降解结晶纤维素极耐热葡聚糖酶重组菌的构建

极耐热纤维素酶在纤维素生物转化中具有潜在的开发前景,但极耐热酶缺乏对天然纤维素的分解能力。采用基因工程方法,将极耐热内切葡聚糖酶Cel12B基因和同样极端嗜热菌来源的纤维素结合域(CBD)区域融合,构建重组质粒pET-20b-Cel12B-CBD,转化至大肠杆菌JM109(DE3)诱导表达后,融合基因表达产物对结晶纤维素具有一定的分解能力。     

The Rab5 effector EEA1 is a core component of endosome docking

Intracellular membrane docking and fusion requires the interplay between soluble factors and SNAREs. The SNARE hypothesis postulates that pairing between a vesicular v-SNARE and a target membrane z-SNARE is the primary molecular interaction underlying the specificity of vesicle targeting as well as lipid bilayer fusion. This proposal is supported by recent studies using a minimal artificial system. However, several observations demonstrate that SNAREs function at multiple transport steps and can pair promiscuously, questioning the role of SNAREs in conveying vesicle targeting. Moreover, other proteins have been shown to be important in membrane docking or tethering. Therefore, if the minimal machinery is defined as the set of proteins sufficient to reproduce in vitro the fidelity of vesicle targeting, docking and fusion as in vivo, then SNAREs are not sufficient to specify vesicle targeting. Endosome fusion also requires cytosolic factors and is regulated by the small GTPase Rab5. Here we show that Rab5-interacting soluble proteins can completely substitute for cytosol in an in vivo endosome-fusion assay, and that the Rab5 effector EEA1 is the only factor necessary to confer minimal fusion activity. Rab5 and other associated proteins seem to act upstream of EEA1, implying that Rab5 effectors comprise both regulatory molecules and mechanical components of the membrane transport machinery. We further show that EEA1 mediates endosome docking and, together with SNAREs, leads to membrane fusion.     

Structural basis for the subunit assembly of the anaphase-promoting complex

The anaphase-promoting complex or cyclosome (APC/C) is an unusually large E3 ubiquitin ligase responsible for regulating defined cell cycle transitions. Information on how its 13 constituent proteins are assembled, and how they interact with co-activators, substrates and regulatory proteins is limited. Here, we describe a recombinant expression system that allows the reconstitution of holo APC/C and its sub-complexes that, when combined with electron microscopy, mass spectrometry and docking of crystallographic and homology-derived coordinates, provides a precise definition of the organization and structure of all essential APC/C subunits, resulting in a pseudo-atomic model for 70% of the APC/C. A lattice-like appearance of the APC/C is generated by multiple repeat motifs of most APC/C subunits. Three conserved tetratricopeptide repeat (TPR) subunits (Cdc16, Cdc23 and Cdc27) share related superhelical homo-dimeric architectures that assemble to generate a quasi-symmetrical structure. Our structure explains how this TPR sub-complex, together with additional scaffolding subunits (Apc1, Apc4 and Apc5), coordinate the juxtaposition of the catalytic and substrate recognition module (Apc2, Apc11 and Apc10 (also known as Doc1)), and TPR-phosphorylation sites, relative to co-activator, regulatory proteins and substrates.     

Synapsin I is a spectrin-binding protein immunologically related to erythrocyte protein 4.1

The membrane-associated cytoskeleton is considered to be the apparatus by which cells regulate the properties of their plasma membranes, although recent evidence has indicated additional roles for the proteins of this structure, including an involvement in intracellular transport and exocytosis (see refs 1-3 for review). Of the membrane skeletal proteins, to date only spectrin (fodrin) and ankyrin have been purified and characterized from non-erythroid sources. Protein 4.1 in the red cell is a spectrin-binding protein that enhances the binding of spectrin to actin and can apparently bind to at least one transmembrane protein Immunoreactive forms of 4.1 have been detected in several cell types, including brain. Here we report the purification of brain 4.1 on the basis of its cross-reactivity with erythrocyte 4.1 and spectrin-binding activity. We further show that brain 4.1 is identical to the synaptic vesicle protein, synapsin I, one of the brain's major substrates for cyclic AMP and Ca2+-calmodulin-dependent kinases. Spectrin and synapsin are present in brain homogenates in an approximately 1:1 molar ratio. Although synapsin I has been implicated in synaptic transmission, no activity has been previously ascribed to it.     

