Shake-up and shake-off excitations with associated electron losses in X-ray studies of proteins

Photoionization of an atom by X-rays usually removes an inner shell electron from the atom, leaving behind a perturbed "hollow ion" whose relaxation may take different routes. In light elements, emission of an Auger electron is common. However, the energy and the total number of electrons released from the atom may be modulated by shake-up and shake-off effects. When the inner shell electron leaves, the outer shell electrons may find themselves in a state that is not an eigen-state of the atom in its surroundings. The resulting collective excitation is called shake-up. If this process also involves the release of low energy electrons from the outer shell, then the process is called shake-off. It is not clear how significant shake-up and shake-off contributions are to the overall ionization of biological materials like proteins. In particular, the interaction between the outgoing electron and the remaining system depends on the chemical environment of the atom, which can be studied by quantum chemical methods. Here we present calculations on model compounds to represent the most common chemical environments in proteins. The results show that the shake-up and shake-off processes affect approximately 20% of all emissions from nitrogen, 30% from carbon, 40% from oxygen, and 23% from sulfur. Triple and higher ionizations are rare for carbon, nitrogen, and oxygen, but are frequent for sulfur. The findings are relevant to the design of biological experiments at emerging X-ray free-electron lasers.     

LET,track structure and models

Summary Swift heavy ions when penetrating through matter strip off those electrons having a smaller orbital velocity than the ion velocity. The remaining electrons screen the nuclear charge yielding an effective charge. The effective charge of the ions interacts predominately with the target electrons causing excitation and ionizations of the target atoms. Using the Bethe Bloch formula for the energy loss combined with the Barkas formula for effective charge, the energy loss values as well as unrestricted and restricted linear transfer can be calculated within a few percent of accurancy. From the primary energy loss only a small fraction of 10% or less is transformed into excitation. The major part of the energy loss is used for the ionization of the target atoms and the emission of the corresponding electrons with a high kinetic energy. These electrons form the track around the trajectory of the primary ion in which two thirds of the primary energy is deposited by collisions of primary, secondary and later generations of electrons with the target molecules. In the electron diffusion process the energy is transported from the center of the track into the halo. The radial dose decreases with the square of the radial distance from the center. The diameter of the track is determined by the maximum range of the emitted electrons, i.e. by the maximum energy electrons. All ions having the same velocity i.e. the same specific energy produce electrons of the same energy and therefore tracks of the same diameters independent of the effective charge. But the dose inside the track increases with the square of the effective charge. Track structure models using this continuous dose distributions produce a better agreement with the experiment than models based on microdosimetry. The critical volume as used in microdosimetry is too large compared to the size of the DNA as critical structure inside the biological objects. Track structure models yield better results because the gross-structure of the track i.e. its lateral extension and the thin down toward the end of the track is included in these calculations. In a recent refinement the repair capacity of the cell has been included in a track structure model by using the complete shouldered x-ray survival curve as a template for the local damage produced by the particle tracks. This improved model yields presently the best agreement with the experiment.Invited paper given on the fourth workshop on Heavy Charged Particles in Biology and Medicine GSI, Darmstadt, FRG, September 23–25, 1991     

Cross sections of electron inelastic interactions in DNA

The cross sections of electron inelastic interaction in DNA are calculated using the dielectric response theory and Penn statistical approximation, with the exchange correction included. An empirical approach to obtain optical energy loss function is given for the organic compounds without available optical data. Comparisons of the calculated data with available experimental and theoretical results have been done to show the reliability of the approach proposed in this work. Using this approach, the total inelastic cross sections for five bases: guanine, adenine, thymine, cytosine and uracil have been calculated in the energy range of E10 keV and compared with those recently obtained with the Deutsch-Märk formalism and the Binary-Encounter-Bethe model, respectively. An equivalent unit of the DNA molecule is constructed according to the contents of A-T and G-C base pairs in DNA, and is divided into five constituents, i.e. sugar-phosphate and four bases. The total inelastic cross sections for the constructed unit of the DNA molecule and its constituents have also been calculated.     

Model for radial dependence of frequency distributions for energy imparted in nanometer volumes from HZE particles

This paper develops a deterministic model of frequency distributions for energy imparted (total energy deposition) in small volumes similar to DNA molecules from high-energy ions of interest for space radiation protection and cancer therapy. Frequency distributions for energy imparted are useful for considering radiation quality and for modeling biological damage produced by ionizing radiation. For high-energy ions, secondary electron (delta-ray) tracks originating from a primary ion track make dominant contributions to energy deposition events in small volumes. Our method uses the distribution of electrons produced about an ion's path and incorporates results from Monte Carlo simulation of electron tracks to predict frequency distributions for ions, including their dependence on radial distance. The contribution from primary ion events is treated using an impact parameter formalism of spatially restricted linear energy transfer (LET) and energy-transfer straggling. We validate our model by comparing it directly to results from Monte Carlo simulations for proton and alpha-particle tracks. We show for the first time frequency distributions of energy imparted in DNA structures by several high-energy ions such as cosmic-ray iron ions. Our comparison with results from Monte Carlo simulations at low energies indicates the accuracy of the method.     

