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.     

Long-range structural changes in proteinase K triggered by calcium ion removal

The X-ray crystal structure of the subtilisin-type enzyme proteinase K at 1.5 A resolution shows that is has two binding sites for Ca2+. Scatchard analysis indicates that one Ca2+ binds tightly, with pK 7.6 x 10(-8) M-1, and the other only weakly. Although Ca2+ is not directly involved in the catalytic mechanism and is 16.6 A away from the alpha-carbon atoms of the catalytic triad Asp 39-His 69-Ser 224, the activity of proteinase K towards the synthetic substrate succinyl-Ala-Ala-Ala-p-nitroanilide drops slowly to approximately 20% of its original value when it is depleted of Ca2+. This is not due to autolysis of the enzyme. The X-ray crystal structure of Ca2+-free proteinase K shows that removal of Ca2+ from the tight binding site triggers a concerted domino-like movement of five peripheral loops and of two alpha-helices. At a distance of 25 A from this calcium-binding site, the geometry of both the secondary substrate binding site and of the catalytic triad is affected by this movement thereby reducing the activity of the enzyme.     

Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus

Fusion of biological membranes is mediated by specific lipid-interacting proteins that induce the formation and expansion of an initial fusion pore. Here we report the crystal structure of the ectodomain of the Semliki Forest virus fusion glycoprotein E1 in its low-pH-induced trimeric form. E1 adopts a folded-back conformation that, in the final post-fusion form of the full-length protein, would bring the fusion peptide loop and the transmembrane anchor to the same end of a stable protein rod. The observed conformation of the fusion peptide loop is compatible with interactions only with the outer leaflet of the lipid bilayer. Crystal contacts between fusion peptide loops of adjacent E1 trimers, together with electron microscopy observations, suggest that in an early step of membrane fusion, an intermediate assembly of five trimers creates two opposing nipple-like deformations in the viral and target membranes, leading to formation of the fusion pore.     

Application of C5-C13 light hydrocarbons in depositional envlrOnment diagnosis

Based on the geological background and Gammacerane/C31H(S+R)ratios,source rock depositional environments of the studied oil samples(194)from 13 oilfields were classified into three groups according to salinity:saline-lacustrine facies,fresh to brackish lacustrine facies(including linmetic facies),and semi-saline to saline facies(including marine facies of the Tarim Basin).C5-C13 compound groups in the crude oils were separated by GC,and about 286 compounds were qualitatively analyzed.The geochemical application of the C6-C13 compound groups and their ratios between each group with individual carbon number was investigated.Our studies show that(1)C6-C13 compound groups and their ratios in the crude oils could serve as new reliable parameters for oil-oil correlation because the C6-C13 light fractions are the major oil component,especially in light oil or condensate,in which they account for almost 90%of the whole oil;(2)the compound groups of C7 light hydrocarbons in oils derived from different depositional environments with different salinity have different characteristics;(3)C6-C13 compound groups and ratios may be affected by other factors such as maturity,but they are mainly controlled by salinity of depositional waters.     

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

Functioning and processing of membrane proteins critically depend on the way their transmembrane segments are embedded in the membrane. Sphingolipids are structural components of membranes and can also act as intracellular second messengers. Not much is known of sphingolipids binding to transmembrane domains (TMDs) of proteins within the hydrophobic bilayer, and how this could affect protein function. Here we show a direct and highly specific interaction of exclusively one sphingomyelin species, SM 18, with the TMD of the COPI machinery protein p24 (ref. 2). Strikingly, the interaction depends on both the headgroup and the backbone of the sphingolipid, and on a signature sequence (VXXTLXXIY) within the TMD. Molecular dynamics simulations show a close interaction of SM 18 with the TMD. We suggest a role of SM 18 in regulating the equilibrium between an inactive monomeric and an active oligomeric state of the p24 protein, which in turn regulates COPI-dependent transport. Bioinformatic analyses predict that the signature sequence represents a conserved sphingolipid-binding cavity in a variety of mammalian membrane proteins. Thus, in addition to a function as second messengers, sphingolipids can act as cofactors to regulate the function of transmembrane proteins. Our discovery of an unprecedented specificity of interaction of a TMD with an individual sphingolipid species adds to our understanding of why biological membranes are assembled from such a large variety of different lipids.     

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.     