紫薯花青素的成分鉴定及其抗白血病潜在靶点的筛选验证

为探讨紫薯花青素(Purple Sweet Potato Anthocyanin, PSPA)在急性淋巴细胞白血病(Acute Lymphoblastic Leukemia, ALL)防治中的靶点,本文提取、纯化并鉴定了紫薯花青素,基于分子对接技术预测了紫薯花青素的潜在靶点。结果显示：从川紫4号紫薯中鉴定出25种花青素,分别是矢车菊素、芍药色素、天竺葵色素及其衍生物,各种成分的相对含量为0.1%-23.0%。其中,矢车菊素3-阿魏酸-对羟基苯甲酰槐糖苷-5-葡萄糖苷(Cyanidin 3-feruloyl-p-hydroxybenzoyl sophoroside-5-glucoside)相对含量最高,达到22.63%。基于矢车菊素抗氧化活性较其他两种花青素更强、二乙酰化的花青素更稳定的特点,该化合物被选择作为后续分子对接的配体,分别与程序性细胞死亡(Programmed Cell Death, PCD),如凋亡、焦亡、坏死性凋亡、铁死亡及铜死亡相关的关键蛋白进行分子对接分析。结果表明,紫薯花青素可以结合到抗凋亡蛋白(Bcl-2)、E3泛素连接酶(Parkin)蛋白、胱氨酸转运蛋白(SL...     

Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex

F-box proteins are members of a large family that regulates the cell cycle, the immune response, signalling cascades and developmental programmes by targeting proteins, such as cyclins, cyclin-dependent kinase inhibitors, IkappaBalpha and beta-catenin, for ubiquitination (reviewed in refs 1-3). F-box proteins are the substrate-recognition components of SCF (Skp1-Cullin-F-box protein) ubiquitin-protein ligases. They bind the SCF constant catalytic core by means of the F-box motif interacting with Skp1, and they bind substrates through their variable protein-protein interaction domains. The large number of F-box proteins is thought to allow ubiquitination of numerous, diverse substrates. Most organisms have several Skp1 family members, but the function of these Skp1 homologues and the rules of recognition between different F-box and Skp1 proteins remain unknown. Here we describe the crystal structure of the human F-box protein Skp2 bound to Skp1. Skp1 recruits the F-box protein through a bipartite interface involving both the F-box and the substrate-recognition domain. The structure raises the possibility that different Skp1 family members evolved to function with different subsets of F-box proteins, and suggests that the F-box protein may not only recruit substrate, but may also position it optimally for the ubiquitination reaction.     

Structure and assembly of the Alu domain of the mammalian signal recognition particle

The Alu domain of the mammalian signal recognition particle (SRP) comprises the heterodimer of proteins SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. It retards the ribosomal elongation of signal-peptide-containing proteins before their engagement with the translocation machinery in the endoplasmic reticulum. Here we report two crystal structures of the heterodimer SRP9/14 bound either to the 5' domain or to a construct containing both 5' and 3' domains. We present a model of the complete Alu domain that is consistent with extensive biochemical data. SRP9/14 binds strongly to the conserved core of the 5' domain, which forms a U-turn connecting two helical stacks. Reversible docking of the more weakly bound 3' domain might be functionally important in the mechanism of translational regulation. The Alu domain structure is probably conserved in other cytoplasmic ribonucleoprotein particles and retroposition intermediates containing SRP9/14-bound RNAs transcribed from Alu repeats or related elements in genomic DNA.     

