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At least 19 recordsLinked to original sources
PubMed1978

Nucleosome structure.

Electron microscopic and biochemical results are presented supporting the following conclusions: (1) Two molecules of each histone H2A, H2B, H3 and H4 are necessary and sufficient to form a nucleosome with a diameter of 12.5 +/- 1 nm and containing about 200 base pairs of DNA. (2) H3 plus H4 alone can compact 129 +/- 8 DNA base pairs into a sub-nucleosomal particle with a diameter of 8 +/- 1 nm. In such a particle the DNA duplex is under a constraint equivalent to negative superhelicity. (3) Chromatin should be viewed as a dynamic structure, oscillating between a compact structure (the nucleosome) and more open structures, depending on the environmental conditions.

Animals↗
PubMed2022

Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination.

DNA repair in the context of chromatin is poorly understood. Biochemical studies using nucleosome core particles, the fundamental repeating unit of chromatin, show most DNA repair enzymes remove DNA damage at reduced rates as compared to free DNA. The molecular details on how base excision repair (BER) enzymes recognize and remove DNA damage in nucleosomes have not been elucidated. However, biochemical BER data of nucleosomal substrates suggest the nucleosome presents different structural barriers dependent on the location of the DNA lesion and the enzyme. This indicates the mechanisms employed by these enzymes to remove DNA damage in free DNA may be different than those employed in nucleosomes. Given that the majority of genomic DNA is assembled into nucleosomes, structural information of these complexes is needed. To date, the scientific community lacks detailed protocols to perform technically feasible structural studies of these complexes. Here, we provide two methods to prepare a complex of two genetically fused BER enzymes (Polymerase β and AP Endonuclease1) bound to a single-nucleotide gap near the entry-exit of the nucleosome for cryo-electron microscopy (cryo-EM) structural determination. Both methods of sample preparation are compatible for vitrifying quality grids via plunge freezing. This protocol can be used as a starting point to prepare other nucleosomal complexes with different BER factors, pioneer transcription factors, and chromatin-modifying enzymes.

Chromatin↗
PubMedDate not supplied

[Electron microscopic structure of the mycelium of Actinomyces chrysomallus, the producer of the antibiotic chrysomallin, during the stab fermentation process].

Ultrastructural changes in the mycelium of Actinomyces (Streptomyces) chrysomallus 2703 producing the antibiotic chrysomallin in the process of submerged fermentation are described. When the antibiotic was produced at a high rate, most hyphae remained viable for a long period of time and had the ultrastructure typical of the young cells of actinomycetes. At the same time, a number of degenerative changes due to aging were observed; these resulted in autolysis. A decrease in the antibiotic titre was accompanied with intensive sporulation in a considerable number of the submerged hyphae. Structural changes in the sporeforming hyphae distinctly differed from those in the vegetative ones: the cell walls became thicker and numerous septa were formed. The exogenous formation of submerged spores in the culture under study has been studied in detail for the first time.

Culture Media↗
PubMedDate not supplied

Structure and mechanism of catalytic action of active sites of nitrogenase.

A review of the data on the macromolecular structure of nitrogenase and its individual fragments, the electronic structure of iron- and molybdenum-containing components of the active site, and the functional groups of the ATPase site of the enzyme is given. Reactions of N2 reduction, ATP hydrolysis, and H2 evolution, inhibitory processes, and electron transport reactions catalyzed by the enzyme are analyzed within the framework of a general kinetic model. The results of an investigation of the location of the iron-containing cluster system of electron transport, the ATPase site, and the N2-binding and reducing site on the nitrogenase macro-molecule with the aid of a new complex approach including methods of spin, luminescent, and electron-dense labeling are described. On the basis of a number of physicochemical and kinetic data a model of the structure and mechanism of action of the active site of nitrogenase is proposed, which assumes four-step electron transfer from an external reducing agent along the chain of ferredoxin-like iron-containing clusters of the enzyme and an increase in the reducing potential of the iron clusters through the energy of ATP hydrolysis and four-electron reduction in a binuclear molybdenum-containing complex.

Adenosine Triphosphatases↗
PubMed1975

Interaction of flavins with electron-rich metals.

A complex of the electron-rich ion Cu(I) with the flavoquinone analogue 10-methylisoalloxazine has been synthesized and characterized by x-ray methods. The complex is unstable to oxygen. It is black-green in color, in contrast with the bright yellow, orange, or orange-brown crystalline complexes of 10-methylisoalloxazine or riboflavin with Cu(II), Ag(I), and Pb(II). These results are indicative of strong perturbation of the flavin electronic structure by the Cu(I) ion and suggest that this complex is a reasonable model for incipient transfer of an electron from a reduced metal to flavoquinone. the crystal structure is orthorhombic, Pna2-1, with unit cell constants a = 31.24(1) (figures in parentheses are estimated standard deviations), b = 12.862(4), c = 6.239(2) A, Pobs = 1.76 g per cm-3 and Pcalc = 1.77 g per cm-3 for Z = 4 and asymmetric formula CuClO4-2(C11H8N4O2). HCOOH. The final R factor based on 1250 counter-measured data is 8.8%. The 2 independent 10-methylisoalloxazine molecules, A and B, bind strongly to the cuprous ion throug N(5) of each flavin. The copper is approximately linearly coordinated with an N-Cu-N angle of 153(1) degrees, and Cu-N(5) distances of 1.94(2) A and 1.92(2) A. The next nearest atoms to Cu are the O(4) oxygens of each flavin, forming weak bonds with distances Cu-O(4) = 2.27(2) A and 2.21(2) A for molecules A and B. The dihedral angle between the 2 10-methylisoalloxazine molecules is 65.4 degrees.

