X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor

Nitrogenase is a complex enzyme that catalyzes the reduction of dinitrogen to ammonia. Despite insight from structural and biochemical studies, its structure and mechanism await full characterization. An iron-molybdenum cofactor (FeMoco) is thought to be the site of dinitrogen reduction, but the identity of a central atom in this cofactor remains unknown. Fe Kβ x-ray emission spectroscopy (XES) of intact nitrogenase MoFe protein, isolated FeMoco, and the FeMoco-deficient nifB protein indicates that among the candidate atoms oxygen, nitrogen, and carbon, it is carbon that best fits the XES data. The experimental XES is supported by computational efforts, which show that oxidation and spin states do not affect the assignment of the central atom to C(4-). Identification of the central atom will drive further studies on its role in catalysis.     

Evidence for interstitial carbon in nitrogenase FeMo cofactor

The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species.     

一维链状镍配合物[Ni（C_（14）H_（10）N_2O_2）（Mf）]_n的合成和晶体结构

合成了含水杨醛缩苯甲酰腙的一维链状镍配合物[Ni（C14H10N2O2）（Mf）]n（Mf=C4H9NO,即吗啡啉）,通过元素分析,红外、电子光谱和X-射线单晶衍射进行了表征.晶体属单斜晶系,空间群为P21/c,a=0.9708（4）nm,b=1.4783（7）nm,c=1.2275（4）nm,β=95.728（14）°,V=1.7528（12）nm3,Z=4,Mr=384.07,Dc=1.455 g.cm-3,μ=1.129 mm-1,F（000）=800,R=0.0759,wR=0.2155.中心镍离子与水杨醛缩苯甲酰腙配体提供的2个氧原子与1个氮原子以及1个配位吗啡啉的氮原子配位,形成了N2O2的平面四边形的配位构型.晶体内每个配合物分子通过分子间氢键与相邻另一个配合物分子缔合成一个沿c轴方向的一维链状结构,N…N氢键键长为0.3239（10）nm,N-H…N氢键键角为173.56°.     

Structure of a cofactor-deficient nitrogenase MoFe protein

One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We describe here the crystal structure of an iron-molybdenum cofactor-deficient form of the nitrogenase MoFe protein, into which the cofactor is inserted in the final step of MoFe protein assembly. The MoFe protein folds as a heterotetramer containing two copies each of the homologous alpha and beta subunits. In this structure, one of the three alpha subunit domains exhibits a substantially changed conformation, whereas the rest of the protein remains essentially unchanged. A predominantly positively charged funnel is revealed; this funnel is of sufficient size to accommodate insertion of the negatively charged cofactor.     

X-ray structure of the major adduct of the anticancer drug cisplatin with DNA: cis-[Pt(NH3)2(d(pGpG))

Crystals of the adduct of the anticancer drug cis-diamminedichloroplatinum(II), cis-DDP, with d(pGpG), its putative target on DNA in the cancer cell, have been obtained and used in an x-ray crystallographic study to elucidate the molecular structure to atomic resolution. Each of the four crystallographically independent cis-[Pt(NH3)2(d(pGpG))] molecules is comprised of a square-planar platinum atom bonded to two ammonia ligands and two N(7) atoms of guanosine nucleosides from the same chain. Base stacking of the two adjacent guanine rings is completely disrupted by coordination to the cis-(Pt(NH3)2)2+ unit. Comparison of the backbone and deoxyribose ring torsion angles with those found by previous (nuclear magnetic resonance spectroscopy) studies of this adduct in solution demonstrates that the solid state geometry is substantially the same as that in solution. The relevance of these results to the molecular mechanism of action of cis-DDP is discussed.     

Scavenger Probe Sampling: A Method for Studying Gaseous Free Radicals

Scavenger probe sampling for determining the concentration of certain gaseous free radicals and atoms has been used to study flames and electric discharges. Combining microprobe sampling and chemical scavenging with mass spectral analysis, this technique offers high spatial resolution, absolute concentration determination, and high temperature applicability. The reactions of hydrogen atoms with chlorinated hydrocarbons and oxygen atoms with nitrogen dioxide were used for scavenging. The results were reproducible and proportional to concentration. In an electric discharge oxygen atom concentrations agreed with gas phase titration determinations. The gas phase titration measures atom flux rather than concentration, and differences as high as 20 percent were observed. A method for deriving concentration from flux measurements is discussed.     

Side-on copper-nitrosyl coordination by nitrite reductase

A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.     

In Situ X-ray Absorption Study of Surface Complexes: Selenium Oxyanions on agr-FeOOH

A novel application of x-ray absorption spectroscopy has provided structural information for ions sorbed at oxide-water interfaces. As an example, in situ extended x-ray absorption fine structure (EXAFS) measurements of adsorbed selenate and selenite ions at ah alpha-FeOOH(goethite)-water interface have been performed; these measurements show that selenate forms a weakly bonded, outer-sphere complex and that selenite forms a strongly bonded, inner-sphere complex. The selenite ion is bonded directly to the goethite surface in a bidentate fashion with two iron atoms 3.38 angstroms from the selenium atom. Adsorbed selenate has no iron atom in the second coordination shell of selenium, which indicates retention of its hydration sphere upon sorption. This method provides direct structural information for adsorbed species at solid-liquid interfaces.     