晶体硅光伏电池的材料优化

介绍了调制阳光频率实现太阳光波上下量子剪裁的两种方式:掺杂稀土离子和微纳米结构化硅基材料.以Lu2O3为基质,采用共沉淀法制备了Tb3+和Yb3+共掺的下转换粉末;以NaYF4为基质,采用热水法制备了Er、Yb和Tm共掺的上转换粉末.实验证明Lu2O3:Tb3+,Yb3+纳米粉末中,一个高能光子可剪裁成2个974 nm的近红外光子.而NaYF4:Er3+,Yb3+,Tm3+共掺的上转换材料也有显著的上转换效果,仅用1 122 nm激光照射0.25 cm2实验硅光电池片可增加电池光电流密度0.06 mA/cm2.设计了具有纳米结构的PIN.简述了通过梯度掺杂制结增强光伏效应的原因.     

Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex

The serine proteinase alpha-thrombin causes blood clotting through proteolytic cleavage of fibrinogen and protease-activated receptors and amplifies its own generation by activating the essential clotting factors V and VIII. Thrombomodulin, a transmembrane thrombin receptor with six contiguous epidermal growth factor-like domains (TME1-6), profoundly alters the substrate specificity of thrombin from pro- to anticoagulant by activating protein C. Activated protein C then deactivates the coagulation cascade by degrading activated factors V and VIII. The thrombin-thrombomodulin complex inhibits fibrinolysis by activating the procarboxypeptidase thrombin-activatable fibrinolysis inhibitor. Here we present the 2.3 A crystal structure of human alpha-thrombin bound to the smallest thrombomodulin fragment required for full protein-C co-factor activity, TME456. The Y-shaped thrombomodulin fragment binds to thrombin's anion-binding exosite-I, preventing binding of procoagulant substrates. Thrombomodulin binding does not seem to induce marked allosteric structural rearrangements at the thrombin active site. Rather, docking of a protein C model to thrombin-TME456 indicates that TME45 may bind substrates in such a manner that their zymogen-activation cleavage sites are presented optimally to the unaltered thrombin active site.     

麻疯树核糖体失活蛋白Curcin和Curcin C与腺苷及腺嘌呤的互作方式分析

麻疯树核糖体失活蛋白Curcin和Curcin C均具N-糖苷酶活性，然而两者的体外翻译抑制能力却具有明显差异，这暗示着两者的N-糖苷酶活性也存在差异.为了探究造成这一差异的结构基础，本研究使用trRosetta对两种蛋白进行了三级结构的预测，通过PROCHECK和Qmean对预测得到的三级结构模型进行了质量评估，利用Chem3D对小分子配体腺嘌呤和腺苷进行了结构优化，借助UCSF Chimera对Curcin及Curcin C活性位点的氨基酸组成进行了预测.最终使用分子对接软件AutoDock将预测得到的模型与小分子腺嘌呤及腺苷进行分子对接.对接结果显示，两种蛋白与腺嘌呤的相互作用模式具有较高的相似性，但Curcin的关键氨基酸Arg并未参与到与配体的相互作用.此外Curcin C与腺嘌呤和腺苷之间的结合能都低于Curcin,且其和腺苷与腺嘌呤之间结合能的差值也要高于Curcin.这一结果暗示着Curcin和Curcin C之间的活性差异与其活性位点处的结构特征有关，Curcin C中的关键氨基酸Arg与腺嘌呤及腺苷的结合位点更为靠近，从而导致Curcin C与底物之间的结合能更低，...     

