Structural evidence for a two-metal-ion mechanism of group I intron splicing

We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.     

Three-dimensional structure of favin: saccharide binding-cyclic permutation in leguminous lectins

The three-dimensional structure of favin, the glucose- and mannose-binding lectin of Vicia faba (vetch, broad bean), has been determined at a resolution of 2.8 angstroms by molecular replacement. The crystals contain specifically bound glucose and provide the first high-resolution view of specific saccharide binding in a leguminous lectin. The structure is similar to those of concanavalin A (Con A) and green pea lectin; differences from Con A show that minimal changes are needed to accommodate the cyclic permutation in amino acid sequence between the two molecules. The molecule is an ellipsoidal dimer dominated by extensive beta structures. Each protomer contains binding sites for two divalent metal ions (Mn2+ and Ca2+) and a specific saccharide. Glucose is bound by favin in a cleft in the molecular surface and has noncovalent contacts primarily with two peptide loops, one of which contains several metal ion ligands. The specific carbohydrate-binding site is similar to that of Con A in location and general peptide folding, despite several differences in specific amino acid residues.     

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA 's, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNA's.     

Molecular recognition and metal ion template synthesis

Methods for the design and synthesis of ligands intended to be specific for a metal ion have been a recent chemical development. This article describes how this process can be inverted so that the specifics of the coordination environment around the metal ion can be used as a template in large-scale ligand synthesis. The synthesis of macrobicyclic ligands for ferric ion has been accomplished by using active esters of catechol ligands in which catecholate coordination to iron is a prelude to the organic chemical reactions that link the coordination subunits together into one ligand system surrounding a central metal ion coordination site. The lanthanide(III) ions, which are among the most labile metal ions known, have coordination numbers of 8 or higher, and thus their encapsulation into a macrobicyclic structure is a challenging problem. Lanthanide amine complexes have been used as metal templates in the synthesis of such macrobicyclic lanthanide complexes. There is evidence that such a complex is inert to exchange in aqueous solution.     

Reversible cleavage and ligation of hepatitis delta virus RNA

A 148-nucleotide subfragment of hepatitis delta virus RNA was shown to undergo cleavage and ligation reversibly. The direction of the reaction is determined by the presence or absence of Mg2+ ions, with the presence of Mg2+ favoring the cleavage reaction. Ligation requires specific conformation of the RNA molecules involved and occurs only between two cleaved RNA fragments that are still held together by hydrogen bonds. The ligation reaction occurs rapidly on removal of Mg2+ by EDTA. This represents a new class of RNA enzymes.     

去除猪场沼液重金属Pb(Ⅱ)的离子印迹膜制备及其应用

应用羧甲基纤维素钠(CMC)和聚乙烯醇(PVA)等基材制备Pb(Ⅱ)离子印迹膜,开展该印迹膜去除猪场沼液重金属铅的试验研究。结果表明:Pb(Ⅱ)离子印迹膜具有疏松沟壑状的膜结构,内部存在许多规则的约0.24nm左右的空腔结构,与Pb(Ⅱ)的尺寸相匹配;印迹后的Pb(Ⅱ)-ⅡM表面的亲水性能得到明显改善,这有利于水中金属离子Pb(Ⅱ)与膜表面印迹位点的结合;Pb(Ⅱ)-ⅡM对各种金属离子的选择渗透顺序为Pb(Ⅱ)Zn(Ⅱ)Cu(Ⅱ)Cd(Ⅱ)Co(Ⅱ),对铅离子具有良好的选择渗透性能。该铅离子印迹膜对福建省3家猪场沼液重金属铅的去除率为93%~95%,沼液出水均达到《无公害食品蔬菜产地环境条件》标准。     

RNA structure: reading the ribosome

The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.     

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction

Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.     

The structure of catalytically active gold on titania

The high catalytic activity of gold clusters on oxides has been attributed to structural effects (including particle thickness and shape and metal oxidation state), as well as to support effects. We have created well-ordered gold mono-layers and bilayers that completely wet (cover) the oxide support, thus eliminating particle shape and direct support effects. High-resolution electron energy loss spectroscopy and carbon monoxide adsorption confirm that the gold atoms are bonded to titanium atoms. Kinetic measurements for the catalytic oxidation of carbon monoxide show that the gold bilayer structure is significantly more active (by more than an order of magnitude) than the monolayer.     

金属离子在铁(氢)氧化物与腐殖质微界面上的吸附机理和模型研究进展

铁（氢）氧化物和腐殖质是广泛分布在土壤中的重要天然活性物质,因其具有较大的比表面积并且铁（氢）氧化物表面的-OH 与腐殖质表面的-COOH、-OH 等活性官能团可通过静电作用、配体交换等多种机制对重金属离子产生较强吸附,从而影响重金属离子在环境中的迁移、转化和生物效应。深入了解重金属离子在铁（氢）氧化物-腐殖质复合体微界面相互作用的分子机理,对于阐明重金属离子在环境中的迁移、转化过程具有重要意义。本文综述了金属离子在铁（氢）氧化物与腐殖质上吸附机理和模型的研究进展,为重金属污染土壤的风险评估和控制提供理论依据。     

Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein

Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein.     

