Structure of D-ribulose-l,5-bisphosphate carboxylase/oxygenase from Alcaligenes eutrophyus H16

RuBPcase, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (EC4.1.1.39) is the key enzyme of the reductive pentose phosphate cycle. Because of its biological significance, many structural studies on a number of plant and bacterial RuBPCases have been undertaken, including the enzyme isolated from the autotrophic hydrogen-oxidizing bacterium Alcaligenes eutrophus H16 (refs 2-6). Although both the higher plant enzyme and the A. eutrophus enzyme consist of eight large and eight small subunits (L(8)S(8)), no model describing the quaternary structure is generally accepted. Here we present a model for the A. eutrophus RuBPCase derived from X-ray crystallography of three-dimensional (3D) crystals, and electron microscopy and image analysis of two-dimensional (2D) crystals of the enzyme. The X-ray electron density of RuBPCase in the presence of HCO(-)(3), Mg(2+), and the transition state analogue 2-carboxyarabinitol-1,5-bisphosphate (CABP) shows an L(8)S(8) molecule in which the L(4)S(4) half molecules have local 4-fold symmetry (C4). The local 4-fold axes of the two L(4)S(4) halves do not coincide but are shifted by 36 ? and are related by a crystallographic 2-fold axis perpendicular to and between the local 4-fold axes. Electron microscope data of the enzyme without CABP, which can be perfectly modelled using the X-ray densities, do not show this shift and the low-resolution point group of the molecules in the 2D crystals is D4. Both structures are presented.     

X-ray structure of a DNA hairpin molecule

We have solved the crystal structure of a synthetic DNA hexadecanucleotide of sequence: C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G, at 2.1 A resolution, and observed that it adopts a monomeric hairpin configuration with a Z-DNA hexamer stem. In the T4 loop the bases stack with one another and with neighbouring molecules of the crystal, and not with base pairs of their own hexamer stem. Two thymine T10 rings from different molecules stack between the C1-G16 ends of a third and a fourth hairpin helix, in a manner that suggests T-T base 'pairing' and simulates a long, 13-base-pair helix. Although such T-T interactions would not be present in solution, they illustrate a remarkable tendency of thymines for self-association. Purine-purine G-A base pairs are known to exist in the anti-anti conformation with an increase in local helix width; it may be that more serious consideration should be given to the possible existence of pyrimidine-pyrimidine C-T base pairs with decreased local helix width, particularly where several such base pairs occur sequentially.     

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.     

Receptor-binding region of insulin.

X-ray analysis, circular dichroism, receptor binding and biological potencies of chemically modified insulins suggest that the conformation of the insulin molecule is critical to the formation of both the zinc insulin hexamer and the insulin-receptor complex. Results are consistent with an insulin receptor-binding region including many of the hydrophobic residues important to dimerisation in addition to more polar surface residues. There is a further possibility of formation of an antiparallel sheet structure between the insulin and receptor molecules in the complex similar to that between monomers in the insulin dimer.     

Crystallization and preliminary crystallographic analyses of human insulin mutant B9(Ser→Asp) in different aggregation forms

B9(Ser→Asp) insulin, one of the fast-acting insulin mutants produced by protein engineering, has been crystallized. Three crystal forms have been obtained, which belong to or-thorhombic, tetragonal and rhombohedral system, respectively. Each crystal form contains different aggregation units of the mutant, i.e. dimer or hexamer. The diffraction data of the former two have been collected beyond 0.2 nm resolution. The structural analyses and comparisons will provide some information about insulin' s self-association and the structural basis of the fast absorption produced from the mutation.     

锌与羟基的配位作用及晶状氢氧化锌的溶度积

为对文献[1]报道的ε-Zn（OH）2的溶度积值作更准确的测定,用溶解度法研究了Zn2+与羟基的配位作用,在25℃下测定了ε-Zn（OH）2在不同浓度氢氧化钠溶液中的溶解度（μ=2）.在所研究体系中揭示出存在Zn（OH）+,Zn（OH）20,Zn（OH）3-和Zn（OH）42-配离子.用图解法和松驰法计算出相应配离子的稳定常数相一致,结果为:β1=8.1×104,β2=6.3×1011,β3=3.9×1014,β4=1.2×1018.同时求出了更为准确的ε-Zn（OH）2的溶度积Ksp=10×10-17.     