Virtual substrates screening model of triacylglycerol lipase from <Emphasis Type="Italic">Bacillus thermocatenulanatus</Emphasis>

A reliable 3-D structure of Triacylglycerol lipase from Bacillus thermocatenulanatus was constructed by homology modeling. Under molecular dynamics simulation, it was refined and checked. The model was further used as a receptor to search binding sites and carry out flexible docking with a range of substrates, whose enzyme activities were already measured. By inputting a series of docking results, virtual substrates screening models were established and assessed. Monadic nonlinear solution demanded less data but was weak in fitting enzyme activity data with little difference; its mean absolute percentage error (MAPE) of regression was 0.67 and mean square error (MSE) was 1.73 U/mg. Both quadratic stepwise regression and BP neural network were good in regression and prediction; however, more data were required. In the cross-validation of 12 groups, overall MAPE of regression and prediction for the former were 0.18 and 0.49, while the latter was 0.55 and 0.36. MSE values for these two methods were 0.95 and 1.20 U/mg, respectively. Therefore, monadic nonlinear regression model can be used as a preliminary screening one; quadratic stepwise regression and BP neural network approach can be applied to precise screening.     

分子对接技术筛选沉香中抗新型冠状病毒活性成分

从沉香中筛选潜在的抗新型冠状病毒活性成分,指导以沉香小分子作为SARS-CoV-2潜在阻断剂和抑制剂药物的研发.根据沉香已知的化学成分,采用分子对接的方法,以血管紧张素转化酶-2(ACE2)、SARS-CoV-2的3CL水解酶(3CLpro)为靶标,通过结合打分值以及与靶蛋白受体的相互作用模式,获得沉香中具有潜在抗SA...     

Structural mechanism for sterol sensing and transport by OSBP-related proteins

The oxysterol-binding-protein (OSBP)-related proteins (ORPs) are conserved from yeast to humans, and are implicated in the regulation of sterol homeostasis and in signal transduction pathways. Here we report the structure of the full-length yeast ORP Osh4 (also known as Kes1) at 1.5-1.9 A resolution in complexes with ergosterol, cholesterol, and 7-, 20- and 25-hydroxycholesterol. We find that a single sterol molecule binds within a hydrophobic tunnel in a manner consistent with a transport function for ORPs. The entrance is blocked by a flexible amino-terminal lid and surrounded by basic residues that are critical for Osh4 function. The structure of the open state of a lid-truncated form of Osh4 was determined at 2.5 A resolution. Structural analysis and limited proteolysis show that sterol binding closes the lid and stabilizes a conformation favouring transport across aqueous barriers and signal transmission. The structure of Osh4 in the absence of ligand exposes potential phospholipid-binding sites that are positioned for membrane docking and sterol exchange. On the basis of these observations, we propose a model in which sterol and membrane binding promote reciprocal conformational changes that facilitate a sterol transfer and signalling cycle.     

Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine

Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish substrates that can be refolded from those that need to be degraded. To investigate the molecular basis of this process, we have solved the crystal structure of DegP (also known as HtrA), a widely conserved heat shock protein that combines refolding and proteolytic activities. The DegP hexamer is formed by staggered association of trimeric rings. The proteolytic sites are located in a central cavity that is only accessible laterally. The mobile side-walls are constructed by twelve PDZ domains, which mediate the opening and closing of the particle and probably the initial binding of substrate. The inner cavity is lined by several hydrophobic patches that may act as docking sites for unfolded polypeptides. In the chaperone conformation, the protease domain of DegP exists in an inactive state, in which substrate binding in addition to catalysis is abolished.     

Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor.

Many motile species of bacteria are propelled by flagella, which are rigid helical filaments turned by rotary motors in the cell membrane. The motors are powered by the transmembrane gradient of protons or sodium ions. Although bacterial flagella contain many proteins, only three-MotA, MotB and FliG-participate closely in torque generation. MotA and MotB are ion-conducting membrane proteins that form the stator of the motor. FliG is a component of the rotor, present in about 25 copies per flagellum. It is composed of an amino-terminal domain that functions in flagellar assembly and a carboxy-terminal domain (FliG-C) that functions specifically in motor rotation. Here we report the crystal structure of FliG-C from the hyperthermophilic eubacterium Thermotoga maritima. Charged residues that are important for function, and which interact with the stator protein MotA, cluster along a prominent ridge on FliG-C. On the basis of the disposition of these residues, we present a hypothesis for the orientation of FliG-C domains in the flagellar motor, and propose a structural model for the part of the rotor that interacts with the stator.     

