Investigation of the active site of Escherichia coli Cu,Zn superoxide dismutase reveals the absence of the copper-coordinated water molecule. is the water molecule really necessary for the enzymatic mechanism?

The active site of the Cu,Zn superoxide dismutase from Escherichia coli in the oxidized Cu(II) state has been studied by nuclear magnetic relaxation dispersion (NMRD), optical and nuclear magnetic resonance spectroscopy. The orientation of some metal ligands is different with respect to all the other Cu,Zn superoxide dismutases. Moreover, NMRD measurements demonstrate the lack of a copper-coordinated water molecule. In spite of these differences the enzymatic activity is still high. Azide also binds copper with normal affinity and induces modifications in the active site comparable to those previously observed in the eukaryotic enzymes. Our results suggest that, in this enzyme, the copper-coordinated water molecule appears not necessary for the enzymatic reaction. A role for the copper-coordinated water molecule is discussed in the light of recent crystallographic studies.     

Water Exchange at the Active Site of Carbonic Anhydrase: A Synthesis of the OH- and H2O-Models

We have measured the paramagnetic contribution to the magnetic relaxation rate of solvent protons in highly purified, buffer- and salt-free solutions of Co(2+)-substituted human carbonic anhydrase B (HCAB), as a function of pH in the range 5.5-10 and as a function of magnetic field. We have also measured the optical absorption at 640 nm to characterize the enzyme. The relaxation rates vary with pH much as does the CO(2) hydration activity, increasing with increasing pH. We find that the relaxation rates at all intermediate values of pH can be described as linear combinations of the rates obtained at the extremes of pH used, indicating the existence of low- and high-pH forms of the enzyme with pH-dependent concentrations. The optical data can be similarly represented. The fraction of high-pH form present, determined from either the relaxation or optical data, has a pK(a) of approximately 7.6 when approximated by a single ionization. The data are very similar to that for HCAB in the presence of buffer, in contrast to the bovine enzyme for which the pK(a) is affected substantially by the presence of sulfate. Previous analysis of the high relaxation rates at high pH indicated rapid exchange of Co(2+)-liganded protons, possible only if these exchanging protons were conveyed by water molecules. On the other hand, the present demonstration of the existence of two forms of HCAB in highly purified solutions, coupled with other data, argues strongly for ionization of a water molecule ligand of the metal ion at the active site, with OH(-) as the solvent-donated ligand at high pH. We propose a mechanism of ligand exchange at high pH that reconciles these ostensibly conflicting requirements by invoking a pentacoordinate intermediate having both OH(-) and H(2)O as ligands. Proton exchange can be rapid between these ligands because charge transfer without net ionization can occur, so that the leaving water can carry away the initial OH(-). The low-pH form is a thermal mixture of tetra- and pentacoordinate species, the latter having low relaxation rates by analogy with inhibitor derivatives of the enzyme and model systems. The proposed associative ligand-exchange mechanism reconciles the distinctions between the OH- and H(2)O-models of carbonic anhydrase by merging them, providing the first model is consistent with the observed pH dependence of hydration activity, optical absorption, and solvent magnetic relaxation.     

Interaction of ethidium bromide with DNA. Optical and electrooptical study

The binding of ethidium bromide to DNA has been studied by various optical methods. From fluorescence polarization studies, and film, electric linear dichroism, and circular dichroism spectra, we propose assignments of the absorption bands of the dye, which are discussed in connection with wave-mechanical calculations recently reported. The optical activity induced in the dye absorption bands upon binding to DNA was attributed to various origins depending on the electronic transition considered. The visible absorption band displayed a circular dichroism due to the asymmetry of the binding site and independent of the amount of binding. The transition identified at 378 nm from the circular dichroism and electric dichroism observations was thought to be due to a magnetic-dipole transition. It remained constant with increasing amounts of dye bound. The main ultraviolet band showed circular dichroism characteristics corresponding to exciton interactions between dye molecules bound to neighboring sites. The electric dichroism observed for the strongly bound dye molecules indicated that the phenanthridinium ring of ethidium bromide was probably not perfectly parallel to the DNA base planes. When the amount of dye bound to DNA exceeded the maximum amount compatible with the exclusion of adjacent binding sites, the electric dichroism decreased owing to the appearance of externally bound dye molecules with no contribution to the dichroism. Sonicated DNA was used to study the lengthening of the DNA molecule upon complexation. Although the viscosity of the complexes increased with the amount of binding, the rotational diffusion coefficient measured by the electric birefringence relaxation was not detectably affected. The absence of variation in the electric birefringence with the binding indicated that the DNA base stacking remained unaltered.     