富勒烯(C60)的钼配合物Mo(η2-C60)(CO)2(phen)(dbm)的晶体结构

富勒烯（C60）的钼配合物Mo（η^2-C60）（CO2）（phen)(phen）=1,10-phenanthroline,dbm=dibutyl maleate）的晶体结构在低温下被测定。此晶体属于正交晶系,Pbea空间群。晶胞参数α=2.5318（5）nm,b=2.7257(5)nm,c=1.4577(3）nm,V=10.059（3)nm^3,Z=8 and R1=0.0908,钼原子与配体呈变型八面体配位。因为晶胞中没有溶剂分子存在,此晶体在空气中很稳定。     

酸碱连续改性木质活性炭及其吸附水中苯酚的动力学研究

为了了解木质活性炭酸碱连续改性前后其表征变化及对水中苯酚的吸附机理,对市售木质活性炭进行先酸(12mol/L HCl)后碱(1mol/L NaOH)改性处理,测定了改性前后其表面灰分变化并进行了红外光谱(FTIR)分析,并对改性前后活性炭吸附水中苯酚的动力学进行了研究.结果表明,经酸碱改性后,活性炭表面灰分含量降低了37.5%;增加了活性炭表面官能团累积双键(=C=C=C=)和三键(-C≡C-)的数量;常温下,二级动力学模型能更好地模拟木质活性炭对水中苯酚的吸附过程.     

半氟烃链作桥链的对称酯类二聚体的合成及介晶性

合成全氟烃链或半氟烃链作为中心桥链的二聚体化合物可能出现新的性能,作为液晶材料具有较大的研究价值.合成了7个以半氟烃链作为桥链的对称酯类二聚体化合物H2n+1CnO-C6H4-COOCH2C6 F12CH2OOC-C6H4-OCnH2n+1(n=4,1a;6,1b;10,1c),H2n+1 CnO-C6H4-C6H4-COOCH2C6F12 CH2OOC-C6H4-C6H4-OCnH2n+1(n=4,2a;6,2b;12,2c)和C6F13CH2CH2COOCH2C6F12CH2OOCCH2CH2C6F13(3).差示扫描量热法(DSC)和偏光显微镜(POM)对其介晶性研究发现:化合物2a具有典型的焦锥扇形织构SA相,化合物2b出现塑晶相.分别比较结构相类似的化合物1a～1c,2a～2c的熔点,发现随着烷氧基链的增长,存在降低趋势.三段半氟烃链的对称酯类二聚体化合物3未观察到介晶性.     

Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport

Cytosolic coat proteins that bind reversibly to membranes have a central function in membrane transport within the secretory pathway. One well-studied example is COPI or coatomer, a heptameric protein complex that is recruited to membranes by the GTP-binding protein Arf1. Assembly into an electron-dense coat then helps in budding off membrane to be transported between the endoplasmic reticulum (ER) and Golgi apparatus. Here we propose and corroborate a simple model for coatomer and Arf1 activity based on results analysing the distribution and lifetime of fluorescently labelled coatomer and Arf1 on Golgi membranes of living cells. We find that activated Arf1 brings coatomer to membranes. However, once associated with membranes, Arf1 and coatomer have different residence times: coatomer remains on membranes after Arf1-GTP has been hydrolysed and dissociated. Rapid membrane binding and dissociation of coatomer and Arf1 occur stochastically, even without vesicle budding. We propose that this continuous activity of coatomer and Arf1 generates kinetically stable membrane domains that are connected to the formation of COPI-containing transport intermediates. This role for Arf1/coatomer might provide a model for investigating the behaviour of other coat protein systems within cells.     

P2X receptors as cell-surface ATP sensors in health and disease

P2X receptors are membrane ion channels activated by the binding of extracellular adenosine triphosphate (ATP). For years their functional significance was consigned to distant regions of the autonomic nervous system, but recent work indicates several further key roles, such as afferent signalling, chronic pain, and in autocrine loops of endothelial and epithelial cells. P2X receptors have a molecular architecture distinct from other ion channel protein families, and have several unique functional properties.     