Whole-cell imaging at nanometer resolutions using fast and slow focused helium ions

Observations of the interior structure of cells and subcellular organelles are important steps in unraveling organelle functions. Microscopy using helium ions can play a major role in both surface and subcellular imaging because it can provide subnanometer resolutions at the cell surface for slow helium ions, and fast helium ions can penetrate cells without a significant loss of resolution. Slow (e.g., 10–50 keV) helium ion beams can now be focused to subnanometer dimensions (∼0.25 nm), and keV helium ion microscopy can be used to image the surfaces of cells at high resolutions. Because of the ease of neutralizing the sample charge using a flood electron beam, surface charging effects are minimal and therefore cell surfaces can be imaged without the need for a conducting metallic coating. Fast (MeV) helium ions maintain a straight path as they pass through a cell. Along the ion trajectory, the helium ion undergoes multiple electron collisions, and for each collision a small amount of energy is lost to the scattered electron. By measuring the total energy loss of each MeV helium ion as it passes through the cell, we can construct an energy-loss image that is representative of the mass distribution of the cell. This work paves the way to use ions for whole-cell investigations at nanometer resolutions through structural, elemental (via nuclear elastic backscattering), and fluorescence (via ion induced fluorescence) imaging.     

A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu2+ complex

Since high-intensity synchrotron radiation is available, extended X-ray absorption fine structure spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu²⁺ complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.     

Application of the Lambert <Emphasis Type="Italic">W</Emphasis> function in mathematical problems of plasma physics

Examples of solutions to transcendental equations that arise in mathematical problems of plasma physics are considered. Earlier, such equations were solved only by approximate methods. The use of a new function—the Lambert W function—has made it possible to obtain explicit exact solutions that can help to refine the existing relevant theories. As examples, the following problems from different branches of plasma physics are considered: the equilibrium charge of a dust grain in a plasma, the structure of the Bohm sheath, the diameter of the separatrix in a Galathea-Belt system, the transverse structure of an electron beam in a plasma, the energy loss rate of a test charged particle in a plasma, and the structure of the Sagdeev pseudopotential for ion acoustic waves.     

Copillaria hepatica: Fine structure of egg shell

The structure of the Capillaria hepatica egg shell was studied with the electron microscope and correlated with light microscope histochemical observations. The shell is composed of fibrous and nonfibrous components, both of which stain for protein. The fibrous component, the major portion of the shell, consists of submicroscopic fibers. The nonfibrous component is located in the outer region of the shell but is not always visible; when present it has a reticulated appearance in electron micrographs. The fibrous component is divided into outer and inner regions. The outer region is composed of radially arranged pillars which are connected at their outer surface by a beam-like network and are anchored at the base to a compact inner region. The inner region consists of a series of concentrically arranged lamellae above which is located a nonlaminated region where the pillar bases originate. At each polar end of the shell is a single opening plugged with a material which contains acid mucopolysaccharide. The fine structure of the body of the plug is unresolvable with the electron microscope; its outer surface is impregnated with electron dense particles. Externally the shell is covered by a 250 Å thick continuous membrane which is in close opposition to the surrounding host tissue.     

Energy metabolism in wheat root cells under modification of plasma membrane permeability by antibiotic nystatin

This paper reports changes in ion transport and energy metabolism of plant cells during short- and long-term expositions, resp., to antibiotic nystatin, which is known to specifically bind with plasma membrane sterols to form channels. The excised roots of 5 days old wheat seedlings were used as a model system in this research. It has been shown that treatment of excised roots with nystatin leads to activation of energy metabolism expressed as an increase of respiration and heat production by root cells. Furthermore, in the presence of nystatin increased pH of incubation medium, plasma membrane depolarization and a significant loss of potassium ions were observed. Nystatin-induced stimulation of respiration was prevented by malonate, an inhibitor of succinate dehydrogenase, electron acceptor dichlorophenolindophenol, and AgNO3, an inhibitor of H(+)-ATPase. Based on the data obtained it can be suggested that nystatin-induced stimulation of respiration is related to electron transport activation via mitochondrial respiratory chain, and is connected with activation of plasmalemma proton pump. Moreover, nystatin-induced increase of oxygen consumption was prevented by cerulenin, an inhibitor of fatty acid and sterol synthesis. This indicates that additional sterols and phospholipids may be synthesized in root cells to "heal" nystatin-caused damage of plasma membrane. A supposed chain of events of cell response to nystatin action may by as following: formation of nystatin channels-influx of protons--depolarization of plasmalemma-efflux of potassium ions-disturbance of ion homeostasis--activation of H(+)-ATPase work-increase in energy "requests" for H(+)-ATPase function--increase in the rate of oxygen consumption and heat production. The increased energy production under the action of nystatin, may provide the work of proton pump and synthesis of sterols and phospholipids, which are necessary for membrane regeneration.     

