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At least 937 records · Page 52Linked to original sources

PubMed2003

The membrane-associated form of methane mono-oxygenase from Methylococcus capsulatus (Bath) is a copper/iron protein.

A protocol has been developed which permits the purification of a membrane-associated methane-oxidizing complex from Methylococcus capsulatus (Bath). This complex has approximately 5 fold higher specific activity than any purified particulate methane mono-oxygenase (pMMO) previously reported from M. capsulatus (Bath). This efficiently functioning methane-oxidizing complex consists of the pMMO hydroxylase (pMMOH) and an unidentified component we have assigned as a potential pMMO reductase (pMMOR). The complex was isolated by solubilizing intracytoplasmic membrane preparations containing the high yields of active membrane-bound pMMO (pMMO(m)), using the non-ionic detergent dodecyl-beta-D-maltoside, to yield solubilized enzyme (pMMO(s)). Further purification gave rise to an active complex (pMMO(c)) that could be resolved (at low levels) by ion-exchange chromatography into two components, the pMMOH (47, 27 and 24 kDa subunits) and the pMMOR (63 and 8 kDa subunits). The purified complex contains two copper atoms and one non-haem iron atom/mol of enzyme. EPR spectra of preparations grown with (63)Cu indicated that the copper ion interacted with three or four nitrogenic ligands. These EPR data, in conjunction with other experimental results, including the oxidation by ferricyanide, EDTA treatment to remove copper and re-addition of copper to the depleted protein, verified the essential role of copper in enzyme catalysis and indicated the implausibility of copper existing as a trinuclear cluster. The EPR measurements also demonstrated the presence of a tightly bound mononuclear Fe(3+) ion in an octahedral environment that may well be exchange-coupled to another paramagnetic species.

Ascorbic Acid↗

PubMed2005

Watching the components of photosynthetic bacterial membranes and their in situ organisation by atomic force microscopy.

The atomic force microscope has developed into a powerful tool in structural biology allowing information to be acquired at submolecular resolution on the protruding structures of membrane proteins. It is now a complementary technique to X-ray crystallography and electron microscopy for structure determination of individual membrane proteins after extraction, purification and reconstitution into lipid bilayers. Moving on from the structures of individual components of biological membranes, atomic force microscopy has recently been demonstrated to be a unique tool to identify in situ the individual components of multi-protein assemblies and to study the supramolecular architecture of these components allowing the efficient performance of a complex biological function. Here, recent atomic force microscopy studies of native membranes of different photosynthetic bacteria with different polypeptide contents are reviewed. Technology, advantages, feasibilities, restrictions and limits of atomic force microscopy for the acquisition of highly resolved images of up to 10 A lateral resolution under native conditions are discussed. From a biological point of view, the new insights contributed by the images are analysed and discussed in the context of the strongly debated organisation of the interconnected network of membrane-associated chlorophyll-protein complexes composing the photosynthetic apparatus in different species of purple bacteria.

Bacteria↗

PubMed2004

The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.

The clamp-loader-helicase interaction is an important feature of the replisome. Although significant biochemical and structural work has been carried out on the clamp-loader-clamp-DNA polymerase alpha interactions in Escherichia coli, the clamp-loader-helicase interaction is poorly understood by comparison. The tau subunit of the clamp-loader mediates the interaction with DnaB. We have recently characterised this interaction in the Bacillus system and established a tau(5)-DnaB(6) stoichiometry. Here, we have obtained atomic force microscopy images of the tau-DnaB complex that reveal the first structural insight into its architecture. We show that despite the reported absence of the shorter gamma version in Bacillus, tau has a domain organisation similar to its E.coli counterpart and possesses an equivalent C-terminal domain that interacts with DnaB. The interaction interface of DnaB is also localised in its C-terminal domain. The combined data contribute towards our understanding of the bacterial replisome.

Adenosine Triphosphatases↗

PubMed2006

Resolution of identity Dirac-Kohn-Sham method using the large component only: Calculations of g-tensor and hyperfine tensor.