Fibulin-5/DANCE is essential for elastogenesis in vivo.

The elastic fibre system has a principal role in the structure and function of various types of organs that require elasticity, such as large arteries, lung and skin. Although elastic fibres are known to be composed of microfibril proteins (for example, fibrillins and latent transforming growth factor (TGF)-beta-binding proteins) and polymerized elastin, the mechanism of their assembly and development is not well understood. Here we report that fibulin-5 (also known as DANCE), a recently discovered integrin ligand, is an essential determinant of elastic fibre organization. fibulin-5-/- mice generated by gene targeting exhibit a severely disorganized elastic fibre system throughout the body. fibulin-5-/- mice survive to adulthood, but have a tortuous aorta with loss of compliance, severe emphysema, and loose skin (cutis laxa). These tissues contain fragmented elastin without an increase of elastase activity, indicating defective development of elastic fibres. Fibulin-5 interacts directly with elastic fibres in vitro, and serves as a ligand for cell surface integrins alphavbeta3, alphavbeta5 and alpha9beta1 through its amino-terminal domain. Thus, fibulin-5 may provide anchorage of elastic fibres to cells, thereby acting to stabilize and organize elastic fibres in the skin, lung and vasculature.     

Slowed recovery of rod photoresponse in mice lacking the GTPase accelerating protein RGS9-1

Timely deactivation of the alpha-subunit of the rod G-protein transducin (Galphat) is essential for the temporal resolution of rod vision. Regulators of G-protein signalling (RGS) proteins accelerate hydrolysis of GTP by the alpha-subunits of heterotrimeric G proteins in vitro. Several retinal RGS proteins can act in vitro as GTPase accelerating proteins (GAP) for Galphat. Recent reconstitution experiments indicate that one of these, RGS9-1, may account for much of the Galphat GAP activity in rod outer segments (ROS). Here we report that ROS membranes from mice lacking RGS9-1 hydrolyse GTP more slowly than ROS membranes from control mice. The Gbeta5-L protein that forms a complex with RGS9-1 was absent from RGS9-/- retinas, although Gbeta5-L messenger RNA was still present. The flash responses of RGS9-/- rods rose normally, but recovered much more slowly than normal. We conclude that RGS9-1, probably in a complex with Gbeta5-L, is essential for acceleration of hydrolysis of GTP by Galphat and for normal recovery of the photoresponse.     

Structural basis for site-specific ribose methylation by box C/D RNA protein complexes

Box C/D RNA protein complexes (RNPs) direct site-specific 2'-O-methylation of RNA and ribosome assembly. The guide RNA in C/D RNP forms base pairs with complementary substrates and selects the modification site using a molecular ruler. Despite many studies of C/D RNP structure, the fundamental questions of how C/D RNAs assemble into RNPs and how they guide modification remain unresolved. Here we report the crystal structure of an entire catalytically active archaeal C/D RNP consisting of a bipartite C/D RNA associated with two substrates and two copies each of Nop5, L7Ae and fibrillarin at 3.15-? resolution. The substrate pairs with the second through the eleventh nucleotide of the 12-nucleotide guide, and the resultant duplex is bracketed in a channel with flexible ends. The methyltransferase fibrillarin binds to an undistorted A-form structure of the guide-substrate duplex and specifically loads the target ribose into the active site. Because interaction with the RNA duplex alone does not determine the site specificity, fibrillarin is further positioned by non-specific and specific protein interactions. Compared with the structure of the inactive C/D RNP, extensive domain movements are induced by substrate loading. Our results reveal the organization of a monomeric C/D RNP and the mechanism underlying its site-specific methylation activity.