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PubMed1975

Environment and conformation dependent sensitivity of the arsanilazotyrosine-248 carboxypeptidase A chromophore.

Reaction of carboxypeptidase A crystals with diazotized arsanilic acid uniquely modifies Tyr-248 to form a monazo derivative, which-in solution-forms an intramolecular inner-sphere coordination complex in the active site zinc atom. tarsanilazocarboxypeptidase exhibits spectral properties that are closely similar to those of the model complex, tetrazolylazo-N-carbobenzoxytyrosine Zn2+, with a distinctive maximum at 510 nm. In addition, its circular dichroic spectrum reveals a negative extremum at this wavelength, also characteristic of this complex. Both spectra are exquisitely responsive to pth changes and serve to monitor formation and dissociation of the metal-azophenol complex. Two pKapp at 7.7 and 9.5 delineate the pH range over which the probe characteristics most effectively gauge conformational features of the active center of arsanilazcarboxypeptidase. Other environmental parameters, e.g., substrates and inhibitors, as well as crystallization of the enzyme also critically influence the formation and dissociation of the complex; the response of the probe suggests that they induce conformational movement of the azoTyr-248 residue away from the zinc atom. tthe now available chemical, functional, structural data bearing on the spatial relationships of Tyr-248 and Zn, both thought critical to catalysis, are evaluated, based on spectra of arsanilazo- and nitrocarboxypeptidase crystals and solutions as well as on detailed kinetic analyses of the native enzyme in both physical states and based on the X-ray structure analysis of the native enzyme and its Gly-L-Tyr complex. Collectively all of the data show that the conformation of carboxypeptidase in crystals differs from that in solution. Moreover, reexamination of the original X-ray maps reported in 1968 and thought to preclude a Tyr-248-Zn interaction now leads to the conclusion that in up to 25 per cent of the molecules in the crystals ttyr-248 interacts with the active site zinc atom (W.D. Lipscomb (1973), Proc. Nat. Acad. Sci U.S. 70, 3797). Thus, even in the crystals the enzyme exists in at least two different conformations. In one of these Tyr-248 is near while in the other it is far from the zinc atom. The spectral effects of Gly-L-Tyr and beta-phenylpropionate on solutions of arsanilazo- and of nitrocarboxypeptidase demonstrate that during the catalytic process Tyr-248 moves away from the zinc atom. This implies a mechanistic role for Tyr-248 different from that postulated on the basis of X-ray crystallographic analysis. Indeed, the proximity of ttyr-248 to the zinc atom, when altered by substrates and inhibitor, may reflect certain of the properties characteristic of the entatic, active site.

Animals↗
PubMed1979

[Comparison of algorithms for the resolution of a secular equation in the vibrational analysis of biological molecules].

A computer analysis of several solution methods for secular equations leads to a determination of their optimum conditions. The results contribute to the application of a new preliminary method of frequency assignment to the vibrational study of the heavy atoms coordination sphere in complex biological structures, such as metalporphyrins and adenosine triphosphate.

Adenine Nucleotides↗
PubMed1975

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.

Animals↗
PubMedDate not supplied

Reactions in glass-ionomer cements: IV. Effect of chelating comonomers on setting behavior.

The oscillating rheometer is a valuable instrument for studying the effects of additives on the setting behavior of a cement system. Using this instrument, it was found that certain chelating comonomers, the hydroxycarboxylic acids, could improve the setting characteristics of the glass-ionomer cement system when added to the PAA solution. The acid chelates probably assign the extraction of metal ions from the glass and also tend to hold them in solution, preventing premature ion binding of the polyanion chains. The effect is to increase the rate of hardening without reducing the working time, which may indeed by slightly increased. Tartaric acid, the most effective of the comonomers, can form a chelate bridge between aluminum atoms, and this metal complex probably acts as a flexible bridge structure linking polyanion chains. This mechanism offers some steric advantages over a simple salt bridge.

Acrylic Resins↗
PubMed1975

Structural and electronic effects on the polarographic half-wave potentials of copper (II) chelate complexes.

Polarographic measurements in dimethylformamide solution have been performed on 37 bis-chelate Cu(II) complexes containing primarily salicylaldimine, geta-ketoamine, beta-iminoamine, and pyrrole-2-aldimine ligand systems. The complexes were selected in order to reveal the effect of stereochemical and donor atom variations on half-wave potentials. Mono- and binuclear complexes undergo one-and two-electron reductions, respectively, which were established for representative cases by controlled potential coulometry. The response of Cu(II)/Cu(I) potentials to these variations reveals that nonplanar bis-chelate complexes are easier to reduce than their planar analogs, rigid planar tetradentate or related planar bis-chelate complexes, and complexes differing only in donor atoms are more readily reduced in the order N4 less than N2O2 less than N2S2. Binuclear complexes are reduced in one two-electron or two resolvable one-electron steps depending on ligand structure. Potentials of these and other complexes previously examined are considered in relation to the markedly positive potentials of "blue" copper proteins and ligand structural features which might afford Cu(II)/Cu(I) potentials in the protein range are noted.