含有金属水链的3,5-吡唑二甲酸铜配位聚合物的合成及热稳定性

在乙腈和水的混合体系中，将硝酸铜和3,5-吡唑二甲酸（H-3pdc）于120 ℃反应72 h, 得到蓝色晶体, 该化合物分子式为{［Cu₃(pdc)₂(H₂O)7］·2H₂O}_n. 通过元素分析、 红外光谱分析、 粉末X射线衍射及单晶X射线衍射对该化合物的结构进行表征, 并研究其热稳定性. 结果表明, 3个铜离子和2个pdc₃-形成中性分子Cu₃(pdc)₂, 水分子作为桥联配体连接Cu₃(pdc)₂形成一维折叠链, 通过氢键作用, 一维链连接形成三维超分子网络, Cu²⁺的配位水分子与晶格水分子通过氢键作用形成了一维金属水链.     

Molecular dynamics simulation of RNA pseudoknot unfolding pathway

Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hairpin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after formation of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure’s unfolding process, which means that both are the unzipping process.     

六元瓜环与[Zn(H2O)6]2+的超分子自组装结构

利用X-射线衍射方法测定六元瓜环(Q[6])与[Zn(H2O)6]2 形成的超分子自组装结构。在该化合物结构中,每一个六元瓜环分子包结了一个1,4二氧六烷分子,与瓜环两端的锌水合离子形成一个分子胶囊结构,并通过锌离子上的配位水分子分别与相邻两瓜环端口的羰基氧原子通过氢键相互作用形成一维超分子链。     

不同离子对氧化锌晶体形貌的影响

以不同Zn盐Zn(CH3COO)2.2H2O,ZnCl2,ZnSO4.7H2O,Zn(NO3)2.6H2O与不同碱NaOH,KOH为原料,制得Zn(OH)42-前驱溶液,使之在水热环境下分解,生成ZnO晶体.产物通过全自动X射线衍射仪(XRD)进行物相分析,扫描电子显微镜(SEM)观测ZnO晶体的形貌和大小.170℃,溶液中的阴离子CH3COO-,SO42-,NO3-,Cl-分别与Na+构成干扰离子对,伴随着晶体生长12 h,晶体成长为片球集状、极性生长明显的花状、极性生长不明显的花状、小尺寸花状ZnO晶体;140℃,溶液中阳离子Na+,K+分别与CH3COO-作为离子对,干扰晶体生长,12 ...     

替加氟-层状双金属氢氧化物纳米杂化物的制备及缓释性能研究

采用共沉淀法制备了非离子型抗癌药物替加氟-LDHs纳米杂化物,依据替加氟分子大小和替加氟-LDHs的通道高度推测出替加氟分子是沿长轴方向垂直于层板以重叠双层方式排列于LDHs层间。药物释放研究表明,替加氟-LDHs纳米杂化物具有明显的缓释效果,表明是有发展潜力的新型药物控释体系。在pH=7.2的缓冲溶液中的释放速率明显低于pH=4.8的缓冲溶液,而在纯水(pH=5.65)中的释放速率明显低于缓冲溶液;释放动力学过程符合准二级动力学方程。     

Orthorhombic crystal structure of an insulin mutant B9Asp at 0.20 nm resolution

Human B9(Ser~i'Asp) insulin, a fast-absorption insulin analogue, was obtained by site-directed mutagenesis at B9 position. The orthorhombic crystal structure of B9Asp insulin was analyzed by crystallography at 0.20 nm resolution. Although no significant change of its overall conformation was observed, the local conformation flanking B9 site differed greatly from native T6 human insulin. The substitution of serine at B9 position by aspartic acid resulted in obvious alteration of local hydrophobic and hydrophilic interactions. As a result, the insulin dimer became unstable and the capability of the hexamer formation was diminished extensively. All these properties contribute to the fast-absorption of B9Asp, In addition, the open state of N-terminus of B-chain, which differs from T- or R- state, might suggest a new conformational state in the monomer or dimer insulin.     

Liquid-like movements in crystalline insulin

Diffuse X-ray scattering from protein crystals provides information about molecular flexibility and packing irregularities. Here we analyse diffraction patterns from insulin crystals that show two types of scattering related to disorder: very diffuse, liquid-like diffraction, and haloes around the Bragg reflections. The haloes are due to coupled displacements of neighbouring molecules in the lattice, and the very diffuse scattering results from variations in atomic positions that are only locally correlated within each molecule. The measured intensity was digitally separated into three components: the Bragg reflections and associated haloes; the water and Compton scattering; and the scattering attributed to internal protein movements. We extend methods used to analyse disorder in membrane structures to simulate the diffuse scattering from crystalline insulin in terms of (1) the Patterson (autocorrelation) function of the ideal, ordered crystal structure, (2) the root-mean-square (r.m.s.) amplitude of the atomic movements, and (3) the mean distance over which these displacements are coupled. Movements of the atoms within the molecules, with r.m.s. amplitudes of 0.4-0.45 A, appear to be coupled over a range of approximately 6 A, as in a liquid. These locally coupled movements account for most of the disorder in the crystal. Also, the protein molecules, as a whole, jiggle in the lattice with r.m.s. amplitudes of approximately 0.25 A that appear to be significantly correlated only between nearest neighbours.     