Sequence-specific peptide cleavage catalyzed by an antibody

Monoclonal antibodies have been induced that are capable of catalyzing specific hydrolysis of the Gly-Phe bond of peptide substrates at neutral pH with a metal complex cofactor. The antibodies were produced by immunizing with a Co(III) triethylenetetramine (trien)-peptide hapten. These antibodies as a group are capable of binding trien complexes of not only Co(III) but also of numerous other metals. Six peptides were examined as possible substrates with the antibodies and various metal complexes. Two of these peptides were cleaved by several of the antibodies. One antibody was studied in detail, and cleavage was observed for the substrates with the trien complexes of Zn(II), Ga(III), Fe(III), In(III), Cu(II), Ni(II), Lu(III), Mg(II), or Mn(II) as cofactors. A turnover number of 6 x 10(-4) per second was observed for these substrates. These results demonstrate the feasibility of the use of cofactor-assisted catalysis in an antibody binding site to accomplish difficult chemical transformations.     

RNA二级结构预测及其在分子分类研究中的应用

文中通过比较RNA二级结构与一级结构和三维结构的差异,说明了RNA二级结构用于系统发育和分子分类研究的优点,并介绍了目前构建RNA二级结构的常用方法以及各种方法的优缺点,并对用于RNA二级结构折叠的软件作了简单介绍。最后从4个方面详细阐述了RNA二级结构在分子分类研究中的应用,即:RNA二级结构应用于分子分类研究的理论和方法;应用RNA二级结构分类与形态分类的区别;三种RNA二级结构在分子分类中的研究现状;RNA二级结构对序列信息的校正与补充。     

Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing

We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNAala by ADAT1.     

Open Framework Structures Based on Sex2- Fragments: Synthesis of (Ph4P)[M(Se6)2] (M = Ga, In, TI) in Molten (Ph4P)2Sex

Polychalcogenide compounds with open polymeric frameworks are rare, and they represent a class of compounds in which microporosity might be achieved. Microporous frameworks that are not oxide-based are now attracting interest because of the combination of catalytic and electronic properties they may simultaneously possess. Three new compounds that may be forerunners to such materials have been discovered and are reported here. The reaction of gallium (Ga), indium (In), and thallium (TI) metal with (Ph(4)P)(2)Se(5) (Ph, phenyl) and an excess of elemental selenium (Se) in a sealed, evacuated Pyrex tube at 200 degrees C yielded small red crystals of (Ph(4)P)[Ga(Se(6))(2)] (I), (Ph(4)P)[In(Se(6))(2)] (II), and (Ph(4)P)[TI(Se(6))(2)] (III), respectively. The [M(Se(6))(2)](-) (M = Ga, In, TI) ions form a two-dimensional, open framework filled with Ph(4)P(+) ions. The [M(Se(6))(2)](n)(n-) structure consists of tetrahedral M(3+) centers and bridging Se(6)(2-) ligands, leading to an extended structure in two dimensions. These layers stack perfectly one on top of the other giving rise to one-dimensional channels running down the c axis that are filled with Ph(4)P(+) cations. These cations are situated in the layers, as opposed to between the layers, and the whole structure can be viewed as a template. Compound II shows remarkable thermal stability and melts congruently at 242 degrees C. Upon cooling to room temperature it gives a glassy phase that recrystallizes upon subsequent heating to 160 degrees C.     

四种金属离子对地图幼鱼淀粉酶活性的影响

以酶学分析的方法研究了4种金属离子Na＋、K＋、Ca2＋、Mg2＋分别在单因子和双因子条件下对地图幼鱼淀粉酶活性的影响。结果表明：在设定的浓度梯度内,单因子条件下,除Ca2＋对淀粉酶活性起强烈的抑制作用外,其余3种离子对淀粉酶活性均起促进作用,其中Mg2＋的促进作用最强。双因子条件下,Na＋和K＋互作对淀粉酶的激活作用高于2者单独作用,Na＋和Mg2＋在一定浓度下互作对淀粉酶的激活作用高于2者单独作用,而K＋和Mg2＋互作则会抑制Mg2＋的激活作用。     

Direct observation of chaperone-induced changes in a protein folding pathway

How chaperone interactions affect protein folding pathways is a central problem in biology. With the use of optical tweezers and all-atom molecular dynamics simulations, we studied the effect of chaperone SecB on the folding and unfolding pathways of maltose binding protein (MBP) at the single-molecule level. In the absence of SecB, we find that the MBP polypeptide first collapses into a molten globulelike compacted state and then folds into a stable core structure onto which several alpha helices are finally wrapped. Interactions with SecB completely prevent stable tertiary contacts in the core structure but have no detectable effect on the folding of the external alpha helices. It appears that SecB only binds to the extended or molten globulelike structure and retains MBP in this latter state. Thus during MBP translocation, no energy is required to disrupt stable tertiary interactions.