Structure of an ABC transporter in complex with its binding protein

ATP-binding cassette (ABC) transporter proteins carry diverse substrates across cell membranes. Whereas clinically relevant ABC exporters are implicated in various diseases or cause multidrug resistance of cancer cells, bacterial ABC importers are essential for the uptake of nutrients, including rare elements such as molybdenum. A detailed understanding of their mechanisms requires direct visualization at high resolution and in distinct conformations. Our recent structure of the multidrug ABC exporter Sav1866 has revealed an outward-facing conformation of the transmembrane domains coupled to a closed conformation of the nucleotide-binding domains, reflecting the ATP-bound state. Here we present the 3.1 A crystal structure of a putative molybdate transporter (ModB2C2) from Archaeoglobus fulgidus in complex with its binding protein (ModA). Twelve transmembrane helices of the ModB subunits provide an inward-facing conformation, with a closed gate near the external membrane boundary. The ATP-hydrolysing ModC subunits reveal a nucleotide-free, open conformation, whereas the attached binding protein aligns the substrate-binding cleft with the entrance to the presumed translocation pathway. Structural comparison of ModB2C2A with Sav1866 suggests a common alternating access and release mechanism, with binding of ATP promoting an outward-facing conformation and dissociation of the hydrolysis products promoting an inward-facing conformation.     

Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2

The regulation of ion channel activity by specific lipid molecules is widely recognized as an integral component of electrical signalling in cells. In particular, phosphatidylinositol 4,5-bisphosphate (PIP(2)), a minor yet dynamic phospholipid component of cell membranes, is known to regulate many different ion channels. PIP(2) is the primary agonist for classical inward rectifier (Kir2) channels, through which this lipid can regulate a cell's resting membrane potential. However, the molecular mechanism by which PIP(2) exerts its action is unknown. Here we present the X-ray crystal structure of a Kir2.2 channel in complex with a short-chain (dioctanoyl) derivative of PIP(2). We found that PIP(2) binds at an interface between the transmembrane domain (TMD) and the cytoplasmic domain (CTD). The PIP(2)-binding site consists of a conserved non-specific phospholipid-binding region in the TMD and a specific phosphatidylinositol-binding region in the CTD. On PIP(2) binding, a flexible expansion linker contracts to a compact helical structure, the CTD translates 6 ? and becomes tethered to the TMD and the inner helix gate begins to open. In contrast, the small anionic lipid dioctanoyl glycerol pyrophosphatidic acid (PPA) also binds to the non-specific TMD region, but not to the specific phosphatidylinositol region, and thus fails to engage the CTD or open the channel. Our results show how PIP(2) can control the resting membrane potential through a specific ion-channel-receptor-ligand interaction that brings about a large conformational change, analogous to neurotransmitter activation of ion channels at synapses.     

Immunogenicity of recombinant fowl-pox virus co-expressing structural protein precursor P1-2A and proteinase 3C of FMDV

Two recombinant plasmids, pUTA2P1 and pUTAL3CP1, were constructed by inserting structural protein precursor P1-2A and proteinase 3C of foot-and-mouth disease virus (FMDV) into fowl-pox virus (FPV) recombinant vectors pUTA-2 and pUTA-16-LacZ respectively, and two recombinant FPVs (vUTA2P1 and vUTAL3CP1) screened by the RT-PCR, IFA assay and Western blotting assay were obtained successfully. Mice injected respectively with rFPVs were induced high level specific anti-FMDV antibodies, increasing of T subtypes, and higher cytotoxicities of splenocytes than those of control groups. These results indicated that a new method was used to construct a potential candidate vaccine of FMDV.     

Crystal structure of nerve growth factor in complex with the ligand-binding domain of the TrkA receptor.

Nerve growth factor (NGF) is involved in a variety of processes involving signalling, such as cell differentiation and survival, growth cessation and apoptosis of neurons. These events are mediated by NGF as a result of binding to its two cell-surface receptors, TrkA and p75. TrkA is a receptor with tyrosine kinase activity that forms a high-affinity binding site for NGF. Of the five domains comprising its extracellular portion, the immunoglobulin-like domain proximal to the membrane (TrkA-d5 domain) is necessary and sufficient for NGF binding. Here we present the crystal structure of human NGF in complex with human TrkA-d5 at 2.2 A resolution. The ligand-receptor interface consists of two patches of similar size. One patch involves the central beta-sheet that forms the core of the homodimeric NGF molecule and the loops at the carboxy-terminal pole of TrkA-d5. The second patch comprises the amino-terminal residues of NGF, which adopt a helical conformation upon complex formation, packing against the 'ABED' sheet of TrkA-d5. The structure is consistent with results from mutagenesis experiments for all neurotrophins, and indicates that the first patch may constitute a conserved binding motif for all family members, whereas the second patch is specific for the interaction between NGF and TrkA.     

