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At least 127 records · Page 7Linked to original sources

PubMed1997

A quantitative analysis of single protein-ligand complex separation with the atomic force microscope.

Force measurements on and within single macromolecular complexes utilizing techniques such as atomic force microscopy, optical trapping, flexible glass fibers, and magnetic beads provide a rich source of quantitative data on biomolecular processes. Stochastic thermal fluctuations, an undesirable source of noise in macroscopic biochemical experiments, are an essential element of these sensitive and novel experiments. With the proper analysis, a great deal of information can be gleaned from measurements of these fluctuations. A quantitative framework for analyzing such measurements, based on Kramers' theory of molecular dissociation, is developed. The analysis reveals the kinetic origin and stochastic nature of the measurements. This framework is presented in the context of protein-ligand separation with the atomic force microscope.

Journal Article↗

PubMed2000

Structural studies of a crystalline insulin analog complex with protamine by atomic force microscopy.

Crystallographic studies of insulin-protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of crystalline neutral protamine Lys(B28)Pro(B29) (NPL), a complex of Lys(B28)Pro(B29) insulin, in which the C-terminal prolyl and lysyl residues of human insulin are inverted, and protamine that is used as an intermediate time-action therapy for treating insulin-dependent diabetes. Tapping mode AFM performed at 6 degrees C on bipyramidally tipped tetragonal rod-shaped NPL crystals revealed large micron-sized islands separated by 44-A tall steps. Lattice images obtained by in situ TMAFM phase and height imaging on these islands were consistent with the arrangement of individual insulin-protamine complexes on the P4(1)2(1)2 (110) crystal plane of NPH, based on a low-resolution x-ray diffraction structure of NPH, arguing that the NPH and NPL insulins are isostructural. Superposition of the height and phase images indicated that tip-sample adhesion was larger in the interstices between NPL complexes in the (110) crystal plane than over the individual complexes. These results demonstrate the utility of low-temperature TMAFM height and phase imaging for the structural characterization of biomolecular complexes.

Crystallization↗

PubMed2005

High resolution electronic spectra of 7-azaindole and its Ar atom van der Waals complex.

Rotationally resolved fluorescence excitation spectra of the S(1)<--S(0) origin band of 7-azaindole [1H-pyrrolo(2,3-b)pyridine] and its argon atom van der Waals complex have been recorded and assigned. The derived rotational constants give information about the geometries of the two molecules in both electronic states. The equilibrium position of the argon atom in the azaindole complex is considerably different from its position in the corresponding indole complex. Furthermore, the argon atom moves when the UV photon is absorbed. There are significant differences in the intermolecular potential energy surfaces in the two electronic states. A large, vibration-state-dependent rotation of the S(1)<--S(0) electronic transition moment vector of 7-azaindole relative to that of indole suggests that these differences have their origin in S(1)/S(2) electronic state mixing in the isolated molecule, a mixing that is enhanced by nitrogen substitution in the six-membered ring.

Journal Article↗

PubMed2005

Oxygen atom transfer reactivity from a dioxo-Mo(VI) complex to tertiary phosphines: synthesis, characterization, and structure of phosphoryl intermediate complexes.

The oxygen atom transfer (OAT) reactivity of TpMoO2Cl with PMe3, PEt3, and PPhMe2 (where Tp = hydrotris(3,5-dimethylpyrazol-1-yl)borate) has been investigated. The OAT reactions proceed through a diamagnetic Mo(IV) phosphoryl intermediate complex of general formula TpMoOCl(OPR3) (OPR3 = OPMe3, OPEt3, OPPhMe2), which have been isolated and characterized by 1H and 31P NMR, UV-visible, and infrared spectroscopies and electrospray ionization mass spectrometry. Solid-state crystal structures of TpMoOCl(OPMe3) and TpMoOCl(OPPhMe2) are also reported, the oxygen-to-phosphorus distances agree with a double-bond formulation and a single bond between the metal and the phosphoryl oxygen atom. The stability of the phosphoryl intermediate complexes depends on the steric properties of the coordinated phosphine-oxides. These intermediate complexes have been converted to solvent-coordinated species, TpMoOCl(solv) (solv = acetonitrile or dmf), and the coordinated solvents exchange with the bulk solvent.

Crystallography↗

PubMed2006

Metastable intermolecular charge-transfer complexes with a pentavalent carbon atom.

