讯作者。我校博士生朱瑞、徐龙发博士后、郑清炳工程师、李少伟教授和美国加州大学洛杉矶分校崔彦祥博士后为该论文共同第一作者。【Abstract】Coxsackievirus A10 (CVA10) recently emerged as a major pathogen of hand, foot, and mouth disease and herpangina in children worldwide, and lack of a vaccine or a cure against CVA10 infections has made therapeutic antibody identification a public health priority. By targeting a local isolate, CVA10-FJ-01, we obtained a potent antibody, 2G8, against all three capsid forms of CVA10. We show that 2G8 exhibited both 100% preventive and 100% therapeutic efficacy against CVA10 infection in mice. Comparisons of the near-atomic cryo–electron microscopy structures of the three forms of CVA10 capsid and their complexes with 2G8 Fab reveal that a single Fab binds a border region across the three capsid proteins (VP1 to VP3) and explain 2G8’s remarkable cross-reactivities against all three capsid forms. The atomic structures of this first neutralizing antibody of CVA10 should inform strategies for designing vaccines and therapeutics against CVA10 infections.This work was supported by grants from the National Science and Technology Major Projects for Major New Drugs Innovation and Development (2018ZX09711003-005-003), the National Science and Technology Major Project of Infectious Diseases (2017ZX10304402-002-003), the National Natural Science Foundation of China (31670933 and 81801646), and the National Institutes of Health (R37-GM33050, GM071940, DE025567, and AI094386). We acknowledge the use of instruments at the Electron Imaging Center for Nanomachines supported by the University of California, Los Angeles and by instrumentation grants from NIH (1S10RR23057 and 1U24GM116792) and NSF (DBI-1338135 and DMR-1548924). 该研究获得了国家自然科学基金、新药创制国家科技重大专项、传染病防治国家科技重大专项和美国国立卫生研究院基金的资助

Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids

VZV是一种广泛存在并且具有高度传染性的人类α-疱疹病毒。初次感染VZV可导致水痘，人群普遍易感（感染率约为61%～100%）。该病毒可在背根神经节潜伏感染，持续终生。夏宁邵教授团队长期开展VZV相关基础与新型疫苗研究，通过系统和精细探索建立了高效的VZV规模化培养和病毒颗粒纯化技术体系，成功获得高质量的VZV颗粒样品。首次揭示了疱疹病毒α家族的水痘-带状疱疹病毒（VZV）不同类型核衣壳的近原子分辨率结构，阐明了VZV核衣壳不同组成蛋白的相互作用网络与衣壳装配机制，可为进一步开展新型载体疫苗设计及抗病毒药物等研究提供重要支持。 我校博士后王玮、高级工程师郑清炳、博士生潘德全和俞海副教授为该论文共同第一作者，我校夏宁邵教授、程通副教授、李少伟教授以及美国罗格斯大学朱桦（Hua Zhu）教授、加利福尼亚大学洛杉矶分校周正洪（Z. Hong Zhou）教授为该论文的共同通讯作者。【Abstract】Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP—the largest among human herpesviruses—uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine.This research was supported by grants from the National Science and Technology Major Projects for Major New Drugs Innovation and Development (no. 2018ZX09711003-005-003), the National Science and Technology Major Project of Infectious Diseases (no. 2017ZX10304402), the National Natural Science Foundation of China (no. 81871648, 81601762), the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences (no. 2019RU022) and the US National Institutes of Health (DE025567/028583). 该研究获得了国家自然科学基金、新药创制国家科技重大专项和传染病防治国家科技重大专项等资助

Identification of antibodies with non-overlapping neutralization sites that target coxsackievirus A16