A study of molecular dynamics and freezing phase transition in tissues by proton spin relaxation

Muscle, spleen, and kidney tissues from 4-wk-old C57 black mice were studied by proton magnetic resonance. Spin-lattice relaxation times at high fields and in the rotating frame, as well as the spin-spin relaxation times, are reported as a function of temperature in the liquid and frozen phase. Motions of large molecules and of water molecules and their changes at the freezing phase transition are studied. The shortcomings of the two-state fast-exchange relaxation model are discussed.     

Dynamics of the First‐Order Metamagnetic Transition in Magnetocaloric La(Fe,Si)13: Reducing Hysteresis

The influence of dynamics and sample shape on the magnetic hysteresis in first‐order magnetocaloric metamagnetic LaFe_13–xSi_x with x = 1.4 is studied. In solid‐state magnetic cooling, reducing magnetic and thermal hysteresis is critical for refrigeration cycle efficiency. From magnetization measurements, it is found that the fast field‐rate dependence of the hysteresis can be attributed to extrinsic heating directly related to the thickness of the sample and the thermal contact with the bath. If the field is paused partway through the transition, the subsequent relaxation is strongly dependent on shape due to both demagnetizing fields and thermal equilibration; magnetic coupling between adjacent sample fragments can also be significant. Judicious shaping of the sample can both increase the onset field of the ferromagnetic–paramagnetic (FM–PM) transition but have little effect on the PM–FM onset, suggesting a route to engineer the hysteresis width by appropriate design. In the field‐paused state, the relaxation from one phase to the other slows with increasing temperature, implying that the process is neither thermally activated or athermal; comparison with the temperature dependence of the latent heat strongly suggests that the dynamics reflect the intrinsic free energy difference between the two phases.     

Identification of molecular-mimicry-based ligands for cholera diagnostics using magnetic relaxation

When covalently bound to an appropriate ligand, iron oxide nanoparticles can bind to a specific target of interest. This interaction can be detected through changes in the solution's spin-spin relaxation times (T2) via magnetic relaxation measurements. In this report, a strategy of molecular mimicry was used in order to identify targeting ligands that bind to the cholera toxin B subunit (CTB). The cellular CTB-receptor, ganglioside GM1, contains a pentasaccharide moiety consisting in part of galactose and glucose units. We therefore predicted that CTB would recognize carbohydrate-conjugated iron oxide nanoparticles as GM1 mimics, thus producing a detectable change in the T2 relaxation times. Magnetic relaxation experiments demonstrated that CTB interacted with the galactose-conjugated nanoparticles. This interaction was confirmed via surface plasmon resonance studies using either the free or nanoparticle-conjugated galactose molecule. The galactose-conjugated nanoparticles were then used as CTB sensors achieving a detection limit of 40 pM. Via magnetic relaxation studies, we found that CTB also interacted with dextran-coated nanoparticles, and surface plasmon resonance studies also confirmed this interaction. Additional experiments demonstrated that the dextran-coated nanoparticle can also be used as CTB sensors and that dextran can prevent the internalization of CTB into GM1-expressing cells. Our work indicates that magnetic nanoparticle conjugates and magnetic relaxation detection can be used as a simple and fast method to identify targeting ligands via molecular mimicry. Furthermore, our results show that the dextran-coated nanoparticles represent a low-cost approach for CTB detection.     