A novel type of metastable complexes of metal (such as Na) atoms with a super-fluorinated carbon molecule is investigated, with a carbon atom exhibiting a unique, pentavalent character. It is induced by the charge transfer from the alkali metal component, followed by a geometric compression of the ion pair system. Analysis of the electron-density distribution confirms the real chemical nature of the extra C-F bond. Structure and stability of the system are characterized ab initio, and a spectrum of electronic perturbations is considered. The ways of forming the systems are discussed, and the spectroscopic parameters are predicted, facilitating their detection in experiments.

Carbon↗

PubMed2006

AFM studies of the supramolecular assembly of bacterial photosynthetic core-complexes.

The atomic force microscope (AFM) allows visualization of the assembly and molecular interactions of single proteins. Most recently, AFM images of bacterial membranes have revealed details of the supramolecular architecture of bacterial photosynthetic apparatus in different species. The near-native experimental conditions used in AFM imaging reduce artefacts and make AFM ideal for studying native conformations. High-resolution AFM of native membranes has revealed variation in core-complex architectures amongst species.

Bacteria↗

PubMed2001

Atomic force microscopy of RecA--DNA complexes using a carbon nanotube tip.

We report high resolution images of RecA-double stranded (ds) DNA complexes obtained by atomic force microscopy (AFM). When a carbon nanotube (CNT) tip was used, AFM images visualized the 10-nm pitch of RecA-dsDNA complexes and RecA filaments as three-dimensional surface topography without reconstruction analysis. The depth of the notch between two pitches was less than 1 nm. When adsorbed on a soft surface covered with proteins, naked DNA, RecA monomers, RecA hexamers, and short RecA filaments were all clearly resolved in one image. The high resolution images with a CNT tip provided valuable information on the initiation process of RecA-dsDNA complex formation.

DNA↗

PubMed2004

Synthesis and characterisation of cyclopentadienyl complexes of barium: precursors for atomic layer deposition of BaTiO3.

Cyclopentadienyl complexes Ba(C5Me5)2(THF)2 (1), Ba(C5Me5)2(A) (A = THF, dien, trien, diglyme, triglyme) (2-5), Ba(Pr(i)3C5H2)2(THF)2 (6), Ba(Bu(t)3C5H2)2(THF) (7), Ba(Me2NC2H4C5Me4)2 (8) and Ba(EtOC2H4C5Me4)2 (9) were prepared and characterised with TGA/SDTA, NMR and MS. Crystal structures of 2, 4, 5, 7, 8 and 9 are presented. All complexes prepared sublime under reduced pressure and complexes 1, 6 and 7 showed volatility also under atmospheric pressure. Complexes 1, 6 and 7 lose the coordinated THF when evaporated while complexes 2-5 are sublimable as complete molecules under reduced pressure. Complexes with bulky cyclopentadienyl ligands (6 and 7) are the most thermally stable and volatile among the prepared barocenes. X-ray structure determinations reveal that all the complexes studied are monomeric. Complexes 1, 7 and 8 were successfully tested in BaTiO3 thin film depositions by atomic layer deposition (ALD).

Journal Article↗

PubMed2005

A computational study of the reactions of a beta-diketiminatoaluminium(I) complex with the hydrogen atom and the electron.

A computational study has been performed to examine the reactions of a model beta-diketiminatoaluminium (I) complex with the hydrogen atom and with the electron. It was found that the hydrogen atom adds to the metal centre exothermically (DeltaH(rxn)=-202 kJ mol(-1)), and the spin density in the resulting radical resides entirely on the beta-diketiminato ligand. The spin density of the corresponding radical anion is very similar to the H-adduct.

Journal Article↗

PubMed2005

Nitrogen-atom exchange mediated by nitrido complexes of molybdenum.

Nitrido complexes NMo(OC(CF3)2Me)3 and NMo(OC(CF3)3)3(NCMe) containing fluorinated alkoxide ancillary ligands are synthesized in 57% and 50% yield, respectively. Both complexes undergo N-atom exchange within hours at 30 degrees C with acetonitrile and benzonitrile in either THF-d8 or CD2Cl2, as shown by 15N NMR studies using labeled 15NCMe. In both solvents, is the more active in this process. Additionally, both compounds are substantially more active in THF-d8 than in CD2Cl2. Complex crystallizes in the space group P2(1)/c, adopting a pseudo-square-pyramidal structure in which the nitrido moiety occupies the apical position, 1.633(3) A away from Mo.

