Interplay of terminal amino group and coordinating side chains in directing regioselective cleavage of natural peptides and proteins with palladium(II) complexes

Palladium(II) ions anchored to side chains of histidine and methionine residues in peptides and proteins in weakly acidic aqueous solutions promote hydrolytic cleavage of proximate amide bonds in the backbone. In this study, we determine how attachment of Pd(II) ions to histidine and methionine anchors and also to the terminal amino group in six natural peptides (chains A and B of insulin, segment 11-14 of angiotensinogen, pentagastrin, angiotensin II, and segment 3-8 of angiotensin II) and two proteins (ubiquitin and cytochrome c) affects regioselectivity and rate of backbone cleavage. These Pd(II)-promoted reactions follow a clear pattern of regioselectivity, directed by the anchoring side chains. When the Pd(II) reagent is nonspecifically anchored to the terminal amino group, the ligating site that is present in almost all proteins, the cleavage is fortunately absent. When the reagent is anchored to a residue in positions 1, 2, or 3, cleavage is absent, because the terminal amino group and deprotonated amide nitrogen atom(s) interposed between it and the anchor "lock" the Pd(II) ion in hydrolytically inactive chelate complexes. When the reagent is anchored to residues in positions beyond 3, the second amide bond upstream from the anchor is regioselectively cleaved in all cases when the anchor was "isolated," that is, flanked by noncoordinating side chains. Segment 3-8 of angiotensin II undergoes additional cleavage, which we explain by determining the rate constants for the cleavage, identifying the rate-limiting displacement of ethylenediamine ligand from the Pd(II) ion, and detecting several intermediates. Experiments with cytochrome c demonstrate that the number of cleavage sites can be controlled by adjusting the mole ratio of the Pd(II) reagent to the substrate. Our inorganic peptidases are useful for biochemical applications because their regioselectivity and reactivity set them apart from proteolytic enzymes and organic chemical reagents.     

The characteristic polynomial of a chemical graph

We list uses of, and the computational methods for the characteristic polynomial of a (chemical) graph. Pour computational methods are singled out for more detailed presentation. These are the graphical methods of Sachs, the recurrence formulae for several classes of simple graphs, the method based on Ulam subgraphs, and the Le Verrier — Faddeev — Franic recursive method. The latter method appears, at present, to be the most efficient procedure for the computation of the characteristic polynomials of graphs of sizes with up to even a few hundred sites.Dedicated to Dennis H. Rouvray, the friend and one of the foremost popularizers of chemical graph theory in our time.Research supported by the Robert A. Welch Foundation of Houston, Texas, USA.     

Combined use of platinum(II) complexes and palladium(II) complexes for selective cleavage of peptides and proteins

This study shows, for the first time, the advantages of combining two transition-metal complexes as selective proteolytic reagents. In this procedure, cis-[Pt(en)(H(2)O)(2)](2+) is followed by [Pd(H(2)O)(4)](2+). In the peptide AcAla-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala, the Pt(II) reagent cleaves the Met6-Ala7 peptide bond, whereas the Pd(II) reagent cleaves the Gly4-Gly5 bond. In the peptide AcVal-Lys-Gly-Gly-His-Ala-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala, the Pt(II) reagent cleaves the Met11-Ala12 peptide bond, whereas the Pd(II) reagent cleaves the Gly3-Gly4 bond. All cleavage reactions are regioselective and complete at pH 2.0 and 60 degrees C. Each metal ion binds to an anchoring side chain and then, as a Lewis acid, activates a proximal peptide bond toward hydrolysis by the solvent water. The selectivity in cleavage is a consequence of the selectivity in this initial anchoring. Both Pt(II) and Pd(II) reagents bind to the methionine side chain, whereas only the Pd(II) reagent binds to the histidine side chain under the reaction conditions. Consequently, only methionine residues direct the cleavage by the Pt(II) reagent, whereas both methionine and histidine residues direct the cleavage by the Pd(II) reagent. The Pt(II) reagent cleaves the first bond downstream from the anchor, i.e., the Met-Z bond. The Pd(II) reagent cleaves the second bond upstream from the anchor, i.e., the X-Y bond in the X-Y-Met-Z and in the X-Y-His-Z segments. The diethylenetriamine complex [Pt(dien)(H(2)O)](2+) cannot promote cleavage. Its prior binding to the Met11 residue in the second peptide prevents the Pd(II) reagents from binding to Met11 and cleaving the Gly9-Gly10 bond and directs the cleavage by the Pd(II) reagent exclusively at the Gly3-Gly4 bond. Our new method was tested on equine myoglobin, which contains 2 methionine residues and 11 histidine residues. The complete methionine-directed cleavage of the Met55-Lys56 and Met131-Thr132 bonds by the Pt(II) reagent produced three fragments, suitable for various biochemical applications because they are relatively long and contain amino and carboxylic terminal groups. The deliberately incomplete histidine-directed cleavage of the long fragments 1.55 and 56.131 at many sites by the Pd(II) reagent produced numerous short fragments, suitable for protein identification by mass spectrometry. The ability of combined Pt(II) and Pd(II) complexes to cleave proteins with explicable and adjustable selectivity and with good yields bodes well for their greater use in biochemical and bioanalytical practice.     