A new relativistic two-component density functional approach, based on the Dirac-Kohn-Sham method and an extensive use of the technique of resolution of identity (RI), has been developed and is termed the DKS2-RI method. It has been applied to relativistic calculations of g and hyperfine tensors of coinage-metal atoms and some mercury complexes. The DKS2-RI method solves the Dirac-Kohn-Sham equations in a two-component framework using explicitly a basis for the large component only, but it retains all contributions coming from the small component. The DKS2-RI results converge to those of the four-component Dirac-Kohn-Sham with an increasing basis set since the error associated with the use of RI will approach zero. The RI approximation provides a basis for a very efficient implementation by avoiding problems associated with complicated integrals otherwise arising from the elimination of the small component. The approach has been implemented in an unrestricted noncollinear two-component density functional framework. DKS2-RI is related to Dyall's [J. Chem. Phys. 106, 9618 (1997)] unnormalized elimination of the small component method (which was formulated at the Hartree-Fock level and applied to one-electron systems only), but it takes advantage of the local Kohn-Sham exchange-correlation operators (as, e.g., arising from local or gradient-corrected functionals). The DKS2-RI method provides an attractive alternative to existing approximate two-component methods with transformed Hamiltonians (such as Douglas-Kroll-Hess [Ann. Phys. 82, 89 (1974); Phys. Rev. A 33, 3742 (1986)] method, zero-order regular approximation, or related approaches) for relativistic calculations of the structure and properties of heavy-atom systems. In particular, no picture-change effects arise in the property calculations.

Journal Article↗

PubMed2005

Di-mu-formato-1kappa2O:2kappa2O'-di-mu-pyridin-2-olato-1kappaO:2kappaN;1kappaN:2kappaO-bis[(2-pyridone-kappaO)copper(II)] acetonitrile 1.02-solvate.

In the title compound, [Cu2(CHO2)2(C5H4NO)2(C5H5NO)2].1.02CH3CN, the dimeric unit is centrosymmetric, with two bidentate pyridin-2-olate and two bidentate formate syn-syn bridges, and two apical 2-pyridone ligands coordinated through the O atoms. The N atom from the apical 2-pyridone ligand is a donor of a hydrogen bond to the O atom of the bridging pyridinolate ligand of the same complex. The coordination polyhedron of the Cu atom is a distorted square pyramid.

Journal Article↗

PubMed1985

Characterization of a cyanobacterial photosystem I complex.

A simple procedure is described for the preparation of photosystem I (PSI) particles from Triton X-100-solubilized thylakoid membranes of the unicellular cyanobacterium Synechococcus 6301. The purified PSI complex contained the full complement of antenna chlorophylls, 130 +/- 5/P700, displayed the electron paramagnetic resonance signals characteristic of iron-sulfur centers X, A, and B, and had a protein/chlorophyll ratio of 2.9. Determination of the polypeptide composition, utilizing a uniformly 14C-labeled complex, showed that it contained polypeptides of 70, 18, 17.7, 16, and 10 kDa, in a molar ratio of 4.0:0.7:1.0:0.5:1.6. The relative amount of the lower molecular weight polypeptides showed progressive decrease with increase in Triton X-100 concentration and time of exposure to detergent. Consequently, it is proposed that in vivo the composition of the complex is [70 kDa]4 [18 kDa]1 [17.7 kDa]1 [16 kDa]1 [10 kDa]2. Relative to 130 mol of chlorophyll a, the PSI complex contained 16 mol of carotenoids, 13.7 +/- 1.0 g atoms of Fe, and 12.2 +/- 1.1 g atoms of labile sulfide. The properties of complexes fully depleted of the low-molecular weight polypeptides by treatment with sodium dodecyl sulfate or with proteinase K are also described.

Chlorophyll↗

PubMed2006

Nanomechanical properties of desmin intermediate filaments.

Desmin intermediate filaments play important role in the mechanical integrity and elasticity of muscle cells. The mechanisms of how desmin contributes to cellular mechanics are little understood. Here, we explored the nanomechanics of desmin by manipulating individual filaments with atomic force microscopy. In complex, hierarchical force responses we identified recurring features which likely correspond to distinct properties and structural transitions related to desmin's extensibility and elasticity. The most frequently observed feature is an initial unbinding transition that corresponds to the removal of approximately 45-nm-long coiled-coil dimers from the filament surface with 20-60 pN forces in usually two discrete steps. In tethers longer than 60 nm we most often observed force plateaus studded with bumps spaced approximately 16 nm apart, which are likely caused by a combination of protofilament unzipping, dimer-dimer sliding and coiled-coil-domain unfolding events. At high stresses and strains non-linear, entropic elasticity was dominant, and sometimes repetitive sawtooth force transitions were seen which might arise because of slippage within the desmin protofilament. A model is proposed in which mechanical yielding is caused by coiled-coil domain unfolding and dimer-dimer sliding/slippage, and strain hardening by the entropic elasticity of partially unfolded protofilaments.