Journal Article↗

PubMed2004

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex.

The atomic view of the active site coupling termed channelling is a major subject in molecular biology. We have determined two distinct crystal structures of the bacterial multienzyme complex that catalyzes the last three sequential reactions in the fatty acid beta-oxidation cycle. The alpha2beta2 heterotetrameric structure shows the uneven ring architecture, where all the catalytic centers of 2-enoyl-CoA hydratase (ECH), L-3-hydroxyacyl-CoA dehydrogenase (HACD) and 3-ketoacyl-CoA thiolase (KACT) face a large inner solvent region. The substrate, anchored through the 3'-phosphate ADP moiety, allows the fatty acid tail to pivot from the ECH to HACD active sites, and finally to the KACT active site. Coupling with striking domain rearrangements, the incorporation of the tail into the KACT cavity and the relocation of 3'-phosphate ADP bring the reactive C2-C3 bond to the correct position for cleavage. The alpha-helical linker specific for the multienzyme contributes to the pivoting center formation and the substrate transfer through its deformation. This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex.

3-Hydroxyacyl CoA Dehydrogenases↗

PubMed2001

Rhenium(I) carbonyl complexes of 2,4,6-tris(2-pyridyl)-1,3,5-triazine (TPT). Rhenium(I)-promoted methoxylation of the triazine ring carbon atom in dinuclear rhenium complexes.

2,4,6-Tris(2-pyridyl)-1,3,5-triazine (TPT) bridged dinuclear rhenium(I) tricarbonyl halide complexes with the composition (mu-TPT)[ReX(CO)(3)](2) (3, X = Cl; 4, X = Br) can be made either by one-pot reaction of TPT with 2 equiv of [ReX(CO)(5)] (X = Cl and Br) in chloroform or by reacting mononuclear [ReX(CO)(3)(TPT)] (2) (1, X = Cl; 2, X = Br) with an excess amount of [ReX(CO)(5)]. Crystal data are as follows. 1: monoclinic, P2(1)/c, a = 11.751(1) A, b = 11.376(1) A, c = 15.562(2) A, beta = 103.584(2) degrees, V = 2022.0(4) A(3), Z = 4. 2: monoclinic, P2(1)/c, a = 11.896(1) A, b = 11.396(1) A, c = 15.655(1) A, beta = 104.474(2) degrees, V = 2054.9(3) A(3), Z = 4. 3: triclinic, P1, a = 11.541(2) A, b = 12.119(2) A, c = 13.199(2) A, alpha = 80.377(2) degrees, beta = 76.204(3) degrees, gamma = 66.826(2) degrees, V = 1642.5(4) A(3), Z = 2. Crystals of 4 crystallized from acetone: triclinic, P1, a = 11.586(5) A, b = 12.144(5) A, c = 13.364(6) A, alpha = 80.599(7) degrees, beta = 76.271(8) degrees, gamma = 67.158(8) degrees, V = 1678.0(12) A(3), Z = 2. Crystals of 4' are obtained from CH(2)Cl(2)-pentane solution: monoclinic, C2/c, a = 17.555(4) A, b = 15.277(3) A, c = 13.093(3) A, beta = 111.179(3) degrees, V = 3274.0(12) A(3), Z = 4. By contrast, similar reactions in the presence of methanol yielded complexes with the composition [mu-C(3)N(3)(OMe)(py)(2)(pyH)][ReX(CO)(3)](2) (5, X = Cl; 6, X = Br). Crystal data for 5: monoclinic, C2/c, a = 26.952(2) A, b = 16.602(1) A, c = 14.641(1) A, beta = 116.147(1) degrees, V = 5880.5(8) A(3), Z = 8. 6: monoclinic, C2/c, a = 27.513(3) A, b = 16.740(2) A, c = 14.837(2) A, beta = 116.925(2) degrees, V = 6092.8(10) A(3), Z = 8. An unusual metal-induced methoxylation at the carbon atom of the triazine ring of the bridging TPT ligand was observed. The nucleophilic attack of MeO(-) on C(3) results in a tetrahedral geometry around the carbon atom. Concomitantly, the uncoordinated pyridyl ring is protonated and rotated into a perpendicular orientation relative to the central C(3)N(3) ring. Reaction of TPT with [NEt(4)](2)[ReBr(3)(CO)(3)] in benzene-methanol resulted in an unexpected dinuclear complex 7, with formulation [mu-C(3)N(3)(OMe)(py)(3)][Re(CO)(3)][ReBr(CO)(3)]. The methoxylated TPT ligand functions simultaneously as a tridentate and bidentate ligand with two fac-Re(CO)(3)(+) cores. Crystal data for 7: monoclinic, P2(1)/n, a = 12.114(1) A, b = 14.878(1) A, c = 15.807(1) A, beta = 104.601(1) degrees, V = 2756.9(3) A(3), Z = 4.