Interaction between perdeuterated dimyristoylphosphatidylcholine and low molecular weight pulmonary surfactant protein SP-C

A low molecular weight hydrophobic protein was isolated from porcine lung lavage fluid using silicic acid and Sephadex LH-20 chromatography. The protein migrated with an apparent molecular weight of 5000-6000 on SDS-PAGE under reducing and nonreducing conditions. Gels run under reducing conditions also showed a minor band migrating with a molecular weight of 12,000. Amino acid compositional analysis and sequencing data suggest that this protein preparation contains intact surfactant protein SP-C and about 30% of truncated SP-C (N-terminal leucine absent). The surfactant protein was combined with perdeuterated dimyristoylphosphatidylcholine (DMPC-d54) in multilamellar vesicles. The protein enhanced the rate of adsorption of the lipid at air-water interfaces. The ability of the protein to alter normal lipid organization was examined by using high-sensitivity differential scanning calorimetry (DSC) and 2H nuclear magnetic resonance spectroscopy (2H NMR). The calorimetric measurements indicated that the protein caused a decrease in the temperature maximum (Tm) and a broadening of the phase transition. At a protein concentration of 8% (w/w), the enthalpy change of transition was reduced to 4.4 kcal/mol compared to 6.3 kcal/mol determined for the pure lipid. NMR spectral moment studies indicated that protein had no effect on lipid chain order in the liquid-crystal phase but reduced orientational order in the gel phase. Two-phase coexistence in the presence of protein was observed over a small temperature range below the pure lipid transition temperature. Spin-lattice relaxation times (T1) were not substantially affected by the protein. Transverse relaxation time (T2e) studies suggest that the protein influences slow lipid motions.     

Freezing of phosphocholine headgroup in fully hydrated sphingomyelin bilayers and its effect on the dynamics of nonfreezable water at subzero temperatures.

Differential scanning calorimetry (DSC) and nuclear magnetic resonance (NMR) spectroscopy are applied to characterize the nonfreezable water molecules in fully hydrated D2O/sphingomyelin at temperatures below 0 degrees C. Upon cooling, DSC thermogram displays two thermal transitions peaked at -11 and -34 degrees C. The high-temperature exothermic transition corresponds to the freezing of the bulk D2O, and the low-temperature transition, which has not previously been reported, can be ascribed to the freezing of the phosphocholine headgroup in the lipid bilayer. The dynamics of nonfreezable water are also studied by 2H NMR T1 (spin-lattice relaxation time) and T2e (spin-spin relaxation time obtained by two pulse echo) measurements at 30.7 MHz and at temperatures down to -110 degrees C. The temperature dependence of the T1 relaxation time is characterized by a distinct minimum value of 2.1 +/- 0.1 ms at -30 degrees C. T2e is discontinuous at temperature around -70 degrees C, indicating another freezing-like event for the bound water at this temperature. Analysis of the relaxation data suggest that nonfreezable water undergoes both fast and slow motions at characteristic NMR time scales. The slow motions are affected when the lipid headgroup freezes.     

Structural studies of lipophorin in insect blood by differential scanning calorimetry and 13C nuclear magnetic relaxation measurements. Location of hydrocarbons

The possible structure of lipophorin in insect blood (hemolymph) was investigated by differential scanning calorimetry (DSC) and 13C nuclear magnetic relaxation studies. The DSC heating curves of intact lipophorins showed endothermic peaks between -3 and 40 degrees C for lipophorins which contain hydrocarbons, whereas no such peaks were observed for lipophorins which do not contain this lipid. Hydrocarbon fractions isolated from the lipophorins showed endothermic peaks similar to those obtained from intact lipophorin in terms of the transition temperatures, the shapes, and the enthalpy changes. 13C spin lattice relaxation times of the (CH2)n resonance of hydrocarbons of intact lipophorin were measured as a function of temperature and revealed that the motions of hydrocarbon chains changed coincidentally with the onset and offset of phase transition. These data suggest the presence of a hydrocarbon-rich region within the lipophorin particles.     