Simultaneous electrical and X-ray diffraction studies on neodymium metal to 152 GPa

Using designer diamond anvils and angle dispersive X-ray diffraction technique at a synchrotron source, we have performed simultaneous electrical and structural studies on neodymium metal to 152 GPa in a diamond anvil cell. Four-probe electrical resistance measurement shows a 38% decrease in the electrical resistivity, associated with the delocalization of the 4f-shell electrons, starting at 100 GPa up to a final pressure of 152 GPa. The continuous decrease in electrical resistivity is consistent with the observation of a gradual phase transition to α-U structure in this pressure range. The (1 1 1) diffraction peak of α-U structure first appears at 100 GPa and increases in intensity with increasing pressure to 152 GPa. This increase in intensity is attributed to an increasing volume fraction of α-U phase and an increase in structural y-parameter from 0.07 at 118 GPa to 0.095 at 152 GPa. In contrast to the abrupt pressure-induced f-electron transition seen in cerium and praseodymium, the continuous evolution of α-U structure and electrical resistivity in neodymium confirms the gradual nature of 4f delocalization process in this element.     

No More Tears in Heaven: Two Views of Response-Dependence

The paper defends a neo-Lockean view of secondary qualities, in particular color, according to which the being of a given color amounts to having the disposition to produce in normal viewers under normal circumstances the response of seeing an objective manifest simple color. It also defends the view that the naïve color-concept, the simple color concept, so to speak, is a fully objective property. The defense of this view is carried against its “nearest cousin”, the view proposed and defended by Philip Pettit and Frank Jackson, according to which the naive color concept is response dependent, whereas color itself is fully objective. It is argued that the neo-Lockean alternative better captures the phenomenology of color, and better predicts or accounts for the dramatic character of the historical scientific discoveries (of Newton and his followers). Against metaphysical response dependence, the paper proposes a brief positive argument from the unity of color properties, and a criticism of Jackson’s counter-argument against metaphysical response-dependence from the naïve intuitions about causal properties of color.     

Variable neighborhood search for harmonic means clustering

Harmonic means clustering is a variant of minimum sum of squares clustering (which is sometimes called K-means clustering), designed to alleviate the dependance of the results on the choice of the initial solution. In the harmonic means clustering problem, the sum of harmonic averages of the distances from the data points to all cluster centroids is minimized. In this paper, we propose a variable neighborhood search heuristic for solving it. This heuristic has been tested on numerous datasets from the literature. It appears that our results compare favorably with recent ones from tabu search and simulated annealing heuristics.     

Determination of the soil-to-grass transfer of 137Cs and its relation to several soil properties at various locations in Serbia

Transfer coefficients of (137)Cs from soil to grass were determined for the terrain around the city of Kragujevac in central Serbia. Mass activity concentrations of (137)Cs in soil and grass samples were determined with a high-purity Ge-detector (HPGe). The activity concentration at the depth of 20 cm was found to be in the range of 14.92-124.05 Bq kg(-1), whereas the activity in grass for the same location was in the range of 4.60-84.95 Bq kg(-1). Transfer factors (TFs) were in the range of 0.07 up to 1.94. Dependences of TFs on different soil characteristics were presented graphically. Weak dependences were determined between them. Absalom's model was used to predict TFs based on soil characteristics: pH value, contents of clay, exchangeable potassium and humus. A comparison of measured and predicted values from Absalom's model is shown graphically. It has been found that Absalom's model might be carefully used for the prediction of (137)Cs in grass for specific regions.     