Journal Article↗

PubMed2003

Binuclear manganese compounds of potential biological significance. Part 2. Mechanistic study of hydrogen peroxide disproportionation by dimanganese complexes: the two oxygen atoms of the peroxide end up in a dioxo intermediate.

The dimanganese(II,II) complexes 1a [Mn(2)(L)(OAc)(2)(CH(3)OH)](ClO(4)) and 1b [Mn(2)(L)(OBz)(2)(H(2)O)](ClO(4)), where HL is the unsymmetrical phenol ligand 2-(bis-(2-pyridylmethyl)aminomethyl)-6-((2-pyridylmethyl)(benzyl)aminomethyl)-4-methylphenol, react with hydrogen peroxide in acetonitrile solution. The disproportionation reaction was monitored by electrospray ionization mass spectrometry (ESI-MS) and EPR and UV-visible spectroscopies. Extensive EPR studies have shown that a species (2) exhibiting a 16-line spectrum at g approximately 2 persists during catalysis. ESI-MS experiments conducted similarly during catalysis associate 2a with a peak at 729 (791 for 2b) corresponding to the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) ([Mn(III)Mn(IV)(L)(O)(2)(OBz)](+) for 2b). At the end of the reaction, it is partly replaced by a species (3) possessing a broad unfeatured signal at g approximately 2. ESI-MS associates 3a with a peak at 713 (775 for 3b) corresponding to the formula [Mn(II)Mn(III)(L)(O)(OAc)](+) ([Mn(II)Mn(III)(L)(O)(OBz)](+) for 3b). In the presence of H(2)(18)O, these two peaks move to 733 and to 715 indicating the presence of two and one oxo ligands, respectively. When H(2)(18)O(2) is used, 2a and 3a are labeled showing that the oxo ligands come from H(2)O(2). Interestingly, when an equimolar mixture of H(2)O(2) and H(2)(18)O(2) is used, only unlabeled and doubly labeled 2a/b are formed, showing that its two oxo ligands come from the same H(2)O(2) molecule. All these experiments lead to attribute the formula [Mn(III)Mn(IV)(L)(O)(2)(OAc)](+) to 2a and to 3a the formula [Mn(II)Mn(III)(L)(O)(OAc)](+). Freeze-quench/EPR experiments revealed that 2a appears at 500 ms and that another species with a 6-line spectrum is formed transiently at ca. 100 ms. 2a was prepared by reaction of 1a with tert-butyl hydroperoxide as shown by EPR and UV-visible spectroscopies and ESI-MS experiments. Its structure was studied by X-ray absorption experiments which revealed the presence of two or three O atoms at 1.87 A and three or two N/O atoms at 2.14 A. In addition one N atom was found at a longer distance (2.3 A) and one Mn at 2.63 A. 2a can be one-electron oxidized at E(1/2) = 0.91 V(NHE) (DeltaE(1/2) = 0.08 V) leading to its Mn(IV)Mn(IV) analogue. The formation of 2a from 1a was monitored by UV-visible and X-ray absorption spectroscopies. Both concur to show that an intermediate Mn(II)Mn(III) species, resembling 4a [Mn(2)(L)(OAc)(2)(H(2)O)](ClO(4))(2), the one-electron-oxidized form of 1a, is formed initially and transforms into 2a. The structures of the active intermediates 2 and 3 are discussed in light of their spectroscopic properties, and potential mechanisms are considered and discussed in the context of the biological reaction.

Crystallography, X-Ray↗

PubMed1998

Visualization of trp repressor and its complexes with DNA by atomic force microscopy.