Scanning electron microscopy of the shell membranes of the hen's egg

Summary Scanning and transmission electron microscopy have been used to study the structure of the hen's shell membranes and their relationship to the shell and to the chorioallantoic membrane.We have confirmed previous observations that the fibres of the outer shell membrane are of larger diameter than those of the inner shell membrane, and that the fibres of the outer shell membrane extend into the mammillary knobs of the shell.The shell membrane fibres are arranged in layers parallel to the surface of the egg and there is no interweaving between the layers. Individual fibres are randomly orientated and may extend for distances of at least 25 m. It is suggested that relative movement between the oviduct and the developing membrane is random in direction and location.Each fibre consists of a core with a covering cortex, but the idea that the core may consist of keratin is criticised. A limiting membrane separating the surface of the albumen from the fibres of the shell membrane is also formed from this cortex. During incubation the chorioallantoic membrane becomes pressed against this inner limiting membrane.No correlation could be found between the positioning of the mammillary knobs and the patterning of the shell membrane fibres. It is suggested that the positioning of the mammillary knobs reflects the pattern of certain secretory cells in the genital tract of the hen.No significant changes in structure of thickness of the shell membrane could be found during incubation. The tips of the mammillary knobs, however, become detached from the shell and remain adherent to the shell membrane.The Cambridge Scientific InstrumentsStereoscan scanning electron microscope was provided by the Science Research Council (UK).We should like to thank Mr.R. F. Moss and Mr.P. S. Reynolds for technical assistance, and Mrs.Jeanne Mills for secretarial assistance.     

A theoretical study of Na+ and Mg+2 binding to the carbonyl oxygen of N-methyl acetamide.

Molecular orbital calculations (CNDO/2) are reported for the interaction of Na+ and Mg+2 with the carbonyl of a model peptide moiety (N-methyl acetamide) as a function of the C--O ... Me distance and angle and with variation in the number of ligands for the purpose of determining the steepness of the distance dependence of the binding energy and for the purpose of determining the reduction of charge on the ion with increasing numbers of ligands. The greater energy derived on divalent ion binding and the steeper distance dependence indicate that selective, divalent over monovalent, ion binding will occur whenever the liganding system can provide a coordination shell of appropriate dimension. The calculations indicate that the preferred C--O ... Me angle is not 180 degrees. Of particular note is the decrease of charge on the cation on binding to N-methyl acetamide. One ligand bound to Na+ reduces the charge from 1.0 to 0.7 electron units and four ligands bound to Mg+2 reduces the charge from 2.0 to 0.7 electron units. This is of primary significance in carrier and channel mechanisms for cation permeation of lipid membranes; and although the numerical values are qualitative, the implication is for allowance of multiple occupancy of channels by monovalent cations.     

Energy loss of hydrogen- and helium-ion beams in DNA: calculations based on a realistic energy-loss function of the target

We have calculated the electronic energy loss of proton and α-particle beams in dry DNA using the dielectric formalism. The electronic response of DNA is described by the MELF-GOS model, in which the outer electron excitations of the target are accounted for by a linear combination of Mermin-type energy-loss functions that accurately matches the available experimental data for DNA obtained from optical measurements, whereas the inner-shell electron excitations are modeled by the generalized oscillator strengths of the constituent atoms. Using this procedure we have calculated the stopping power and the energy-loss straggling of DNA for hydrogen- and helium-ion beams at incident energies ranging from 10 keV/nucleon to 10 MeV/nucleon. The mean excitation energy of dry DNA is found to be I = 81.5 eV. Our present results are compared with available calculations for liquid water showing noticeable differences between these important biological materials. We have also evaluated the electron excitation probability of DNA as a function of the transferred energy by the swift projectile as well as the average energy of the target electronic excitations as a function of the projectile energy. Our results show that projectiles with energy ?100 keV/nucleon (i.e., around the stopping-power maximum) are more suitable for producing low-energy secondary electrons in DNA, which could be very effective for the biological damage of malignant cells.     

Initial studies with high resolution TEM and electron energy loss spectroscopy studies of ferritin cores extracted from brains of patients with progressive supranuclear palsy and Alzheimer disease.

