Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.     

胞嘧啶脱氨基酶APOBEC1研究进展

为全面理解载脂蛋白B mRNA(ApoB mRNA)编辑酶催化多肽-1(APOBEC1)的作用机制,介绍了APOBEC1和ApoB mRNA的蛋白及核酸序列,总结并绘制了APOBEC1与不同的辅助蛋白的结合模型,阐述了APOBEC1催化ApoB mRNA第6 666位的胞嘧啶(C_(6666))脱氨基化分子机制.列举了啮齿动物APOBEC1抑制多种逆转录病毒的研究报道,介绍了兔源APOBEC1结合人类免疫缺陷病毒1(HIV-1)的病毒粒子并编辑病毒基因组的机理.同时介绍了APOBEC1通过编辑胞嘧啶或与AU富集元件(ARE)结合来调控癌症等疾病相关的细胞因子表达.     

SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx

The primate lentivirus auxiliary protein Vpx counteracts an unknown restriction factor that renders human dendritic and myeloid cells largely refractory to HIV-1 infection. Here we identify SAMHD1 as this restriction factor. SAMHD1 is a protein involved in Aicardi-Goutières syndrome, a genetic encephalopathy with symptoms mimicking congenital viral infection, that has been proposed to act as a negative regulator of the interferon response. We show that Vpx induces proteasomal degradation of SAMHD1. Silencing of SAMHD1 in non-permissive cell lines alleviates HIV-1 restriction and is associated with a significant accumulation of viral DNA in infected cells. Concurrently, overexpression of SAMHD1 in sensitive cells inhibits HIV-1 infection. The putative phosphohydrolase activity of SAMHD1 is probably required for HIV-1 restriction. Vpx-mediated relief of restriction is abolished in SAMHD1-negative cells. Finally, silencing of SAMHD1 markedly increases the susceptibility of monocytic-derived dendritic cells to infection. Our results demonstrate that SAMHD1 is an antiretroviral protein expressed in cells of the myeloid lineage that inhibits an early step of the viral life cycle.     

Structure of the molybdopterin-bound Cnx1G domain links molybdenum and copper metabolism

The molybdenum cofactor is part of the active site of all molybdenum-dependent enzymes, except nitrogenase. The molybdenum cofactor consists of molybdopterin, a phosphorylated pyranopterin, with an ene-dithiolate coordinating molybdenum. The same pyranopterin-based cofactor is involved in metal coordination of the homologous tungsten-containing enzymes found in archea. The molybdenum cofactor is synthesized by a highly conserved biosynthetic pathway. In plants, the multidomain protein Cnx1 catalyses the insertion of molybdenum into molybdopterin. The Cnx1 G domain (Cnx1G), whose crystal structure has been determined in its apo form, binds molybdopterin with high affinity and participates in the catalysis of molybdenum insertion. Here we present two high-resolution crystal structures of Cnx1G in complex with molybdopterin and with adenylated molybdopterin (molybdopterin-AMP), a mechanistically important intermediate. Molybdopterin-AMP is the reaction product of Cnx1G and is subsequently processed in a magnesium-dependent reaction by the amino-terminal E domain of Cnx1 to yield active molybdenum cofactor. The unexpected identification of copper bound to the molybdopterin dithiolate sulphurs in both structures, coupled with the observed copper inhibition of Cnx1G activity, provides a molecular link between molybdenum and copper metabolism.     

APOBEC3家族蛋白的进化分析和3D结构比对分析

为探寻HIV-1的种间传播路线与范畴进而发现有效的控制物,选取灵长类天然抗病毒因子APOBEC3家族的22种蛋白（以A3G为主）与17例灵长类线粒体（mtDNA）全基因组序列做进化分析研究．结果一致显示除黑猩猩（Pan troglodytes troglodytes,以下简称Pan）,大猩猩（Gorilla）以外,猩猩（Pongo）中的某些种也可能是HIV／SIV的贮主或宿主,值得从实践中有目的追溯．不同种属A3G蛋白活性位点与Zn^2＋结合位点的3D结构比较结果显示人与其他灵长类物种极为相似,预示着A3G蛋白在结构和功能上是非常保守的．人的APOBEC3蛋白有A～H7种,对它们的活性位点和Zn^2＋结合位点进行3D比较,hA3B与hA3G的重合度最好,hA3B不会被HIV-i的Vif作用与降解,提示进一步探讨hA3B的结构与功能对于控制HIV-1的感染与传播很重要．     

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.     

HIV-1和HBV复合型DNA免疫的初步研究

近年的研究表明,在啮齿类和非人灵长类免疫带有编码病毒和细菌抗原基因的质粒ＤＮＡ可以激发体液和细胞免疫应答．在本实验中,将ＨＢＶ的Ｓ基因和ＨＩＶ－１的ｇｐ１６０基因以融合形式插入到载体ｐｃＤＮＡ３中,其能表达ＨＢｓＡｇ和ｇｐ１６０的融合蛋白,并将此质粒ＤＮＡ分别直接注射到Ｂａｌｂ／ｃ小鼠和Ｓｗｉｓ小鼠．三次免疫后,用ＥＬＩＳＡ的方法初步检测ＨＢｓＡｇ和ｇｐ１６０抗原特异的抗体免疫应答均为阳性．结果说明,带有ＨＢＶ和ＨＩＶ－１融合基因的质粒ＤＮＡ直接免疫小鼠后,均激发了小鼠产生相应的免疫应答反应,这个结果为研究和生产多价疫苗提供了新的思路     

Structure of the small G protein Cdc42 bound to the GTPase-binding domain of ACK.