Uncoupled photonic band gaps

We theoretically investigated the symmetry properties of the modes in two-dimensional square lattice photonic crystals in order to study phenomena that would enable new frontiers in the applications of photonic crystals. Using group theory, symmetry analysis of the photonic crystals bands has been done. Particular attention was given to the search for the uncoupled B modes that cannot be excited by the external plane wave because they are symmetry forbidden. The existence of the uncoupled modes enabled to define new physics phenomena: uncoupled photonic band gaps. For the frequency ranges inside the uncoupled photonic band gaps, zero transmission is obtained. Therefore, there are two different types of photonic gaps in the photonic crystals: photonic band gaps and uncoupled photonic band gaps. The appearance of uncoupled photonic band gaps in photonic crystals could at least improve the application of the existing photonic materials and structures or even enable the usage of new ones for devices like waveguides, filters, and lasers.     

Analysis of Error Propagation from NMR-Derived Internuclear Distances into Molecular Structure ofCyclo-Pro-Gly

Analytical expressions have been derived that translate uncertainties in distance constraints (obtained from NMR investigations) into uncertainties in atom positions in the maximum likelihood (ML) structure consistent with these inputs. As a test of this approach, a comparison was made between test structures reconstructed by the new ML approach, which yields a single structure and a covariance matrix for coordinates, and those reconstructed by metric matrix distance-geometry (MMDG), which yields a family of structures that sample uncertainty space. The test structures used were 560 polyhedra, with edges of arbitrary length containing up to 50 vertices, and one polyhedron, with 100 vertices; randomized distance constraints generated from these structures were used in reconstructing the polyhedra. The uncertainties derived from the two methods showed excellent agreement, and the correlation improved, as expected, with increasingly larger numbers of MMDG structures. This agreement supports the validity of the rapid analytical ML approach, which requires the calculation of only a single structure. As a second test of the ML method, the approach was applied to the determination of uncertainties in the structure of a cyclic dipeptide,cyclo(DL-Pro-Gly) (cPG), derived from NMR cross-relaxation data. The input data were interproton distances calculated from NOEs measured for a solution of the peptide in 2:1 DMSO:H₂O at −40°C (so as to yield large negative NOEs). In order to evaluate effects of the quality of the input spectral parameters on the precision of the resulting NMR structure, information from the covalent geometry of cPG was not used in the structure calculations. Results obtained from the analytical ML approach compared favorably with those from the much slower random-walk variant of the Monte Carlo method applied to the same input data. As a third test, the ML approach was used with synthetic structural constraints for a small protein; the results indicate that it will be feasible to use this rapid method to translate uncertainties associated with a given set of distance restraints into uncertainties in atom positions in larger molecules.     

Imaging of the reaction zone in a 100 kW oil-burning furnace by use of a broad-band excimer laser

The reaction zone in the hostile combustion environment of a 100 kW oil-burning furnace has been imaged by laser-induced fluorescence using a broad-band XeCl-excimer laser. Upon excitation, the averaged images obtained by using an interference filter around 320 nm (FWHM of 10 nm) show three distinct areas along the direction of the gas flow. An intense emission spreads around the spray axis and is attributed to the fluorescence of large hydrocarbons in the unburned fuel. Approximately 12 cm downstream of the nozzle, a narrow dark region is displayed suggesting the preheat zone of the combustion process where large hydrocarbons are considerably degraded. The third distinct region is characterized by a strong onset of the fluorescence intensity localized downstream of the dark region. This feature is strongly suppressed by replacing the interference filter by a broad-band transmission filter passing light from 350 to 500 nm. Since OH strongly absorbs at the laser wavelength and its fluorescence is significantly lower above 345 nm, the findings imply that the major contribution to the observed intensity in this region originates from the OH radical. This molecule reaches its maximum concentration immediately downstream of the flame front. However, a contribution from other flame species fluorescing around 320 nm cannot be ruled out. Nevertheless, the combined spatial and spectral information obtained imply that the reaction zone of the combustion process can be localized accurately. The results are compared with simultaneously performed numerical simulations of the burner and are in reasonable agreement.