Animals↗

PubMed2004

Coordination complexes of 2-(4-quinolyl)nitronyl nitroxide with M(hfac)(2) [M = Mn(II), Co(II), and Cu(II)]: syntheses, crystal structures, and magnetic characterization.

Three new complexes of the formula M(2)L(2) derived from 2-(4-quinolyl)nitronyl nitroxide (4-QNNN) and M(hfac)(2) [M = Mn(II), Co(II), and Cu(II)], (4-QNNN)(2).[Mn(hfac)(2)](2) (1), (4-QNNN)(2).[Co(hfac)(2)](2).2H(2)O (2), and (4-QNNN)(2).Cu(hfac)(2).Cu'(hfac)(2) (3), were synthesized and characterized structurally as well as magnetically. Complexes 1 and 2 are four-spin complexes with quadrangle geometry, in which both the nitrogen atoms of quinoline rings and oxygen atoms of nitronyl nitroxides are involved in the formation of coordination bonds. For complex 3, however, the nitrogen atoms of quinoline rings are coordinated with Cu(II) ion to afford a three-spin complex, which is further linked to another molecule of Cu(hfac)(2) (referred to as Cu'(hfac)(2)) to form a 1D alternating chain. The magnetic behaviors of the three complexes were investigated. For complex 1, as the nitronyl nitroxides and Mn(II) ions are strongly antiferromagnetically coupled, consequently its temperature dependence of magnetic susceptibility was fitted to the model of spin-dimer with S = 2, yielding the intradimer magnetic exchange constant of J = -0.82 cm(-1). For complex 2, the temperature dependence of the magnetic susceptibility in the T > 50 K region was simulated with the model of two-spin unit with S(1) = 3/2 and S(2) = 1/2, leading to J = -321.9 cm(-1) for the magnetic interaction due to Co(II).O coordination bonding, D = -16.3 cm(-1) (the zero-field splitting parameter), g = 2.26, and zJ = -3.8 cm(-1) for the magnetic interactions between Co(II) ions and nitronyl nitroxides through quinoline rings and those between nitronyl nitroxides due to the short O.O short contacts. The temperature dependence of magnetic susceptibility of 3 was approximately fitted to a model described previously affording J(1) = -6.52 cm(-1) and J(2) = 3.64 cm(-1) for the magnetic interaction between nitronyl nitroxides and Cu(II) ions through the quinoline unit via spin polarization mechanism and the weak O.Cu coordination bonding, respectively.

Journal Article↗

PubMed2006

Nonfluorinated volatile copper(I) 1,3-diketiminates as precursors for Cu metal deposition via atomic layer deposition.

Novel nonfluorinated Cu(diketiminate)L complexes with L = neutral olefinic ligand have been prepared as stable, volatile Cu(I) precursors for the deposition of copper films by an atomic layer deposition (ALD) process. Among them, the complexes of 4-a and 5-a are the most volatile and stable at low temperature (55 degrees C). A clean, conformal copper film was deposited at 120 degrees C in an ALD process. These Cu(I) complexes are the first examples of nonfluorinated copper(I) diketiminates that can be readily applied to an industrial microelectronic fabrication process.

Journal Article↗

PubMed1994

X-ray analysis at 2.0 A resolution of mouse submaxillary renin complexed with a decapeptide inhibitor CH-66, based on the 4-16 fragment of rat angiotensinogen.