Conformational and kinetic studies of synthetic polypeptides by NMR

The α-helix–coil transition of poly-L -leucine, poly-L -alanine and poly-L -methionine in chloroform–trifluoroacetic acid system was studied by nuclear magnetic resonance (NMR) and optical rotatory dispersion (ORD). The kinetics of the hydrogen–deuterium exchange in the peptide was also followed in these polymers by means of NMR. Two types of the NMR spectra and the hydrogen–deuterium exchange reaction were found, corresponding to the high and low molecular weight polypeptides. In high molecular weights, the NH and α-CH resonance lines gave single peaks and the hydrogen–deuterium exchange was expressed as a single first order reaction. In low molecular weights, the NH and α-CH lines were separated into two peaks, corresponding to helical and random-coiled states, respectively, and the exchange react ion was expressed as super-position of a very rapid exchange reaction in the random-coiled part and another slow exchange reaction of the first order in the helical part. These results suggest that the helix–coil interconversion of low molecular weight polypeptides has a longer relaxation time (? 4.5 × 10^?3 sec) than that of high molecular weight polypeptides.     

Paramagnetic form of ribonucleotide reductase in human tissues

The paramagnetic form of ribonucleotide reductase was detected by ESR method in human cervix tissues, especially in tumor ones. The magnetic relaxation rate was proved to be slower for this form than for that in normal animal tissues having a high level of proliferative activity or in Ehrlich tumor cells studied before.     

Protein conformational relaxation following photodissociation of CO from carbonmonoxymyoglobin: picosecond circular dichroism and absorption studies

Picosecond time-resolved polarization spectroscopy is used to study relaxation dynamics in myoglobin following photoelimination of CO from carbonmonoxymyoglobin. Evolution of the transient circular dichroism signal of the N band of myoglobin (probed at 355 nm) to that characteristic of equilibrium myoglobin requires approximately 300 ps. This time scale is significantly longer than that corresponding to the photoinitiated bond cleavage. Transient linear dichroism of the Soret band and picosecond time-resolved magnetic circular dichroism measurements of the Q band demonstrate that the circular dichroism kinetics do not result from either time-dependent changes in the orientation of the transition moments of the heme ring or the doming of the heme that accompanies the out-of-plane motion of the iron. Finally, transient absorption data of the near-IR optical transition of photogenerated myoglobin suggest that the circular dichroism data are not a measure of the tilting of the proximal histidine. The circular dichroism data are discussed in terms of a relaxation in the tertiary structure of the protein following dissociation.     

Electrostatic interactions at charged lipid membranes Kinetics of the electrostatically triggered phase transition

Charged lipid membranes of dimyristoylmethylphosphatidic acid were mixed rapidly in a stopped-flow cell with protons or Ca²⁺ to compensate the charges and thereby trigger the ordered-fluid phase transition. The kinetics of the transition was studied by following the time development of the fluorescence anisotropy of diphenylhexatriene. A relaxation process was observed with a characteristic time in the range 10–200 ms. By comparison with existing theories of non-equilibrium relaxation it was concluded that the relaxation process is governed by a nucleation step.     

The effect of lattice spacing change on cross-bridge kinetics in chemically skinned rabbit psoas muscle fibers. I. Proportionality between the lattice spacing and the fiber width.

Chemically skinned rabbit psoas muscle fibers/bundles were osmotically compressed with a macromolecule dextran T-500 (0-16%, g/100 ml) at 20 degrees C, 200 mM ionic strength, and pH 7.0. The lattice spacing of psoas bundles was measured by equatorial x-ray diffraction studies during relaxation and after rigor induction, and the results were compared with the fiber width measurements by optical microscopy. The purpose of the present study is to determine whether fiber width is a reliable measure of the lattice spacing, and to determine the available spacing for myosin cross-bridges between the thick and thin filaments. We observed that both the lattice spacing and the fiber width decreased with an increase in the dextran concentration during relaxation or after rigor induction, and that the spacing and the fiber width were proportionately related. We further observed that, in the absence of dextran, the lattice spacing (and the fiber width) shrank on a relax-to-rigor transition, whereas in the presence of 16% dextran, the spacing expanded on a relax-to-rigor transition. The cross-over of these plots occurred at the 4-7% dextran concentration. During Ca activation, the fiber width shrank in the absence of dextran, and it slightly expanded in the presence of 14.4% dextran. The degree of expansion was not as large as in the relax-to-rigor transition, and the cross-over occurred at about 11% dextran concentration. We also carried out experiments with dextran T-40 and T-10 to determine the upper limit of the molecular weight that enters the lattice space. We found that the upper limit is about 20 kD.     