A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA

A nucleosomal core particle is composed of two each of histones H2A, H2B, H3 and H4 located inside the particle with approximately 47 base pairs (bp) of DNA wrapped around the octamer in about 1.8 turns of a left-handed superhelix. The path of the superhelix is not smooth; the DNA is sharply bent, or kinked, at positions symmetrically disposed at a distance of about one and four double-helical turns in both directions from the nucleosomal dyad axis (designated as sites +/- 1 and +/- 4 respectively). This non-uniform bending is considered archetypal to other DNA-protein complexes, but its mechanism is not clear (reviewed in ref. 4). DNA-histone chemical cross-linking within the core particle has revealed strong binding of each of the two histone H4 molecules to DNA at a distance of 1.5 helical turns either side of the nucleosomal dyad axis (sites +/- 1.5). In each of these sites, a single flexible domain of H4 was previously shown to contact three points, at about nucleotides 55 and 65 on one strand and nucleotide 88 on the complementary strand, numbering from the 5' terminus of each 147-base strand; these three locations are closely juxtaposed across the highly compressed minor and major grooves (Fig. 1). Here we report that the amino-acid residue of histone H4 cross-linked at the 1.5 site is histidine-18, embedded in a highly basic cluster Lys-Arg-His-Arg-Lys-Val-Leu-Arg which is probably involved in the sharp bending of the DNA double helix at the +/- 1 sites.     

苯三羧酸锌配合物的水热合成、结构表征及发光性质研究

通过使用晶体设计规则,合成了新型的含有1,2,4-苯三羧酸和4,4’-联吡啶多齿混合配体的有机锌金属配位聚合物,并通过元素分析仪,红外光谱仪及X-射线单晶衍射仪对其结构进行表征,配合物展示了一个二维面状的超分子结构.在反应过程中,4,4’-联吡啶是作为后期进攻锌原子中心的二次配体,这在锌聚合物中是很罕见的,由于4,4’-联吡啶是一个线性分子,通常4,4’-联吡啶中的两个氮原子用来连接两个金属中心原子.配合物在紫外光照射下有较强的光致发光性质,探索了结构与性质之间的关系,为光敏材料的制备提供了实验支持及理论指导.     

Three-dimensional structure of calmodulin

The three-dimensional structure of calmodulin has been determined crystallographically at 3.0 A resolution. The molecule consists of two globular lobes connected by a long exposed alpha-helix. Each lobe binds two calcium ions through helix-loop-helix domains similar to those of other calcium-binding proteins. The long helix between the lobes may be involved in interactions of calmodulin with drugs and various proteins.     

The three-dimensional structure of an intact monoclonal antibody for canine lymphoma.

Crystal structures of Fab antibody fragments determined by X-ray diffraction characteristically feature four-domain, beta-barrel arrangements. A human antibody Fc fragment has also been found to have four beta-barrel domains. The structures of a few intact antibodies have been solved: in two myeloma proteins, the flexible hinge regions that connect the Fc to the Fab segments were deleted so the molecules were non-functional, structurally restrained, T-shaped antibodies; a third antibody, Kol, had no hinge residues missing but the Fc region was sufficiently disordered that it was not possible to relate its disposition accurately with respect to the Fab components. Here we report the structure at 3.5 A resolution of an IgG2a antitumour monoclonal antibody which contains an intact hinge region and was solved in a triclinic crystal by molecular replacement using known Fc and Fab fragments. The antibody is asymmetric, reflecting its dynamic character. There are two local, apparently independent, dyads in the molecule. One relates the heavy chains in the Fc, the other relates the constant domains of the Fabs. The variable domains are not related by this 2-fold axis because of the different Fab elbow angles of 159 degrees and 143 degrees. The Fc has assumed an asymmetric, oblique orientation with respect to loosely tethered yet almost collinear Fabs. Our study enables the two antigen-binding segments as well as the Fc portion of a functional molecule to be visualized and illustrates the flexibility of these immune response proteins.     

Atomic model of the actin filament

The F-actin filament has been constructed from the atomic structure of the actin monomer to fit the observed X-ray fibre diagram from oriented gels of F-actin. A unique orientation of the monomer with respect to the actin helix has been found. The main interactions are along the two-start helix with a contribution from a loop extending across the filament axis provided by the molecule in the adjacent strand. There are also contacts along the left-handed genetic helix.