Argonaute蛋白结构及其在植物中的研究进展

在真核细胞中,许多小的非编码RNA与Argonaute蛋白结合形成RNA诱导沉默复合体,并通过识别互补的靶标RNA来调控基因表达,此过程叫RNA干扰。在植物的RNA干扰途径中,Argonaute-sRNA复合物可以通过多种不同的机制发挥作用,进而参与病原体防御、植物发育调控等关键的生物过程。综述了Argonaute蛋白的分类和结构特征、在植物体中参与RNA干扰的机制及生物学功能等研究进展。     

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.     

The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist

The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.     

Crystal structure of Argonaute and its implications for RISC slicer activity

Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage.     

Argonaute2 is the catalytic engine of mammalian RNAi

Gene silencing through RNA interference (RNAi) is carried out by RISC, the RNA-induced silencing complex. RISC contains two signature components, small interfering RNAs (siRNAs) and Argonaute family proteins. Here, we show that the multiple Argonaute proteins present in mammals are both biologically and biochemically distinct, with a single mammalian family member, Argonaute2, being responsible for messenger RNA cleavage activity. This protein is essential for mouse development, and cells lacking Argonaute2 are unable to mount an experimental response to siRNAs. Mutations within a cryptic ribonuclease H domain within Argonaute2, as identified by comparison with the structure of an archeal Argonaute protein, inactivate RISC. Thus, our evidence supports a model in which Argonaute contributes "Slicer" activity to RISC, providing the catalytic engine for RNAi.     

A crystal structure of the complex between human complement receptor 2 and its ligand C3d

The interaction of complement receptor 2 (CR2)--which is present on B cells and follicular dendritic cells--with its antigen-bound ligand C3d results in an enhanced antibody response, thus providing an important link between the innate and adaptive immune systems. Although a cocrystal structure of a complex between C3d and the ligand-binding domains of CR2 has been published, several aspects of this structure, including the position in C3d of the binding interface, remained controversial because of disagreement with biochemical data. We now report a cocrystal structure of a CR2(SCR1-2):C3d complex at 3.2 angstrom resolution in which the interaction interfaces differ markedly from the previously published structure and are consistent with the biochemical data. It is likely that, in the previous structure, the interaction was influenced by the presence of zinc acetate additive in the crystallization buffer, leading to a nonphysiological complex. Detailed knowledge of the binding interface now at hand gives the potential to exploit the interaction in vaccine design or in therapeutics directed against autoreactive B cells.     

Tuhualite crystal structure

As judged by crystal structure analysis, the crystallochemical formula of tuhualite is (Na,K)(2)(VI) (Fe(+3))(2)(VI) (Fe(+2))(2)(VI) Si(12)O(30) . H(2)O, with four such formulas in the unit cell. The structure is characterized by six-repeat double chains of silicon tetrahedrons and chains of edge-sharing, alternating iron tetrahedrons and octahedrons. Chains of each kind are connected by corner sharing to four chains of the other type. The iron cations appear to be anomalously ordered with Fe(+2) in tetrahedral and Fe(+3) in octahedral sites.     

利用CRISPR_Cas9技术创建拟南芥Argonaute2基因缺失突变体

Argonaute2(AGO2)在植物抗病和发育过程中发挥重要作用。为创制拟南芥ago2核苷酸插入/缺失突变体材料,分析了拟南芥AGO2基因结构,选择其外显子上3个靶点构建了CRISPR_Cas9基因编辑载体,并通过农杆菌介导的花序浸染法转化野生型拟南芥,利用潮霉素对T₀代种子进行筛选,获得62株T₁代抗性苗;然后提取T₁代抗性苗DNA,进行潮霉素特异引物PCR扩增检测,确定获得53棵转基因阳性苗。随机选择10株T₁代阳性苗,扩增包含靶点的基因片段进行测序,结果显示,在第1个靶点附近6株苗产生了编辑,第2靶点附近10株苗全部成功编辑,第3个靶点未发生编辑。编辑位点附近产生了多种编辑形式,以PAM前删除或者增加1个碱基的形式出现频率最高,也有删除大于10碱基的编辑形式,最长可删除106个碱基。这些突变株系的获得为深入研究拟南芥AGO2的功能提供了丰富的遗传材料。     

The crystal structure of a mammalian fatty acid synthase

Mammalian fatty acid synthase is a large multienzyme that catalyzes all steps of fatty acid synthesis. We have determined its crystal structure at 3.2 angstrom resolution covering five catalytic domains, whereas the flexibly tethered terminal acyl carrier protein and thioesterase domains remain unresolved. The structure reveals a complex architecture of alternating linkers and enzymatic domains. Substrate shuttling is facilitated by flexible tethering of the acyl carrier protein domain and by the limited contact between the condensing and modifying portions of the multienzyme, which are mainly connected by linkers rather than direct interaction. The structure identifies two additional nonenzymatic domains: (i) a pseudo-ketoreductase and (ii) a peripheral pseudo-methyltransferase that is probably a remnant of an ancestral methyltransferase domain maintained in some related polyketide synthases. The structural comparison of mammalian fatty acid synthase with modular polyketide synthases shows how their segmental construction allows the variation of domain composition to achieve diverse product synthesis.     

Automatic determination of crystal structure

Several crystallographic computer programs have been organized into one large automatic program for solving crystal structures. The emphasis of this organization has been to produce a noninteractive system, that is, to have all decisions made by the computer. Input data are the raw intensity data, cell constants, space group, chemical formula, and other miscellaneous items. The output is a stereo picture of the contents in a unit cell. The program, operating in a noninteractive mode, has successfully solved compounds of unknown structure; in addition, for a test compound of completely unknown composition, this program deduced the correct structure with an average error in bond distance of 0.05 angstrom and an average error in bond angle of 7 degrees .     