不同温度下CeO2预煅烧对甲醇氧化反应中Pt/CeO2–C电催化剂性能的影响

Pt/CeO₂–C catalysts with CeO₂ pre-calcined at 300–600°C were synthesized by combining hydrothermal calcination and wet impregnation. The effects of the pre-calcined CeO₂ on the performance of Pt/CeO₂–C catalysts in methanol oxidation were investigated. The Pt/CeO₂–C catalysts with pre-calcined CeO₂ at 300–600°C showed an average particle size of 2.6–2.9 nm and exhibited better methanol electro-oxidation catalytic activity than the commercial Pt/C catalyst. In specific, the Pt/CeO₂–C catalysts with pre-calcined CeO₂ at 400°C displayed the highest electrochemical surface area value of 68.14 m2·g?1 and I_f/I_b ratio (the ratio of the forward scanning peak current density (I_f) and the backward scanning peak current density (I_b)) of 1.26, which are considerably larger than those (53.23 m2·g?1 and 0.79, respectively) of the commercial Pt/C catalyst, implying greatly enhanced CO tolerance.     

Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation

Many bacterial pathogens secrete proteins that activate host trypsinogen-like enzyme precursors, most notably the proenzymes of the blood coagulation and fibrinolysis systems. Staphylococcus aureus, an important human pathogen implicated in sepsis and endocarditis, secretes the cofactor staphylocoagulase, which activates prothrombin, without the usual proteolytic cleavages, to directly initiate blood clotting. Here we present the 2.2 A crystal structures of human alpha-thrombin and prethrombin-2 bound to a fully active staphylocoagulase variant. The cofactor consists of two domains, each with three-helix bundles; this is a novel fold that is distinct from known serine proteinase activators, particularly the streptococcal plasminogen activator streptokinase. The staphylocoagulase fold is conserved in other bacterial plasma-protein-binding factors and extracellular-matrix-binding factors. Kinetic studies confirm the importance of isoleucine 1 and valine 2 at the amino terminus of staphylocoagulase for zymogen activation. In addition to making contacts with the 148 loop and (pro)exosite I of prethrombin-2, staphylocoagulase inserts its N-terminal peptide into the activation pocket of bound prethrombin-2, allosterically inducing functional catalytic machinery. These investigations demonstrate unambiguously the validity of the zymogen-activation mechanism known as 'molecular sexuality'.     

Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A

The crystal structure of the RNA binding domain of the U1 small nuclear ribonucleoprotein A, which forms part of the ribonucleoprotein complex involved in the excision of introns, has been solved. It contains a four-stranded beta sheet and two alpha helices. The highly conserved segments designated RNP1 and RNP2 lie side by side on the middle two beta strands. U1 RNA binding studies of mutant proteins suggest that the RNA binds to the four-stranded beta sheet and to the flexible loops on one end.     

全氟代蒽、菲、芘、并四苯、1,2苯并菲及三苯围苯的量子化学计算

采用密度泛函理论方法(DFT):BHLYP,B3LYP,BP86,BLYP,在全电子的双ξ基组加极化函数和弥散函数(DZP )基组下,计算了全氟代多环芳香族碳氢化合物:全氟代蒽(1-C14F10)、全氟代菲(2-C14F10)、全氟代芘(C16F10)、全氟代并四苯(1-C18F12)、全氟代1,2苯并菲(2-C18F12)及全氟代三苯围苯(3-C18F12)的总能量、优化几何构型、电子亲合势和谐振频率.在B3LYP水平上得到了可靠的绝热电子亲合势(EAad):1-C14F10为1.84 eV;2-C14F10为1.41 eV;C16F10为1.72 eV;1-C18F12为2.39 eV;2-C18为F121.83 eV(Ci)和1.88 eV(C2);3-C18F12为1.69 eV.     

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for maintenance methylation by interacting with DNA nucleotide methyltransferase 1 (DNMT1), the maintenance methyltransferase, and with hemimethylated CpG, the substrate for DNMT1 (refs 1 and 2). Here we present the crystal structure of the SET and RING-associated (SRA) domain of mouse UHRF1 in complex with DNA containing a hemimethylated CpG site. The DNA is contacted in both the major and minor grooves by two loops that penetrate into the middle of the DNA helix. The 5-methylcytosine has flipped completely out of the DNA helix and is positioned in a binding pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5-methylcytosine. Hence, UHRF1 contains a previously unknown DNA-binding module and is the first example of a non-enzymatic, sequence-specific DNA-binding protein domain to use the base flipping mechanism to interact with DNA.