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PubMed1997

[Thermometry by measuring the chemical shift of lanthanide complex].

BACKGROUND: In the long-term, non-invasive thermometry is vital for the continued clinical and technological development of regional hyperthermia. In magnetic resonance tomography. T1 relaxation time, diffusion and proton resonance frequency are used to measure temperature distributions. When used clinically in the pelvic region, all of these methods are plagued with errors and artefacts on account of the tissue relationships, tissue changes under hyperthermia, physiological and stochastic movements, inhomogeneities, drift phenomena and instabilities. MATERIAL AND METHOD: We tested the relationship between the temperature and the chemical shift of a methyl group of a lanthanide complex with central atom praseodymium (Pr-MOE-DO3A. Schering AG). To do this we used cylindrical phantoms containing a 5-mmol-solution of this temperature-sensitive substance. High resolution spectra and relaxation times were determined in a Bruker AMX at 11.5 T. A calibration curve was then recorded by a Siemens Magnetom SP63 at 1.5 T. Local temperature distributions were determined using the chemical shift imaging method, with a matrix size of 16 x 8 and a narrow-band excitation pulse. The temperature distribution was created using a Nd:YAG laser applicator. RESULTS: At a distance of -25.7 ppm from the water line, we found a singlet line with a temperature-dependent chemical shift of 0.13 ppm/C. In the phantom experiment we found that the chemical shift had a linear relationship with a gradient independent of the surroundings, and a temperature resolution of +/-0.6 degree C. With a concentration of 1 mmol/l, a matrix size of 8 x 8 and a measurement period of 5 s per acquisition, phantom measurements using the CSI method produced a signal to noise ratio of 3.5 per acquisition, i.e a measurement period of 10 to 20 s per spectrum. CONCLUSIONS: Our in vitro data show that spectroscopic temperature measurement using a temperature-sensitive praseodymium complex with a therapeutically practical concentration of 1 mmol/l already appears to be suitable for clinical use Compared with the methods tested so far (T1, diffusion, proton resonance), this method has the special advantage of not being very susceptible to artefacts. The competing methods of non-invasive thermometry using magnetic resonance tomography/spectroscopy will be investigated next.

Artifacts↗

PubMed2001

Preconcentration by coprecipitation of arsenic and tin in natural waters with a Ni-pyrrolidine dithiocarbamate complex and their direct determination by solid-sampling atomic-absorption spectrometry.

A method for the determination of trace amounts of arsenic and tin in natural waters is described. Trace amounts of arsenic and tin were preconcentrated by coprecipitation with a Ni-ammonium pyrrolidine dithiocarbamate (APDC) complex. The coprecipitates obtained were directly analyzed by graphite-furnace atomic-absorption spectrometry (GFAAS) using the Ni-APDC complex solid-sampling technique. The coprecipitation conditions used for the trace amounts of arsenic and tin in natural water were investigated in detail. It was found that arsenic and tin at sub-ng mL(-1) levels were both coprecipitated quantitatively by Ni(PDC)2 in the pH range 2-3. The concentration factors by coprecipitation reached approximately 40,000 when 2 mg nickel was added as a carrier element to 500 mL of the water sample. The proposed method has been applied to the determination of trace amounts of arsenic and tin in river water and seawater reference materials, and the detection limits for arsenic and tin, which were calculated from three times of the standard deviation of the procedural blanks, are 0.02 ng mL(-1) and 0.04 ng mL(-1), respectively, for 500-mL volumes of water sample.

Arsenic↗

PubMed2003

Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p.

Mitochondrial and nuclear DNA are packaged by proteins in a very different manner. Although protein-DNA complexes called "nucleoids" have been identified as the genetic units of mitochondrial inheritance in yeast and man, little is known about their physical structure. The yeast mitochondrial protein Abf2p was shown to be sufficient to compact linear dsDNA, without the benefit of supercoiling, using optical and atomic force microscopy single molecule techniques. The packaging of DNA by Abf2p was observed to be very weak as evidenced by a fast Abf2p off-rate (k(off) = 0.014 +/- 0.001 s(-1)) and the extremely small forces (<0.6 pN) stabilizing the condensed protein-DNA complex. Atomic force microscopy images of individual complexes showed the 190-nm structures are loosely packaged relative to nuclear chromatin. This organization may leave mtDNA accessible for transcription and replication, while making it more vulnerable to damage.