The proteins Cdc42 and Rac are members of the Rho family of small GTPases (G proteins), which control signal-transduction pathways that lead to rearrangements of the cell cytoskeleton, cell differentiation and cell proliferation. They do so by binding to downstream effector proteins. Some of these, known as CRIB (for Cdc42/Rac interactive-binding) proteins, bind to both Cdc42 and Rac, such as the PAK1-3 serine/threonine kinases, whereas others are specific for Cdc42, such as the ACK tyrosine kinases and the Wiscott-Aldrich-syndrome proteins (WASPs). The effector loop of Cdc42 and Rac (comprising residues 30-40, also called switch I), is one of two regions which change conformation on exchange of GDP for GTP. This region is almost identical in Cdc42 and Racs, indicating that it does not determine the specificity of these G proteins. Here we report the solution structure of the complex of Cdc42 with the GTPase-binding domain ofACK. Both proteins undergo significant conformational changes on binding, to form a new type of G-protein/effector complex. The interaction extends the beta-sheet in Cdc42 by binding an extended strand from ACK, as seen in Ras/effector interactions, but it also involves other regions of the G protein that are important for determining the specificity of effector binding.     

Structure of the C2 domain of human factor VIII at 1.5 A resolution

Human factor VIII is a plasma glycoprotein that has a critical role in blood coagulation. Factor VIII circulates as a complex with von Willebrand factor. After cleavage by thrombin, factor VIIIa associates with factor IXa at the surface of activated platelets or endothelial cells. This complex activates factor X (refs 6, 7), which in turn converts prothrombin to thrombin in the presence of factor Va (refs 8, 9). The carboxyl-terminal C2 domain of factor VIII contains sites that are essential for its binding to von Willebrand factor and to negatively charged phospholipid surfaces. Here we report the structure of human factor VIII C2 domain at 1.5 A resolution. The structure reveals a beta-sandwich core, from which two beta-turns and a loop display a group of solvent-exposed hydrophobic residues. Behind the hydrophobic surface lies a ring of positively charged residues. This motif suggests a mechanism for membrane binding involving both hydrophobic and electrostatic interactions. The structure explains, in part, mutations in the C2 region of factor VIII that lead to bleeding disorders in haemophilia A.     

满足｜a_1(G)｜=24的图G的结构

让ａ１（Ｇ）表示图Ｇ的色多项式的一次项系数．给出了满足条件｜ａ１（Ｇ）｜＝２４的图Ｇ的结构．     

Structure of the apoptotic protease-activating factor 1 bound to ADP

Apoptosis is executed by caspases, which undergo proteolytic activation in response to cell death stimuli. The apoptotic protease-activating factor 1 (Apaf-1) controls caspase activation downstream of mitochondria. During apoptosis, Apaf-1 binds to cytochrome c and in the presence of ATP/dATP forms an apoptosome, leading to the recruitment and activation of the initiator caspase, caspase-9 (ref. 2). The mechanisms underlying Apaf-1 function are largely unknown. Here we report the 2.2-A crystal structure of an ADP-bound, WD40-deleted Apaf-1, which reveals the molecular mechanism by which Apaf-1 exists in an inactive state before ATP binding. The amino-terminal caspase recruitment domain packs against a three-layered alpha/beta fold, a short helical motif and a winged-helix domain, resulting in the burial of the caspase-9-binding interface. The deeply buried ADP molecule serves as an organizing centre to strengthen interactions between these four adjoining domains, thus locking Apaf-1 in an inactive conformation. Apaf-1 binds to and hydrolyses ATP/dATP and their analogues. The binding and hydrolysis of nucleotides seem to drive conformational changes that are essential for the formation of the apoptosome and the activation of caspase-9.     

3G(WCDMA)架构和网络承载技术

为了阐明3G（WCDMA）承载网络将采用IP协议,介绍了WCDMA的网络架构,其核心结构采用NGN架构,根据IP和ATM承载语音协议栈的分析,分别计算出承载一个语音通话ATM所占用的骨干带宽远大于IP的占用量,如采用IP协议承载语音,将节省大量的骨干带宽,在未来建设3G承载网络时,IP协议将是承载核心。     

Immune responses of a designed HIV-1 DNA vaccine on rhesus monkeys

According to the UNAIDS/WHO report (http:// www.unaids.org/Epi2005/doc/report.html), there are about 40.3 million HIV/AIDS survivors, and the new HIV infection number amounts to about 4.9 million, while the death number is some 3.1 million in the world in…