Optical activity of simple cyclic amides in solution

The cyclic dipeptide, L -alanylglycyl anhydride, has been studied by optical rotatory dispersion; both L -alanylglycyl anhydride and the lactam, L -3-aminopyrrolidin-2-one, have been studied by circular dichroism. In hydroxylic solvents the circular dichroism spectra of 3-aminopyrrolidin-2-one can be attributed to an n–π* transition near 220 mμ and a π–π* transition near 190 mμ. In these solvents the optical activity of L -alanylglycyl anhydride can be explained as being due to contributions of n–π* transitions and a split π–π* transition. In acetonitrile, however, the circular dichroism spectrum of 3-aminopyrrolidin-2-one shows an additional apparent minimum near 200 mμ. The CD spectrum of the dipeptide is also quite distinctive in this solvent. The possible nature of the band at 200 mμ and the implications of these findings are discussed.     

Optical and magnetic resonance studies of formate binding to horse liver catalase and sperm whale myoglobin.

The binding of formate ion, a substrate for the peroxidatic reaction of catalase, has been investigated by magnetic resonance techniques. Comparative studies of formate binding to ferric myoglobin have also been performed. The nuclear magnetic relaxation (NMR) rate of formate and water protons is enhanced by the presence of ferric horse liver catalase. The enhancement is not changed significantly by the addition of cyanide, indicating that water and formate are still bound in the presence of cyanide. Formate proton to heme iron distances determined by magnetic resonance techniques indicate that formate does not directly bind to the heme iron of catalase or myoglobin but to the globin, and NMR relaxation occurs as a result of outersphere mechanisms. Evidence that water forms an innersphere complex with the iron atom of the catalase heme is presented. In similar experiments with ferric myoglobin, the addition of cyanide caused a large decrease in the enhancement of the proton relaxation rate of both formate and water, indicating the displacement of water and formate from the heme and the vicinity of the heme, respectively. Broad, high-spin, ferric ion electron paramagnetic resonance absorptions of catalase and myoglobin at room temperature obtained in the presence and absence of formate show that formate does not alter appreciably the heme environment of catalase or myoglobin or the spin state of the heme iron. Studies on the binding of formate to catalase as monitored by changes in the heme absorption spectrum in the visible region show one-to-one stoichiometry with heme concentration. However, the small changes observed in the visible region of the optical spectrum on addition of formate ion are attributed to a secondary effect of formate on the heme environment, rather than direct binding of formate to the heme moiety.     

A magnetic study of acidic ferric hemoglobin

In this article, we have extensively studied and discussed the magnetic properties of acidic ferric hemoglobin and its isolated chains. The magnetic susceptibility, EPR and optical spectra of those samples were measured in the temperature region below 77 degrees K. By the magnetic susceptibility measurements, it could be made clear that at an acidic pH value, both ferric hemoglobin and its isolated chains were constituted of a mixture of two spin states (high-spin state S = 5/2 and low-spin state S = 1/2) and the ratio of this mixture varied in each protein sample, but was independent of the temperature change below 77 degrees K. The co-existence of these two components could be ascertained by the observation of EPR spectra at liquid hydrogen temperature. Acidic ferric hemoglobin and its isolated chains exhibited the two components of EPR spectra which corresponded to their magnetic susceptibility, and it was found that the relaxation time of the low-spin state was longer than that of the high-spin state. The low-spin component of EPR spectra was almost undetectable at liquid nitrogen temperature. The three principal g values of this low-spin were gz = 2.80, gy = 2.20, and gx = 1.70. At alkaline pH values these low-spin components and the high-spin component of EPR spectra were displaced by the different low-spin spectra which corresponded to the ferric hemoglobin-hydroxide complex. It seems that the magnetic properties of the high-spin component are the same as the acidic ferric myoglobin, and the fine structure of the iron ion also seems to be same. Optical spectroscopy also gave similar magnetic properties which corresponded to the magnetic measurements.     