The structure of mouse submaxillary renin complexed with a decapeptide inhibitor, CH-66 (Piv-His-Pro-Phe-His-Leu-OH-Leu-Tyr-Tyr-Ser-NH2), where Piv denotes a pivaloyl blocking group, and -OH- denotes a hydroxyethylene (-(S)CHOH-CH2-) transition state isostere as a scissile bond surrogate, has been refined to an agreement factor of 0.18 at 2.0 A resolution. The positions of 10,038 protein atoms and 364 inhibitor atoms (4 independent protein inhibitor complexes), as well as of 613 solvent atoms, have been determined with an estimated root-mean-square (r.m.s.) error of 0.21 A. The r.m.s. deviation from ideality for bond distances is 0.026 A, and for angle distances is 0.0543 A. We have compared the three-dimensional structure of mouse renin with other aspartic proteinases, using rigid-body analysis with respect to shifts involving the domain comprising residues 190 to 302. In terms of the relative orientation of domains, mouse submaxillary renin is closest to human renin with only a 1.7 degrees difference in domain orientation. Porcine pepsin (the molecular replacement model) differs structurally from mouse renin by a 6.9 degrees domain rotation, whereas endothiapepsin, a fungal aspartic proteinase, differs by 18.8 degrees. The triple proline loop (residues 292 to 294), which is structurally opposite the active-site "flap" (residues 72 to 83), gives renin a superficial resemblance to the fold of the retroviral proteinases. The inhibitor is bound in an extended conformation along the active-site cleft, and the hydroxyethylene moiety forms hydrogen bonds with both catalytic aspartate carboxylates. The complex is stabilized by hydrogen bonds between the main chain of the inhibitor and the enzyme. All side-chains of the inhibitor are in van der Waals contact with groups in the enzyme and define ten specificity sub-sites. This study shows how renin has compact sub-sites due to the positioning of secondary structure elements, to complementary substitutions and to the residue composition of its loops close to the active site, leading to extreme specificity towards its prohormone substrate, angiotensinogen. We have analysed the micro-environment of each of the buried charged groups in order to predict their ionization states.

Amino Acid Sequence↗

PubMed2005

Signal complexity and synchrony of epileptic seizures: is there an identifiable preictal period?

OBJECTIVE: Epileptic seizures are characterized by increases in synchronized activity and increased signal complexity. Prediction of seizures depends upon detectable preictal changes before the actual ictal event. The studies reported here test whether two methods designed to detect changes in synchrony and complexity can identify any changes in a preictal period before visual EEG changes or clinical manifestations. METHODS: Two methods are used to characterize different, but linked, properties of the signal-complexity and synchrony. The Gabor atom density (GAD) method allows for quantification of the time-frequency components of the EEG and characterizes the complexity of the EEG signal. The measure S, based on the goodness of fit of a multivariable autoregressive model, allows for characterization of the degree of synchrony of the EEG signal. RESULTS: Complex partial seizures produce very specific patterns of increased signal complexity and subsequent postictal low complexity states. The measure S shows increased synchronization later including a prolonged period of increased synchrony in the postictal period. No significant preictal changes were seen unless contaminated by residual postictal changes in closely clustered seizures. CONCLUSIONS: Both GAD and S measures reveal ictal and prolonged postictal changes; however, there were no significant preictal changes in either complexity or synchrony. Any application of methods to detect preictal changes must be tested on seizures sufficiently separated to avoid residual postictal changes in the potential preictal period.

Algorithms↗

PubMed2002

Determination of verapamil in pharmaceutical formulations using atomic emission spectrometry.

Ion-associate complexes of verapamil hydrochloride (VpCl) with (Cd(II), Co(II), Mn(II), and Zn(II)) thiocyanates, potassium ferricyanide, and ammonium reineckate are precipitated. The solubility of the solid complexes at the recommended optimum conditions of pH and ionic strength values have been studied. Saturated solutions of each ion associate at different temperatures under the optimum precipitation conditions were prepared and the metal ion contents in the supernatant were determined. The solubility products were thus calculated at different temperatures and the thermodynamic parameters DeltaH, DeltaG, and DeltaS were calculated. A new accurate and precise method based on direct coupled plasma atomic emission spectrometry for the determination of VpCl (1.96-62.86 microg ml(-1)) in pure solutions and pharmaceutical preparations is given.

Calcium Channel Blockers↗

PubMed2006

Interatomic electronic decay in endohedral fullerenes.

Ionization of an atom in an endohedral fullerene complex can lead to a wealth of nonradiative decay processes. These interatomic processes occur due to the correlation existing between the atomic and the fullerene electrons and do not take place in the free species . Considering as an example, we calculate the rates of the interatomic decay processes and show that the interatomic decay in is ultrafast. Moreover, our analysis suggests that interatomic decay in an endohedral fullerene does not necessarily lead to the destruction of the complex.