Binding Sites↗

PubMed2005

Predation, death, and survival in a biofilm: Bdellovibrio investigated by atomic force microscopy.

Biofilms are complex microbial communities that are resistant to attack by bacteriophages and to removal by drugs and chemicals. Here we use atomic force microscopy (AFM) to image the attack on Escherichia coli biofilms by Bdellovibrio bacteriovorus 109J. Bdellovibrio is a small, predatory bacterium that invades and devours other Gram-negative bacteria. We demonstrate that under dilute nutrient conditions, bdellovibrios can prevent the formation of simple bacterial biofilms and destroy established biofilms; under richer conditions the prey bacteria persist and are not eradicated, but may be shifted toward solution populations. Using AFM we explore these bacterial interactions with more detail and accuracy than available by more traditional staining assays or optical microscopy. AFM also allows us to investigate the nanoscale morphological changes of the predator, especially those related to motility. This demonstration of Bdellovibrio's successful predation in a biofilm inspires us to consider ways that it might be used productively for industrial, medical, agricultural, and biodefensive purposes.

Adhesiveness↗

PubMed2000

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

The complexes of phage T4 lysozyme L99A with noble gases have been studied by molecular dynamics simulation. In a long simulation of the complex with one Xe atom, the structure was found to undergo global conformation change involving a reversible opening and closing of the entrance to the substrate-binding site, during which the conformations of the N and C-terminal domains varied little. The distributions of Xe positions sampled in dynamics simulations were refined in terms of anisotropic Gaussian distributions via least-squares minimization of the difference between Fourier transforms. In addition, molecular transformation simulations have been applied in order to calculate the binding free energies of Xe, Kr and Ar relative to a standard state at a pressure of 1 bar. A single bound Xe is found to assume an equilibrium distribution over three adjacent preferred sites, while in a two-Xe complex, the two Xe atoms preferentially occupy two of these. The positions of the three sites agree closely with the positions of bound Xe determined in the refined crystal structure of a complex formed at a pressure of 8 bar Xe, and the calculated affinities agree well with the observed partial occupancies. At a pressure of 8 bar, a mixture of one-Xe and two-Xe complexes is present, and similarly for complexes with Kr and Ar, with single occupancy relatively more prevalent with Kr and Ar. (Binding of a third Xe atom is found to be quite unfavorable.) A comparison with simulation results for the binding of benzene to the same site leads to the conclusion that binding of Xe within cavities in proteins is common because of several favorable factors: (1) Xe has a large atomic polarizability; (2) Xe can be applied at a relatively high pressure, i.e. high chemical potential; (3) an unfavorable entropic term related to the need to orient the ligand in the binding site is absent. Finally, it is found that the model's binding energy of a water molecule in the cavity is insufficient to overcome the unfavorable binding entropy.

Amino Acid Substitution↗

PubMed2006

Infrared spectra of the CH3-MX, CH2=MHX, and CH[triple bond]MH2X- complexes formed by reaction of methyl halides with laser-ablated group 5 metal atoms.

Reactions of group 5 metal atoms and methyl halides give carbon-metal single, double, and triple bonded complexes that are identified from matrix IR spectra and vibrational frequencies computed by DFT. Two different pairs of complexes are prepared in reactions of methyl fluoride with laser-ablated vanadium and tantalum atoms. The two vanadium complexes (CH(3)-VF and CH(2)=VHF) are persistently photoreversible and show a kinetic isotope effect on the yield of CD(2)=VDF. Identification of CH(2)=TaHF and CH[triple bond]TaH(2)F(-), along with the similar anionic Nb complex, suggests that the anionic methylidyne complex is a general property of the heavy group 5 metals. Reactions of Nb and Ta with CH(3)Cl and CH(3)Br have also been carried out to understand the ligand effects on the calculated structures and the vibrational characteristics. The methylidene complexes become more distorted with increasing halogen size, while the calculated C=M bond lengths and stretching frequencies decrease and increase, respectively. The anionic methylidyne complexes are less favored with increasing halogen size. Infrared spectra show a dramatic increase of the Ta methylidenes upon annealing, suggesting that the formation of CH(3)-TaX and its conversion to CH(2)=TaHX require essentially no activation energy.