We used tapping mode atomic force microscopy to visualize the protein/protein and the protein/DNA complexes involved in transcriptional regulation by the trp repressor (TR). Plasmid fragments bearing the natural operators trp EDCBA and trp R, as well as nonspecific fragments, were deposited onto mica in the presence of varying concentrations of TR and imaged. In the presence of L-tryptophan, both specific and nonspecific complexes of TR with DNA are apparent, as well as free TR assemblies directly deposited onto the mica surface. We observed the expected decrease in specificity of TR for its operators with increasing protein concentration (1-5 nM). This loss of DNA-binding specificity is accompanied by the formation of large protein assemblies of varying sizes on the mica surface, consistent with the known tendency of the repressor to oligomerize in solution. When the co-repressor is omitted, no repressor molecules are seen, either on the plasmid fragments or free on the mica surface, probably because of the formation of larger aggregates that are removed from the surface upon washing. All these findings support a role for protein/protein interactions as an additional mechanism of transcriptional regulation by the trp repressor.

Bacterial Proteins↗

PubMed2001

Anomalous properties in ferroelectrics induced by atomic ordering.

Complex insulating perovskite alloys are of considerable technological interest because of their large dielectric and piezoelectric responses. Examples of such alloys include (Ba1-xSrx)TiO3, which has emerged as a leading candidate dielectric material for the memory-cell capacitors in dynamic random access memories; and Pb(Zr1-xTix)O3 (PZT), which is widely used in transducers and actuators. The rich variety of structural phases that these alloys can exhibit, and the challenge of relating their anomalous properties to the microscopic structure, make them attractive from a fundamental point of view. Theoretical investigations of modifications to the atomic ordering of these alloys suggest the existence of further unexpected structural properties and hold promise for the development of new functional materials with improved electromechanical properties. Here we report ab initio calculations that show that a certain class of atomic rearrangement should lead simultaneously to large electromechanical responses and to unusual structural phases in a given class of perovskite alloys. Our simulations also reveal the microscopic mechanism responsible for these anomalies.

Journal Article↗

PubMed2003

[Cr(N)Cl4]2-: a simple nitrido complex synthesized by nitrogen-atom transfer.

A new general route to nitrido complexes of Cr(V) based on nitrogen-atom transfer from Mn(N)(salen) to labile CrCl3(THF)3 is presented. By this approach, the simplest nitrido complex of a first row transition metal, [Cr(N)Cl4]2-, has been synthesized and isolated. [[N(CH3)4]2[Cr(N)Cl4].H2O crystallizes in the cubic space group Fm-3m with disordered anions. Cr-N is 1.555(19) A, Cr-Cl is 2.2912(16) A, and N-Cr-Cl is 101.24(4) degrees . The orbital splitting scheme of [Cr(N)Cl4]2- is extreme with the dx2-y2 orbital 10 000 cm-1 lower in energy than the degenerate {dzx, dyz} set of orbitals destabilized by pi-bonding with the nitrido ligand. Hydrolysis of [Cr(N)Cl4]2 preserves the {CrN}2+ moiety.

Journal Article↗

PubMed2005

Nitrogen atom transfer between manganese complexes of salen, porphyrin, and corrole and characterization of a (nitrido)manganese(VI) corrole.

The investigations of complete nitrogen atom transfer reactions from (nitrido)manganese(V) salen to manganese(III) complexes of porphyrins and corroles revealed that stabilization of the [Mn(N)]2+ moiety is in the order of corrole > porphyrin > salen. The first kinetic examination of this quite fundamental reaction exposed a large solvent effect on both the enthalpy and entropy activation energies. Oxidation of the (nitrido)manganese(V) corroles leads to the first (nitrido)manganese(VI) complexes that are coordinated by tetrapyrrolic ligands.

Journal Article↗

PubMed2002

Molecular and atomic analysis of uranium complexes formed by three eco-types of Acidithiobacillus ferrooxidans.

A combination of EXAFS, transmission electron microscopy and energy-dispersive X-ray was used to conduct a molecular and atomic analysis of the uranium complexes formed by Acidithiobacillus ferrooxidans. The results demonstrate that this bacterium accumulates uranium as phosphate compounds. We suggest that at toxic levels when the uranium enters the bacterial cells, A. ferrooxidans can detoxify and efflux this metal by a process in which its polyphosphate bodies are involved.

Biodegradation, Environmental↗