生物固氮基因簇结构与进化研究进展

在固氮菌基因组中,固氮相关基因都是作为一个或几个基因簇存在,是细菌生物固氮的遗传基础。这其中包括固氮酶结构基因nifHDK,以及参与电子转运和铁钼辅因子合成及组装的其他相关基因。对不同菌中固氮基因簇的结构和进化进行了简要的比较分析。比较所有已测序固氮菌中的固氮基因簇,发现均至少含有六个保守基因:nifH、nifD、nifK、nifE、nifN和nifB,并且这6个基因在所有已鉴定的系统中都是固氮所必需的。尽管在不同种类的固氮微生物中,固氮基因簇的构成及组织模式有所不同,但是它们在结构、催化机制和系统进化上紧密相关。同时也对固氮基因的研究方向提出了展望。旨在为今后进一步研究生物固氮机制,了解固氮微生物的进化,扩展生物固氮多样性提供理论基础。     

A steric mechanism for inhibition of CO binding to heme proteins

The crystal structures of myoglobin in the deoxy- and carbon monoxide-ligated states at a resolution of 1.15 angstroms show that carbon monoxide binding at ambient temperatures requires concerted motions of the heme, the iron, and helices E and F for relief of steric inhibition. These steps constitute the main mechanism by which heme proteins lower the affinity of the heme group for the toxic ligand carbon monoxide.     

Synthesis and Structure of an Iron(III) Sulfide-Ferritin Bioinorganic Nanocomposite

Amorphous iron sulfide minerals containing either 500 or 3000 iron atoms in each cluster have been synthesized in situ within the nanodimensional cavity of horse spleen ferritin. Iron-57 M?ssbauer spectroscopy indicated that most of the iron atoms in the 3000-iron atom cores are trivalent, whereas in the 500-iron atom clusters, approximately 50 percent of the iron atoms are Fe(III), with the remaining atoms having an effective oxidation state of about +2.5. Iron K-edge extended x-ray absorption fine structure data for the 500-iron atom nanocomposite are consistent with a disordered array of edge-shared FeS(4) tetrahedra, connected by Fe(S)(2)Fe bridges with bond lengths similar to those of the cubane-type motif of iron-sulfur clusters. The approach used here for the controlled synthesis of bioinorganic nanocomposites could be useful for the nanoscale engineering of dispersed materials with biocompatible and bioactive properties.     

Structure of precursor-bound NifEN: a nitrogenase FeMo cofactor maturase/insertase

NifEN plays an essential role in the biosynthesis of the nitrogenase iron-molybdenum (FeMo) cofactor (M cluster). It is an α(2)β(2) tetramer that is homologous to the catalytic molybdenum-iron (MoFe) protein (NifDK) component of nitrogenase. NifEN serves as a scaffold for the conversion of an iron-only precursor to a matured form of the M cluster before delivering the latter to its target location within NifDK. Here, we present the structure of the precursor-bound NifEN of Azotobacter vinelandii at 2.6 angstrom resolution. From a structural comparison of NifEN with des-M-cluster NifDK and holo NifDK, we propose similar pathways of cluster insertion for the homologous NifEN and NifDK proteins.     

The structure of a complex of recombinant hirudin and human alpha-thrombin

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.     

Magnetism from the atom to the bulk in iron, cobalt, and nickel clusters

Molecular beam deflection measurements of small iron, cobalt, and nickel clusters show how magnetism develops as the cluster size is increased from several tens to several hundreds of atoms for temperatures between 80 and 1000 K. Ferromagnetism occurs even for the smallest sizes: for clusters with fewer than about 30 atoms the magnetic moments are atomlike; as the size is increased up to 700 atoms, the magnetic moments approach the bulk limit, with oscillations probably caused by surface-induced spin-density waves. The trends are explained in a magnetic shell model. A crystallographic phase transition from high moment to low moment in iron clusters has also been identified.     

Atomic resolution imaging of adsorbates on metal surfaces in air: iodine adsorption on pt(111)

The adsorption of iodine on platinum single crystals was studied with the scanning tunneling microscope (STM) to define the limits of resolution that can be obtained while imaging in air and to set a target resolution for STM imaging of metal surfaces immersed in an electrochemical cell. Two iodine adlattice unit cells of slightly different iodine packing density were clearly imaged: ( radical7 x radical7) R19.1 degrees -I, surface coverage ?(I) = 3/7; and (3 x 3)-I, ?(I) = 4/9. The three iodine atoms in the ( radical7 x radical7) unit cell form a regular hexagonal lattice interatomic distance d(I) = 0.424 nanometer, with two atoms adsorbed in threefold hollow sites and one atom adsorbed at an atop site. The (3 x 3) unit cell showed two different packing arrangements of the four iodine atoms exit. In one of the (3 x 3) structures, the iodine atoms pack to form a hexagonal lattice, d(I) = 0.417 nanometer, with three of the iodine atoms at twofold adsorption sites and one atom at an atop site. Another packing arrangement of iodine into the (3 x 3) unit cell was imaged in which the iodine atoms are not arranged symmetrically.     

Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints

Model calculations were performed to test the possibility of solving crystal structures of proteins by Patterson search techniques with three-dimensional structures obtained from nuclear magnetic resonance (NMR) interproton distance restraints. Structures for crambin obtained from simulated NMR data were used as the test system; the root-mean-square deviations of the NMR structures from the x-ray structure were 1.5 to 2.2 A for backbone atoms and 2.0 to 2.8 A for side-chain atoms. Patterson searches were made to determine the orientation and position of the NMR structures in the unit cell. The correct solution was obtained by comparing the rotation function results of several of the NMR structures and the average structure derived from them. Conventional refinement techniques reduced the R factor from 0.43 at 4 A resolution to 0.27 at 2 A resolution without inclusion of water molecules. The partially refined structure has root-mean-square backbone and side-chain atom deviations from the x-ray structure of 0.5 and 1.3 A, respectively.     

由乙二胺、α-萘乙酸构筑的镍(Ⅱ)配合物的合成、结构和抑菌性质研究

[目的]α-萘乙酸是一种植物生长调节剂,乙二胺是一类很好的有机配体,二者与金属离子共同反应合成金属配合物,并研究配合物的抑菌活性。[方法]通过水热合成法合成新的配合物,利用牛津杯法研究配合物的抑菌活性。[结果]成功合成了配合物[Ni(C12H9O2)2(C2H8N2)3]2,采用单晶X-射线、元素分析和FT-IR对合成配合物[Ni(C12H9O2)2(C2H8N2)3]2进行结构表征。同时,研究了该配合物的抑菌活性。[结论]该晶体属于三斜晶系,P-1空间群:a=9.145(6),b=13.146(8),c=14.385(9);α=70.120(7)°,β=74.272(7)°,γ=69.819(7)°,Z=2。Ni(II)与来自3个乙二胺分子的六个氮原子配位,形成扭曲的八面体配位构型。配合物有一定的抑菌活性。     

Ion binding by synthetic macrocyclic compounds

The existence of synthetic macrocyclic molecules with hydrophilic cavities containing multiple binding atoms and with hydrophobic exteriors gives rise to extraordinary possibilities with respect to the design and synthesis of molecules with specific cation and anion binding properties. The preparation of many new macrocyclic compounds has recently been reported, but few practical applications for them have been suggested. From the information available, it is becoming clear that it should be possible to synthesize macrocycles that will have specified, or selected, ion binding properties. Cavity size can be varied to accommodate only those cations or anions within a specified narrow band of sizes. Numbers and types of coordinating atoms can be chosen to give essentially electrostatic or covalent bonding or a combination of the two in a metalmacrocycle complex. The metal ligand bond appears to be predominantly ionic in the case of the cyclic polyethers but the covalent character increases on substitution of sulfur or nitrogen for oxygen donor atoms. The essential hydrophobic exteriors of the macrocycles can be modified by the addition of side chains and groups to facilitate the solution of anions and cations in organic solvents. The structures of many macrocycles can be made to approximate naturally occurring molecules, that is, cyclic polyethers similar to macrocyclic antibiotics of the valinomycin and nonactin types and cyclic polyamines similar to porphyrins. Macrocycles are also useful as model compounds for the study of metal interactions with biological systems. The synthetic macrocycles thus represent an intriguing new area of coordination chemistry, the systematic study of which should lead to many interesting and useful chemical applications in the field of metal complexation in solution.     

Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations

The crystal structure of a murine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, has been determined and refined at 2.4 angstrom resolution. The structure is folded as an eight-stranded parallel alpha/beta barrel with a deep pocket at the beta-barrel COOH-terminal end wherein the inhibitor and a zinc are bound and completely sequestered. The presence of the zinc cofactor and the precise structure of the bound analog were not previously known. The 6R isomer of the analog is very tightly held in place by the coordination of the 6-hydroxyl to the zinc and the formation of nine hydrogen bonds. On the basis of the structure of the complex a stereoselective addition-elimination or SN2 mechanism of the enzyme is proposed with the zinc atom and the Glu and Asp residues playing key roles. A molecular explanation of a hereditary disease caused by several point mutations of an enzyme is also presented.     

Rhodizite: structure and composition

The mineral rhodizite could not be assigned a chemical formula on the basis of chemical analyses. The solution of the crystal structure reported here reveals that CsB(12)Be(4)Al(4)O(28) is the ideal formula. The oxygen atoms occupy all but four sites per cell of cubic close packing whose period is (1/2)a. The boron, beryllium, and aluminum atoms occupy interstices of this array, the first two in tetrahedral coordination, the last in octahedral coordination. Together these atoms form a continuous network whose composition is B(12)Be(4)Al(4)O(28), which should be neutral. The alkali atom is enclosed in a cage in this network and presumably is not behaving as an ion.