Journal Article↗

PubMed2001

Complex gamma-ray hologram: solution to twin images problem in atomic resolution imaging.

A new technique for high fidelity three-dimensional imaging of atomic structure with gamma-ray holography is demonstrated. A complex hologram was constructed from holograms recorded for different values of the nuclear scattering amplitude on both sides of the (57)Fe Mössbauer resonance. The holographic reconstruction was applied to this complex hologram resulting in a twin-image-free image of the bcc Fe local structure. The proposed procedure allows the removal of the twin images for all real space, making gamma-ray holography an unambiguous tool for atomic and magnetic structure imaging.

Journal Article↗

PubMed2001

Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model.

This study describes a computational method for ab inito protein structure prediction. Protein conformation has been modeled by using six optimized backbone torsion angles and fixed side chains approximating rotationally averaged real side chains. The approximations aim to keep complexity of the structure description to a minimum without seriously compromising the accuracy of the structural representation. An evolutionary Monte Carlo algorithm has been developed to search through this restricted conformational space to locate low-energy protein structures. A simple physicochemical force field has been developed to assess the energies of different conformations within this structural description. The corresponding residue interaction energies are based on hydrophobic, hydrophilic, steric, and hydrogen-bonding potentials. The search procedure has been used to locate native energy minima from primary sequence alone. The 3-D structures of polypeptides up to 38 residues with both beta and alpha secondary structural elements have been accurately predicted. The search procedure has been found to be highly efficient and follows an energetically and structurally plausible pathway to locate native populations. The simple force field described in the study has been compared with a more complex all-atom model and been found to be similarly effective in predicting the structures of proposed independent folding units. Proteins 2001;43:186-202.

Algorithms↗

PubMed2002

Cold molecules.

During the last years there has been a rapidly growing interest in the field of cold molecules. This has obviously been inspired by the spectacular successes in the closely related field of cold atoms, which have recently been recognized by the award of the 2001 Nobel Prize in Physics to Cornell, Ketterle, and Wieman. But molecules have much more to offer than simply extending the experiments already performed with atoms to more complex species.

Journal Article↗

PubMed2002

Reversible bulk photorelease of strontium ion from a crown ether-linked merocyanine.

The use of a crown-ether-linked merocyanine, DCM-crown, for producing photoinduced, long-lived and reversible concentration jumps of metal cations is reexamined. In this new investigation, the excited-state behavior of DCM-crown complexed with a strontium ion in acetonitrile is found to exhibit the same trends as those previously reported with calcium and lithium ions. However, some new features provide evidence for cation photorelease to the bulk. Subpicosecond transient absorption experiments confirm the initial fast photodisruption of the interaction between the ion and the crown, and the formation of a loose complex after intramolecular charge transfer within the chromophore. Two additional steps are observed. Firstly, a continuous red shift of the gain spectrum is seen on the subnanosecond scale. It is assigned to the movement of the Sr2+ cation away from the chromophore, partly to the bulk of the solvent and partly towards the formation of an ultraloose complex with oxygen atoms of the crown. Secondly, a free-ligand-like absorption remains after the complete decay of the excited state. This band, which signals a total photorelease of the Sr2+ ion, disappears with a characteristic time of about 110 ns, attributed to the recomplexation of the crown in the ground state of the dye.

Journal Article↗

PubMed2007

Crystal and molecular structures of trichloro-cobalt(II) complexes of epiquinine, epiquinidine, and epidihydrocinchonine.