Ultrasonic evidence for structural relaxation in large unilamellar liposomes

The ultrasonic absorption of large unilamellar vesicles (average diameter 0.2 micron) was determined in the frequency range 0.5-5 MHz. The liposomes were composed of a 4:1 mixture by weight of dipalmitoyl phosphatidylcholine and dipalmitoyl phosphatidylglycerol. They were studied with and without cholesterol or gramicidin incorporated into the bilayer. A large increase in absorption occurs at the solid to liquid-crystalline phase transition temperature (42 degrees C) of the pure lipid vesicles. This increase in absorption is interpreted as a structural relaxation of the 'melting' fatty acid chains occurring with an average relaxation time of 76 ns. The liposomes were also found to be extremely permeable near the transition temperature. Essentially complete release of cytosine arabinoside, a small water-soluble molecule, occurred at 42 degrees C. Addition of cholesterol or gramicidin to the bilayer of the liposomes broadened the ultrasonic absorption and reduced the efflux of cytosine arabinoside at the phase transition. No increase in absorption was observed at the transition temperature in the presence of 50 mol% of cholesterol. Gramicidin, in addition to broadening the transition, slows the isomerization of bonds in the hydrocarbon chains of the lipids. A concentration of 5 mol% gramicidin increased the average relaxation time to 211 ns.     

Theory of optical spectra of photosystem II reaction centers: location of the triplet state and the identity of the primary electron donor

Based on the structural analysis of photosystem II of Thermosynechococcus elongatus, a detailed calculation of optical properties of reaction-center (D1-D2) complexes is presented applying a theory developed previously. The calculations of absorption, linear dichroism, circular dichroism, fluorescence spectra, all at 6 K, and the temperature-dependence of the absorption spectrum are used to extract the local optical transition energies of the reaction-center pigments, the so-called site energies, from experimental data. The site energies are verified by calculations and comparison with seven additional independent experiments. Exciton relaxation and primary electron transfer in the reaction center are studied using the site energies. The calculations are used to interpret transient optical data. Evidence is provided for the accessory chlorophyll of the D1-branch as being the primary electron donor and the location of the triplet state at low temperatures.     

Influence of sucrose and water content on molecular mobility in starch-based glasses as assessed through structure and secondary relaxation

Molecular mobility is known to be a key parameter in controlling the physical properties of materials and thus their quality and performance. Beyond glass transition related changes, attention should be called to the impact of local motions remaining in the glassy state. Gelatinized waxy maize starch at different sucrose contents (0-20% solids) was equilibrated between 0 and 14% water and sorption isotherms determined at 25 degrees C. The effect of water and sucrose content on the molecular mobility of glassy starch was investigated by differential scanning calorimetry through enthalpy relaxation studies and dynamical mechanical thermal analysis. The existence of sucrose-starch interactions was suggested by the sorption isotherms not following the expected additivity of the single component sorption curves. Contrary to the glass transition or associated alpha relaxation, water and sucrose affected differently the secondary relaxations. Indeed, the beta relaxation observed around -15 degrees C was shifted to lower temperature upon increasing hydration, and to higher temperature when sucrose content increased, suggesting a hindering of these local motions. Enthalpy relaxation of the ternary mixtures was studied following aging up to 668 h at Tg -15 degrees C. Ternary mixtures exhibited an enthalpy relaxation upon aging lower than starch alone as a sign of lower polymer mobility in the presence of small molecules, contrary to the free volume theory. Relaxation kinetics were characterized with the Cowie-Ferguson model and compared to literature data. The extent of the enthalpy relaxation appeared to be controlled by the distance between the aging temperature and the beta relaxation temperature.