Studies of crystallographic structure and composition of core nanocrystals of ferritin bound to aberrant tau filaments extracted from progressive supranuclear Palsy (PSP) and Alzheimer disease (AD) brain tissues were performed using high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). The results were compared with those obtained from synthetic Fe3O4 crystal (magnetite) and horse spleen ferritin cores. Core dimensions of ferritin molecules from PSP and AD were similar to those found in normal brain. Ferritin cores nanocrystals in AD seems to have less ordered structure than in PSP. Some nanocrystals did not have the hexagonal ferrihydrite structure generally found in healthy ferritin but rather a cubic structure similar to magnetite, a crystalline form in which both Fe2+ and Fe3+ are present. The presence of ferrous ion, Fe2+, may indicate some dysfunction in these pathological ferritins that might contribute to production of free radicals via the Fenton reaction involved in neurodegeneration.     

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH₃ interaction is weak electrostatically.     

Mixing s orbitals into p and d orbitals. An attempt at bridging the angular overlap model and the valence shell electron pair repulsion model. Critique of the cellular ligand-field model

The stereochemistries of main group molecules have been discussed by using the angular overlap model in its molecular orbital oriented form (MO-AOM). Either ligand-field stabilisation of the ground state s²p^q−2 configuration, or s-p mixing, or both, provide a consistent bonding model for the stereochemistries. The transformation of the non-bonding orbitals into equivalent orbitals leads invariably to agreement with the lone-pair locations of the valence shell electron pair repulsion (VSEPR) model. The concepts of Hamiltonian-generated hybrids and pseudohemispherical molecular systems are found useful in this context. The MO-AOM formalism is also used for discussing s-d mixing in transition metal systems, and the energetic consequences within the ligand-field AOM (LF-AOM) are included. This is a second-order effect, which depends on squares and cross-products of radial parameters. It may still be quite large for tetragonal systems and for systems that deviate strongly from orthoaxiality. The usual ligand-additive property of the AOM is lost when the symmetry is lower than tetragonal and so is the energy separability into angular and radial factors. The cellular ligand-field model is found to be identical with the LF-AOM, except that its users consider it important not to acknowledge the formal hierarchy, MO-AOMLF-AOM, as relevant. The unintelligible concept of an active coordination void is found to be unnecessary and insufficient.     

Exploring Advanced Sandwiched Arrays by Vertical Graphene and N‐Doped Carbon for Enhanced Sodium Storage

Smart hybridization of active materials into tailored electrode structure is highly important for developing advanced electrochemical energy storage devices. With the help of sandwiched design, herein a powerful strategy is developed to fabricate three‐layer sandwiched composite core/shell arrays via combined hydrothermal and polymerization approaches. In such a unique architecture, wrinkled MoSe₂ nanosheets are sandwiched by vertical graphene (VG) core and N‐doped carbon (N‐C) shell forming sandwiched core/shell arrays. Interesting advantages including high electrical conductivity, strong mechanical stability, and large porosity are combined in the self‐supported VG/MoSe₂/N‐C sandwiched arrays. As a preliminary test, the sodium ion storage properties of VG/MoSe₂/N‐C sandwiched arrays are characterized and demonstrated with high capacity (540 mA h g^?1), enhanced high rate capability, and long‐term cycling stability (298 mA h g^?1 at 2.0 A g^?1 after 1000 cycles). The sandwiched core/shell structure plays positive roles in the enhancement of electrochemical performances due to dual conductive carbon networks, good volume accommodation, and highly porous structure with fast ion diffusion. The directional electrode design protocol provides a general method for synthesis of high‐performance ternary core/shell electrodes.     

Dynamics of active transmembrane ion transfer in transport enzymes

It has been shown that recent investigations of the electron density distribution and high resolution (approximately 0.5 nm) spatial structure of transport ATPases open new possibilities in the development of general models for the mechanisms of energy of ATP hydrolysis and its use for active transmembrane ion transfer.     

The mathematics of gnomonic seashells

Parametric Cartesian vector-valued functions are constructed for the purpose of systematically describing various features of spiral shell geometry. The underlying geometrical hypothesis is that molluscan shell shapes can usually, to at least a good first approximation, be developed by rotating a generating curve about a fixed axis whilst simultaneously diminishing it by an “equiangular spiral” scale factor. A first-order symmetry equation is derived; then variational calculus is used to construct energy functionals which establish that Hooke's law is inherent in the formalism and that naturally occurring shell geometries are analogous to those of elastic spiral “clock springs”. The biological requirement that shelly structures must exist in a three-dimensional space is shown to be a sufficiently powerful mathematical constraint to ensure the existence of geometrical artifacts which can, perhaps, be likened to the conservation laws, pseudoforces, and fields of classical physics.