Binding Sites↗
PubMed1978

Influence of external potassium concentration on secretory responses to cholecystokinin-pancreozymin and ionophore A23187 in the pancreatic acinar cell.

1. The inhibitory effect of a diminution in [K+]o on the secretory processes of the pancreatic acinar cell was analysed in the isolated and perfused rat pancreas. 2. Partial replacement of KCl with NaCl produced falls in both amylase output and pancreatic juice flow which were induced by 5 m-u. cholecystokinin-pancreozymin (CCK-PZ)/ml., and the responses were slowly regained after reintroduction of a standard concentration of KCl. 3. A quantitative relation was found between the amount of amylase released by CCK-PZ and [K+]o over the range 1.0--5.6 mM. A linear relation was obtained between the ratio of E1K+]3(0)/amylase output and [K+]3(0). 4. A quantitative relation was also found between the pancreatic juice flow induced by CCK-PZ and [K+]o over the range 1.0--5.6 mM. A linear relation was obtained between the ratio of [K+]3(0)/juice flow and [K+]3(0). 5. The results obtained may be explained by a model as follows: (1) amylase output and juice flow induced by CCK-PZ are simply proportional to the amount of complex composed of a carrier molecule bearing one Ca and four Na atoms, (2) the inward movement of the complex is tightly linked to the CCK-PZ-induced activation of pumps which are postulated on both basal and apical sides of the membrane of the acinar cell, and (3) the Na:K coupling ratio of the pumps is close to 3:2. 6. A quantitative relation was also found between the amount of amylase released by Ca reintroduction after pre-treatment with Ca-ionophore A23187 and [K+]o. This may be explained by a model essentially similar to that mentioned above. 7. Total replacement of NaCl with NaBr slightly reduced the CCK-PZ-induced fluid and amylase secretion. Total replacement of NaCl with sodium isethionate or with sodium pyruvate, however, virtually abolished the CCK-PZ-induced fluid and amylase secretion.

Amylases↗
PubMed1978

Atomic absorption spectroscopic determination of lead extracted from acid-solubilized tissues.

A method is presented for determining lead in a variety of tissues. Lyophilized samples are solubilized with nitric acid at room temperature in glass screw-cap culture tubes. Following neutralization with sodium hydroxide and sodium bicarbonate, the lead is extracted into methyl isobutyl ketone as the pyrrolidine dithiocarbamate complex and analyzed by flame atomic absorption spectrophotometry. Brain, heart, liver, lung, and spleen gave recoveries ranging from 92 to 102% with standard deviations of less than 8%. Aorta, kidney, and rib were unsuitable for analysis by this method. A large number of samples can be analyzed without specialized equipment or intricate experimental steps. The detection limit is 35 ng/g tissue (wet weight) and sensitivity is approximately 140 ng/g tissue (wet weight).

Brain Chemistry↗
PubMed1978

Structural and exchange properties of "Co(III)-phenanthroline-ATP": a labeling reagent for the active site of ATPases.

This paper reports on 1H and 31P NMR as well as EPR measurements of the labeling reagent of ATPase sites, "Co(III)-(phen)-ATP." This complex is found to be paramagnetic, as deduced both from its EPR spectrum and from the significant broadening, though almost unshifted, proton and phosphorus resonances. This paramagnetism is a result of the incorporation of the superoxide free-radical anion in the coordination sphere of the trivalent cobalt ion. Evidence for the presence of superoxide in the complex is based on competition experiments with cyanide, which is able to displace the superoxide anion. The latter was identified by its inducing effect on the photoreactivity of luminol. The displacement of superoxide by cyanide was accompanied by the abolition of the paramagnetism of the complex. The relative distances between the protons and phosphorus atoms of ATP and the superoxide anion in the complex were calculated using the NMR line-broadening data. Structural models compatible with the experimental results are proposed. Under conditions of excess of adenine nucleotides or phenanthroline, the coordinated ATP molecule becomes exchangeable. This phenomenon is attributed to the labilization of the cobaltic ion ligands induced by the superoxide anion.

Adenosine Triphosphatases↗
PubMed1979

Disintegration of Rhodospirillum rubrum chromatophore membrane into photoreaction units, reaction centers, and ubiquinone-10 protein with mixture of cholate and deoxycholate.