Cinchona alkaloids are very well known antimalarials but the mechanism of their biological action still remains to be elucidated. The structural studies of active erythro and inactive threo alkaloid complexes are an important step to this aim. In this paper results of crystal structure analysis of three cobalt complexes of threo alkaloids are presented: (epiquininium)trichlorocobalt(II) (EpiQnCoCl3), (epiquinidinium)trichlorocobalt(II) (EpiQdCoCl3) and (epidihydrocinchoninium)trichlorocobalt(II) (EpiCnCoCl3). The complexes are zwitterions in which trichlorocobalt substituents are coordinated to quinoline nitrogen atoms and quinuclidine nitrogen atoms are protonated. EpiQnCoCl3 adopts uncommon conformation with quinoline moiety oriented in the opposite direction in comparison to the analogous uncomplexed alkaloid. The packing in the crystal structures is determined mainly by the hydrogen bonds, in which the chlorine atoms of substituents and solvent molecules contribute. Atoms participating in hydrogen bonds in EpiQnCoCl3 and EpiQdCoCl3 form large rings, while in EpiCnCoCl3 only chains are present. Solvent molecules are very important for the packing mode. In contrast to most erythro alkaloids, the hydroxyl oxygen atom in the title complexes forms weak or not well defined hydrogen bonds. The contribution of very weak intramolecular interactions N1--H1...O12 cannot be excluded. Such "trace" interactions can be considered a relic of the unprotonated status of an epi alkaloid.

Antimalarials↗

PubMed2006

Slater-like model for carbon 1s core ionization energies of halomethanes.

Based on the atomic electron affinity EA, the average energy of the valence-shell electrons EI and the polarizability alpha, the charge effect and the relaxation effect were evaluated for the carbon 1s core ionization energies of halomethanes CHnY4-n-mZm (Y, Z=F, Cl, Br, I). The charge effect was scaled by the electronegativity discrepancy (the discrepancy of EA and the discrepancy of EI between the C and H or halogen atom in the C-H or C-halogen chemical bond). The relaxation effect (induced dipole) was scaled by the charge on the carbon atom together with the polarizability of the H and halogen atoms. Further, the electrostatic relaxation shielding DeltaSi of the carbon 1s electron in the halomethane was expressed by the charge effect together with the relaxation effect. By introducing DeltaSi into the Slater model, a Slater-like model was obtained for calculating the carbon 1s core ionization energy E1,C of halomethane, whose correlation coefficient r is 0.99985 and the average absolute error is only 0.041 eV between the calculated and the experimental carbon 1s core ionization energies for 27 halomethanes. Also the cross-correlation was tested by the leave-one-out (LOO) cross-validation method, and the obtained model has good predictive ability and stability (the correlation coefficient rcv is 0.99976, the average absolute error between the predicted and the experimental values is only 0.052 eV). The proposed model perhaps lays a good foundation for computing the core ionization energies of various atoms in more complex molecules.

Journal Article↗

PubMed1978

The taxonomy of binding sites in proteins.

Conservation of polypeptide fold and mode of ligand binding is frequently found within proteins of related function. Examples illustrating this phenomenon are taken from NAD linked enzymes, nucleotide binding proteins, polysaccharide binding proteins, heme binding proteins and enzymes with essential Fe--S complexes or zinc atoms.

Amino Acid Sequence↗

PubMed2003

X-ray absorption near-edge spectroscopy of transferrins: a theoretical and experimental probe of the metal site local structure.

Proteins of the transferrin (Tf) family have a role in metal transport in vertebrates and have been extensively studied. The results here reported provide, for the first time, a detailed systematic comparison of metal sites in Tf complexes involving several atoms in the whole protein and in two different types of Tfs. The high interest in the structural variations induced in a metalloprotein upon the uptake of different metals is related to the hypothesis of the metals' involvement in some neuropathologies. We propose a comparative study of the X-ray absorption spectra at the K-edge of iron, copper, zinc and nickel in serotransferrin and ovotransferrin. The experimental data are simulated using an algorithm of the full multiple scattering method. Our results show that: (1) the local structure of each site (N-terminal and C-terminal) is correlated to the ligation state of the other site; (2) the difference between the two proteins is related to site local structure and depends on the metal ion nature being greater in the case of copper and zinc with respect to iron and nickel ions; (3) X-ray spectroscopy is confirmed as a suitable technique able to discriminate between coordination models proposed by X-ray diffraction.