The gramicidin pore: crystal structure of a cesium complex

Gramicidin, a linear polypeptide composed of hydrophobic amino acids with alternating L- and D- configurations, forms transmembrane ion channels. The crystal structure of a gramicidin-cesium complex has been determined at 2.0 angstrom resolution. In this structure, gramicidin forms a 26 angstrom long tube comprised of two polypeptide chains arranged as antiparallel beta strands that are wrapped into a left-handed helical coil with 6.4 residues per turn. The polypeptide backbone forms the interior of the hydrophilic, solvent-filled pore and the side chains form a hydrophobic and relatively regular surface on the outside of the pore. This example of a crystal structure of a solvent-filled ion pore provides a basis for understanding the physical nature of ion translocation.     

The crystal structure of uncomplexed actin in the ADP state

The dynamics and polarity of actin filaments are controlled by a conformational change coupled to the hydrolysis of adenosine 5'-triphosphate (ATP) by a mechanism that remains to be elucidated. Actin modified to block polymerization was crystallized in the adenosine 5'-diphosphate (ADP) state, and the structure was solved to 1.54 angstrom resolution. Compared with previous ATP-actin structures from complexes with deoxyribonuclease I, profilin, and gelsolin, monomeric ADP-actin is characterized by a marked conformational change in subdomain 2. The successful crystallization of monomeric actin opens the way to future structure determinations of actin complexes with actin-binding proteins such as myosin.     

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure

Predictions of the structures of the antigen-binding domains of an antibody, recorded before its experimental structure determination and tested subsequently, were based on comparative analysis of known antibody structures or on conformational energy calculations. The framework, the relative positions of the hypervariable regions, and the folds of four of the hypervariable loops were predicted correctly. This portion includes all residues in contact with the antigen, in this case hen egg white lysozyme, implying that the main chain conformation of the antibody combining site does not change upon ligation. The conformations of three residues in each of the other two hypervariable loops are different in the predicted models and the experimental structure.     

Kornerupine: its crystal structure

Three-dimensional analysis of the crystal structure of kornerupine reveals the crystallochemical formula Mg(VI)(2)Mg(VI)AlVI(6)[Si(2)O(7)] [(Al,Si)(2) SiO(10)]O(4)(OH), with four formula units in the structure cell of a = 16.100 (2) A, b = 13.767(2) A, c = 6.735(2) A; space group, Cmcm. The unusual crystal structure includes walls of Al-O edge and corner-sharing octahedra, and chains of alternating Mg-O and Al-O octahedra fused to the walls by further edge-sharing to form dense slabs. These slabs are held together by [Si(2)O(7)] corner-sharing tetrahedral pairs and [(Al,Si)(2)SiO(10)] corner-sharing tetrahedral triplets.     

The structure of human 5-lipoxygenase

The synthesis of both proinflammatory leukotrienes and anti-inflammatory lipoxins requires the enzyme 5-lipoxygenase (5-LOX). 5-LOX activity is short-lived, apparently in part because of an intrinsic instability of the enzyme. We identified a 5-LOX-specific destabilizing sequence that is involved in orienting the carboxyl terminus, which binds the catalytic iron. Here, we report the crystal structure at 2.4 angstrom resolution of human 5-LOX stabilized by replacement of this sequence.     

原核Argonaute的应用研究进展

原核生物Argonautes （pAgos）是参与细胞防御外来DNA入侵的可编程核酸酶。在体外,pAgos可以结合小的单链核酸（ssDNA/ssRNA）向导来识别和切割互补DNA/RNA。在体内,pAgos优先靶向多拷贝遗传元件、噬菌体和质粒,从而抑制入侵核酸的扩增和噬菌体感染。pAgos作为一类新兴的可编程核酸酶,比目前应用最为广泛的CRISPR-Cas系统更具灵活性,在生物技术方面展现出巨大的潜力。早期的研究聚焦于嗜热的pAgo,目前基于嗜热pAgos的主要应用包括分子诊断和体外DNA组装。为了推进基于Ago的体内生物技术,如基因编辑的应用,研究人员的焦点逐渐转移到中温生物来源的pAgos,虽然目前pAgos还未实现基因组编辑,但是随着越来越多的pAgo被发掘以及研究人员对pAgos催化机制的深入研究,有望开发基于pAgos的下一代基因编辑技术。本文总结了已知代表性pAgos和基于pAgos发展的生物技术,并简要分析了pAgos在原核生物和真核生物体内应用面临的挑战和可能的应对策略。     

The structure of the c60 molecule: x-ray crystal structure determination of a twin at 110 k

Single-crystal x-ray diffraction methods were used to determine the crystal and molecular structure of C(60) buckminsterfullerene. At 110 kelvin C(60) is cubic, apparent Laue symmetry m3m, but it exhibits noncrystallographic systematic extinctions indicative of a twin in which I(hkl) and I(khl) are superimposed. In fact, C(60) crystallizes with four molecules in space group [See equation in the PDF file] of the cubic system (Laue symmetry m3) with lattice constant a = 14.052(5) angstroms (A) at 110 kelvin. The twin components are equal. A given component, which has crystallographically imposed symmetry [See equation in the PDF file] displays an ordered structure of a truncated icosahedron. The five independent C=C bonds that join C(6) rings average 1.355(9) A; the ten independent C-C bonds that join C(6) and C(5) rings average 1.467(21) A. The mean atom-to-atom diameter of the C(60) molecule is 7.065(3) A. The molecules are very tightly packed in the crystal structure, with intermolecular C...C distances as short as 3.131(7) A.     

The crystal structure of the signal recognition particle in complex with its receptor

Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.