1. The membrane of Rhodospirillum rubrum chromatophores was disintegrated with mild detergents (cholate and deoxycholate) in order to study the spatial arrangement of the functional proteins in the photochemical apparatus and the electron transport system in the membrane. 2. The components solubilized from the membrane by a mixture of cholate and deoxycholate (C-DOC) were separated into four fractions by molecular-sieve chromatography in the presence of C-DOC; they were designated as F1, F2, F3, and F4 in the order of elution. The fractions were further purified by repeated molecular-sieve chromatography in the presence of C-DOC until each fraction was chromatographically homogeneous. 3. F1 appeared to be conjugated forms of F2. 4. The purified F2 was composed of a rigid complex having a weight of 7 X 10(5) daltons, containing approximately 10 different kinds of protein species with molecular weights of 3.8 X 10(4), 3.6 X 10(4), 3.5 X 10(4), 2.8 X 10(4), 2.7 X 10(4), 2.6 X 10(4), 1.3 X 10(4), 1.2 X 10(4), 1.1 X 10(4), and 1.0 X 10(4). The complex contained 33 bacteriochlorophylls, 4 iron atoms, and 90 phosphates, but no cytochrome, ubiquinone, or phospholipid. It showed the same reaction center activity as chromatophores, indicating that the complex was a unit of the photochemical apparatus (photoreaction unit). Each chromatophore of average size was estimated to possess about 24 photoreaction units. 5. The purified F3 showed an absorbance spectrum characteristic of reaction centers, and contained 3.4 bacteriochlorophylls, 2.0 bacteriopheophytins, and 1.9 acid-labile iron atoms, but no cytochrome or ubiquinone (C-DOC reaction center). It had a weight of 1.2 X 10(5) daltons, and the main components were 4 protein species with molecular weights of 2.8 X 10(4), 2.7 X 10(4), 2.6 X 10(4), and 1.0 X 10(4). 6. The purified F4 showed a molecular weight of about 11,000, and contained one mole of ubiquinone-10 per mole (ubiquinone-10 protein). 7. The reaction center activity of C-DOC reaction centers was stimulated by ubiquinone-10 protein. In addition, the reaction center oxidized reduced cytochrome c2 in the light, provided that ubiquinone-10 protein was present (photo-oxidase activity).

Bacterial Chromatophores↗
PubMed1977

Furildioxime method for nickel analysis in serum and urine by electrothermal atomic absorption spectrometry.

We describe a method of analysis for nickel in serum and urine. After the sample (1 ml) has been subjected to acid digestion, Ni(II) is extracted into methylisobutylketone as a furildioximate complex, and is measured by electrothermal atomic absorption spectrometry. The method is more sensitive and more convenient than previous methods, and is less subject to nickel contamination because the digestion and extraction steps are performed in a single tube. Analytical recovery of Ni(II) (10 or 20 microng/liter) added to 20 specimens of serum or urine averaged 101% (range, 94 to 107). The following values (mean +/- SD) were obtained for nickel concentrations in specimens of serum and urine from 19 healthy adults living in central Connecticut: serum = 3.1 +/- 1.6 microng/liter; urine = 2.7 +/- 1.6 microng/liter. The method provides a practical means for monitoring occupational exposures of workers to nickel compounds.

Adult↗
PubMed1976

Structure of the iron complex in methemerythrin.

The coordination of the ligands about the iron atoms in methemerythrin from Themiste dyscritum has been deduced from a 2.8 A resolution electron density map. The complex can be described in terms of two trigonal antiprisms about the pair of iron atoms in each subunit, the antiprisms having one face in common. Ligands at eight of the nine coordination positions are protein side chains, the ninth presumably being water. Comparison of the electron density map for T. dyscritum methemerythrin with the sequence of Phascolopsis gouldii hemerythrin suggests six aromatic side chain ligands (five histidine and one tyrosine) and two nonaromatic side chain ligands. The latter provide atoms at two of the three vertices of the face shared by the two antiprisms, and these along with the presumed water at the third vertex form bridges between the iron atoms of each pair.

Annelida↗
PubMed2025

CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of CaXML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

Machine Learning↗
PubMed1975

Magnetic studies of the four-iron high-potential, non-heme protein from Chromatium vinosum.

Extensive EPR studies on high-potential, iron-sulfur protein from Chromatium vinosum indicate that the singular spectrum of this four-iron, non-heme protein consists of a superposition of three distinct signals; namely, two principal signals of equal weight, one reflecting axial and the other rhombic symmetry, and a third nearly isotropic minority component. In addition, magnetic susceptibility experiments on two oxidation states of the protein from 4.2 to approx. 260 degrees K indicate antiferromagnetic exchange coupling between iron atoms. Possible origins of the complex EPR signals are discussed, and a preferred model that is consistent with EPR, magnetic susceptibility, NMR, X-ray, and Mössbauer data is presented.

Bacterial Proteins↗
PubMed1975

Electron-paramagnetic-resonance spectroscopy of iron-binding fragments of hen ovotransferrins.

1. It is confirmed that there are two e.p.r. (electron-paramagnetic-resonance) signals associated with fully loaded ovotransferrin, which has two iron-binding sites. 2. Through experiments in which either of the two sites of whole ovotransferrin is occupied, the other being empty, the first occupied site is shown to belong to the N-terminal region of the protein; the second occupied site is in the C-terminal region. 3. When the protein is cleaved with trypsin or subtilisin, the N-terminal fragments are spectroscopically similar to the monoferric ovotransferrin complexes in which the iron atom occupies the N-terminal or C-terminal site respectively. Each fragment displays the same two e.p.r. signals, though not in the same proportions. 4. Computer summations of the e.p.r. spectra confirm that there is no iron-iron interaction which affects the spin Hamiltonian parameters at the iron-binding sites.

Binding Sites↗