Journal Article↗

PubMed2006

High atom-economical one-pot synthesis of secondary phosphines and their borane complexes using recycling phosphorus donor reagent.

[reaction: see text] A general new method for the one-pot preparation of secondary phosphines 11 and in situ generation of their borane complexes 12 is described. This method consists of the sequential addition, at room temperature, of equivalent amounts of R(1)MgBr and R(2)MgBr to 1 equiv of the phosphorus atom donor reagent 1. Final treatment with water gives secondary phosphines R(1)R(2)PH (or the corresponding phosphine-borane complexes if treated with BH(3).THF) and the end product 6, which can be recycled.

Journal Article↗

PubMed2001

RNA-binding properties of the 63 kDa protein encoded by the triple gene block of poa semilatent hordeivirus.

The 63 kDa '63K' movement protein encoded by the triple gene block of poa semilatent virus (PSLV) comprises the C-terminal NTPase/helicase domain and the N-terminal extension domain, which contains two positively charged sequence motifs, A and B. In this study, the in vitro RNA-binding properties of PSLV 63K and its mutants were analysed. Membrane-immobilized 63K and N-63K (isolated N-terminal extension domain) bound RNA at high NaCl concentrations. In contrast, C-63K (isolated NTPase/helicase domain) was able to bind RNA only at NaCl concentrations of up to 50 mM. In gel-shift assays, C-63K bound RNA to form complexes that were unable to enter an agarose gel, whereas complexes formed by N-63K could enter the gel. Full-length 63K formed both types of complexes. Visualization of the RNA-protein complexes formed by 63K, N-63K and C-63K by atomic force microscopy demonstrated that each complex had a different shape. Collectively, these data indicate that 63K has two distinct RNA-binding activities associated with the NTPase/helicase domain and the N-terminal extension domain. Mutations in either of the positively charged sequence motifs A and B had little effect on the RNA binding of the N-terminal extension domain, whereas mutations in both motifs together inhibited RNA binding. Hybrid viruses with mutations in motifs A and B were able to infect inoculated leaves of Nicotiana benthamiana plants, but were unable to move systemically to uninoculated leaves, suggesting that the RNA-binding activity of the N-terminal extension domain of PSLV 63K is associated with virus long-distance movement.

Amino Acid Sequence↗

PubMed2004

Cytochrome bc complexes: a common core of structure and function surrounded by diversity in the outlying provinces.

The atomic-level picture of transmembrane protein complexes in the photosynthetic membrane has now been completed by the recent publication of crystal structures of cytochrome b(6)f and photosystem II. The two structures of cytochrome b(6)f, together with previously reported structures of the cytochrome bc(1) respiratory complex, provide a basis for understanding the central electron and proton transfer events of photosynthesis and respiration. The protein structures and charge transfer events within the core of the complexes are highly similar, but the complexes differ in subunit and chromophore composition in proportion to the distance from the central redox site within the membrane near the electropositive side.

Biological Transport↗

PubMed1985

Active site structures of deoxyhemerythrin and oxyhemerythrin.

The physiologically active forms of the nonheme-iron, oxygen-transport protein hemerythrin have been studied by x-ray crystallographic techniques. At 3.9-A resolution, a difference electron-density map between the deoxy form and met form (methemerythrin) of the protein suggests only small differences in the binuclear iron complexes. The coordination of the iron atoms appears to be the same in both the deoxy and met forms, one iron of the complexes being pentacoordinate, the other iron being hexacoordinate. The iron atoms appear to be somewhat farther apart in the deoxy form. A 2.2-A resolution study of oxyhemerythrin shows that dioxygen binds to one iron atom--the pentacoordinate one in the met form of the protein, the same binding site found for azide in azidomethemerythrin.

Animals↗

PubMed2000

The First Red Azo Lake Pigment whose Structure is Characterized by Single Crystal Diffraction.

A model for red azo pigment Ca4B was characterized structurally using synchrotron radiation. This highly anisotropic ladder structure represents a new structural class in azo pigment chemistry. The picture shows that the calcium atoms coordinate in a complex manner to three azo ligands (one terdentate, one bidentate, and one monodentate) and two water molecules simultaneously.

Journal Article↗