Animals↗

PubMed1982

The location of redox centers in biological membranes determined by resonance x-ray diffraction. I. Observation of the resonance effect.

We have developed resonance X-ray diffraction methods to locate for the first time intrinsic metal atoms associated with redox centers within biological membrane systems. The study of membranes containing dilute concentrations of resonant scatterers has been made possible by the development of synchrotron radiation sources of X-rays. The technique permits altering the scattering power of a particular atom relative to others by varying the incident X-ray energy. Thus, this method may be used to locate a metal atom within a complex integral protein without chemical modification of the membrane. We present resonance diffraction data taken with synchroton radiation for two different membrane systems: cytochrome oxidase incorporated into lipid vesicles and a photosynthetic reaction center-cytochrome c complex also reincorporated into lipid vesicles.

Cell Membrane↗

PubMed1986

Wheat germ phosphoglycerate mutase: evidence for a metalloenzyme.

Wheat germ phosphoglycerate mutase, exposed to 3.4 M guanidinium chloride at 22 degrees C and pH 7.8, slowly undergoes time-dependent inactivation which can be fully reversed by adding excess Co2+ or Mn2+ to a 50-fold dilution of the denaturing medium. Titration of the denatured enzyme with either Co2+ or Mn2+ shows that wheat germ mutase preferentially binds Co2+. Assuming 1:1 complexation between metal atom and protein, the apparent dissociation constants (Kd) for E Co2+ and E Mn2+ at 22 degrees C and pH 8.7 are approximately 1.06 and 1.84, respectively. Other metal atoms (e.g., Cr2+, Cu2+, Fe2+, Fe3+, Mg2+, and Ni2+) have no effect in restoring the apoenzyme's catalytic activity. At low concentrations (0.11-0.23 mM) Zn2+ partially restores activity, but promotes protein precipitation at elevated concentrations. Evidence suggests that all bisphosphoglycerate-independent phosphoglycerate mutases require either an intra- or an extramolecular metal atom in order to function. Attempts to characterize wheat germ mutase as a glycoprotein have yielded negative results.

Bisphosphoglycerate Mutase↗

PubMed1989

Synthesis and characterization of new chromium(III), vanadium(IV), and titanium(III) complexes with biologically active isonicotinic acid hydrazide.

New complexes of the type [Cr(INH)2Cl2]Cl.2H2O, VO(INH)2Cl2 and TiO(INH)2Cl, where INH = isonicotinic acid hydrazide, have been prepared. The complexes were characterized by infrared and UV-vis spectroscopy, proton nuclear magnetic resonance (NMR) and elemental analyses, molar conductivity and x-ray powder diffraction measurements. For the Cr(III)-complex, the ligand was coordinated through its carbonyl group and amino nitrogen atom; for V(IV)-complex and Ti(III)-complex, the ligand was coordinated through its carbonyl oxygen and heterocyclic nitrogen, respectively. Octahedral geometry has been proposed for all the complexes. The complexes of Cr(III) and Ti(III) showed significant tuberculostatic activity.

Antitubercular Agents↗

PubMed1994

Structural aspects of actin-binding proteins.

The three-dimensional structures of myosin subfragment 1 (S1), gelsolin segment 1 complexed with alpha-actin, villin fragment 14T, Acanthamoeba profilin-I, and bovine profilin complexed with beta-actin were completed last year. Together, they expand our understanding of the structural organization of actin-binding proteins. In addition, the segment 1 and bovine profilin complexes provide atomic-level descriptions of their interfaces with actin.

Actins↗