手足口病（Hand, Foot and Mouth Disease，HFMD）是一种由人肠道病毒引起的全球性传染病，主要发生于5岁以下的婴幼儿。2月5日，我校夏宁邵教授团队在《细胞》子刊《细胞•宿主与微生物》（Cell Host & Microbe）上在线发表题为“Identification of antibodies with non-overlapping neutralization sites that target coxsackievirus A16”的研究论文。该研究首次揭示了手足口病主要病原体柯萨奇病毒A组16型（CVA16）三种衣壳颗粒形式与三种不同类型的治疗性中和抗体的全面相互作用细节和非重叠的中和表位结构信息，阐明了CVA16成熟颗粒是疫苗候选主要保护性免疫原的理论基础，建立了可指导疫苗研制的免疫原特异检测方法，为CVA16疫苗及抗病毒药物研究提供关键基础。我校夏宁邵教授、李少伟教授、程通副教授和美国加州大学洛杉矶分校纳米系统研究所Z. Hong Zhou（周正洪）教授为该论文的共同通讯作者。我校博士生何茂洲、徐龙发博士后、郑清炳高级工程师、博士生朱瑞和尹志超为该论文共同第一作者。【Abstract】Hand, foot, and mouth disease is a common childhood illness primarily caused by coxsackievirus A16 (CVA16), for which there are no current vaccines or treatments. We identify three CVA16-specific neutralizing monoclonal antibodies (nAbs) with therapeutic potential: 18A7, 14B10, and NA9D7. We present atomic structures of these nAbs bound to all three viral particle forms—the mature virion, A-particle, and empty particle—and show that each Fab can simultaneously occupy the mature virion. Additionally, 14B10 or NA9D7 provide 100% protection against lethal CVA16 infection in a neonatal mouse model. 18A7 binds to a non-conserved epitope present in all three particles, whereas 14B10 and NA9D7 recognize broad protective epitopes but only bind the mature virion. NA9D7 targets an immunodominant site, which may overlap the receptor-binding site. These findings indicate that CVA16 vaccines should be based on mature virions and that these antibodies could be used to discriminate optimal virion-based immunogens.This work was supported by grants from the Major Program of National Natural Science Foundation of China ( 81991490 ), the National Science and Technology Major Projects for Major New Drugs Innovation and Development ( 2018ZX09711003-005-003 ), the National Science and Technology Major Project of Infectious Diseases ( 2017ZX10304402-002-003 ), the National Natural Science Foundation of China ( 31670933 and 81801646 ), the China Postdoctoral Science Foundation ( 2018M640599 and 2019T120557 ), the Principal Foundation of Xiamen University ( 20720190117 ), and the National Institutes of Health ( R37-GM33050 , GM071940 , DE025567 , and AI094386 ). 该研究获得了国家自然科学基金、新药创制国家科技重大专项、传染病防治国家科技重大专项和美国国立卫生研究院基金的资助

Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody

手足口病是一种由人肠道病毒引起的全球性传染病，主要发生于5岁以下的婴幼儿，严重危害公众健康。根据获得的手足口病流行病学和病原学调查数据，目前认为CVA6与EV71和CVA16一样应作为优先的手足口病疫苗预防对象，亟需研制有效的预防和治疗方法。然而令人遗憾的是，目前对于CVA6的基础病毒学特别是结构生物学知识均缺乏足够了解，严重制约了相关研究的有效开展。 夏宁邵教授团队研究首次揭示了手足口病重要病原体柯萨奇病毒A组6型（CVA6）的病毒颗粒及其与中和抗体复合物的精确三维结构，为新型疫苗和治疗药物的研制提供了重要的理论基础。这项研究发现并精确描绘了CVA6的病毒颗粒及其与优势中和抗体的结构特征，首次完成了对CVA6的高精度“成像”，为新型疫苗和治疗药物研制提供了关键基础。 该研究工作在厦门大学分子疫苗学和分子诊断学国家重点实验室、国家传染病诊断试剂与疫苗工程技术研究中心科研平台完成。夏宁邵教授、颜晓东博士、程通副教授为该研究论文的共同通讯作者。颜晓东博士来自美国加州大学圣地亚哥分校，同时受聘为我校双聘教授。共同第一作者为徐龙发博士生、郑清炳工程师和李少伟教授。【Abstract】Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses. Our near-atomic resolution structure of CVA6 A-particle complexed with a neutralizing antibody maps an immune-dominant neutralizing epitope to the surface loops of VP1. The structure-guided cell-based inhibition studies further demonstrate that these loops could serve as excellent targets for designing anti-CVA6 vaccines.This work was supported by a grant from the National Natural Science Foundation of China (No. 31670933 and 81401669), the National Science and Technology Major Projects for Major New Drugs Innovation and Development (No. 2017ZX09101005-005-003), the National Science and Technology Major Project of Infectious Diseases (No. 2017ZX10304402-002-003) and the Natural Science Foundation of Fujian Province (No. 2015J05073). This work was also supported in part by funding to T.S.B. from the National Institutes of Health (Grant R37-GM33050). 研究工作也得到了国际病毒结构生物学权威专家美国加州大学洛杉矶分校周正洪教授的大力支持和帮助，获得了国家自然科学基金、新药创制国家科技重大专项、传染病防治国家科技重大专项和福建省自然科学基金的资助

求解TSP问题的离散型萤火虫群优化算法

基于求解TSP问题,提出一种离散型萤火虫群优化(DGSO)算法,该算法结合TSP问题特点,给出一种有效编码和解码方法,并定义适合编码的个体间距离计算公式和编码更新公式.同时,为增强算法求解TSP问题的局部搜索能力,加快算法的收敛速度,算法使用了操作简单的2-Opt优化算子.最后,通过对10个TSP问题进行仿真实验,实验结果表明本文提出的算法是在种群规模较小,迭代次数较少的情况下就可以收敛到已知最优解.在大规模TSP算例中算法获得的最优值与理论最优值的误差也在1%以下

金属复氟化物的形成规律

运用化学键参数-模式识别方法,对金属复氟化物的形成规律作了分析。研究表明:在以金属元素的价态,离子半径,电负性和极化率构成的高维空间中,能形成复氟化物的氟化物二元系分布在该空间的一个特定区域。据此可预测一系列可能存在的复氟化物