Binding Sites↗
PubMed1975

[Histochemical and electron microscopical changes in the kidney of pregnant rats at the time of partus (author's transl)].

In the convoluted proximal tubules of the kidney of pregnant rats alkaline phosphatase activity decreases from 21 days gestation till the 2nd day after birth. During the same time the reaction product of the histochemical succinate dehydrogenase assay exhibits an atypical granular character in some of the proximal tubules, which sometimes additionally contain sudanophilic structures. Electron microscopy reveals dilated mitochondria, an increased number of autophagosomes and big lipid vacuoles of low density.

Alkaline Phosphatase↗
PubMed1978

Quantitative structure-activity relationships in the 2,4,5-ring substituted phenylisopropylamines.

The potency of a series of 2,4,5-ring substituted phenylisopropylamines was examined using the rabbit hyperthermia assay. An excellent correlation (r = 0.99) was found between the rabbit hyperthermic and human psychotomimetic potencies. In the hyperthermic model, the 4-X-substituted-2,5-dimethoxyphenylisopropylamines were found to be one to two orders of magnitude more potent than the 2-X- or 5-X-substituted positional isomers (X = -H, -CH3, -SCH3, -Br). Conformational perturbations induced by substituents ortho to the ethylamine side chain were studied with the PCILO and ab initio molecular orbital methods. The variations in the biological activities could not be rationalized in terms of the ability of the ortho substituents to stabilize conformations which mimic LSD. The electronic structures of the positional isomers were examined in the corresponding toluene analogues using the CNDO/2 method. A reasonable correlation (r = 0.98) was found between the Highest Occupied Molecular Orbital (HOMO) energy and the ionization potentials reported from photoelectron spectroscopy studies. In the case of the positional isomers, the HOMO energies were ordered as follows: 4-X greater than 5-X greater than 2-X. However, the regression analysis of the relationship between these orbital energies and Log Biological Activity (B.A.) was not impressive. Examination of the partition coefficients (octanol/water) of the positional isomers indicated that the 4-X- and 5-X-substituted compounds have almost equivalent Log P's, but that the 2-X-substituted-4,5-dimethoxyphenylisopropylamines are unusually hydrophilic. The regression of Log H.P. to the HOMO energies resulted in a marginally significant relationship; addition of the Log P's resulted in no significant improvement. Qualitative models based on both regiospecific lipophilicity or electron densities and also metabolic conversion to reactive intermediates are presented.

Animals↗
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↗
PubMed1977

Studies on aspartase. IV. Reversible denaturation of Escherichia coli aspartase.

Aspartase (L-aspartate ammonia lyase, EC 4.3.1.1) of Escherichia coli, denatured in 4 M guanidine-HCl, was renatured in vitro by simple dilution with a concomitant restoration of the activity. While the native enzyme exhibited a marked negative Cotton effect centered at 233 +/- 1 nm in optical rotatory dispersion, the enzyme denatured in 4 M guanidine-HCl retained little optical activity. Upon dilution of the denatured enzyme, however, more than 90% of the ordered structure was recovered in 1 min, while the restoration of the activity proceeded much more slowly. Estimation of molecular weights by gel permeation chromatography indicated that the tetrameric enzyme is subject to reversible dissociation into monomeric subunits under the experimental conditions. Various environmental factors such as temperature, pH and protein concentration exhibited profound influence on the rate and extent of the reactivation. In order to examine the correlation between the restoration of the activity and the quaternary structure, electron microscopic inspection of the kinetic processes of reversible denaturation was attempted. Upon dilution of the denatured enzyme at 4 degrees C, neither the activity nor tetrameric images were detected over several min. Upon the temperature shift up to 25 degrees C, however, the activity regain was rapidly proceeded concomitant with the appearance of tetrameric molecules. These results are compatible with the possibility that the subunit assembly is an essential prerequisite, thought not sufficient, for enzyme activity.

Ammonia-Lyases↗
PubMed1977

Magnetic circular dichroism studies on acid and alkaline forms of horseradish peroxidase.

The heme vicinities of the acid and alkaline forms of native (Fd(III)) horseradish peroxidase were investigated in terms of the magnetic circular dichroism (MCD) spectroscopy. The MCD spectrum of the acid form of native horseradish peroxidase was characteristic of a ferric high spin heme group. The resemblance in the MCD spectrum between the acid form and acetato-iron (III)protoporphyrin IX dimethyl ester suggests that the heme iron of the acid form has the electronic structure similar to that in a pentocoordinated heme complex. The MCD spectra of native horseradish peroxidase did not shown any substantial pH dependence in the pH range from 5.20 to 9.00. The MCD spectral change indicated the pK value for the equilibrium between the acid and alkaline forms to be 11.0 which agrees with the results from other methods. The alkaline form of native horseradish peroxidase at pH 12.01 exhibited the MCD spectrum of a low spin complex. The near infrared MCD spectrum suggests that the alkaline form of native horseradish peroxidase has a 6th ligand somehow different from a normal nitrogen ligand such as histidine or lysine. It implicates that the alkaline form has an overall ligand field strength of between the low spin component of metmyoglobin hydroxide and metmyoglobin azide.

Circular Dichroism↗
PubMed1978

Electronic and resonance Raman spectra of iron(III) complexes of enterobactin, catechol, and N-methyl-2,3-dihydroxybenzamide.

Resonance Raman electronic absorption and circular dichroism spectra and pH titration curves are reported for the trianionic ferric complexes of enterobactin, catechol, and N-methyl-2,3-dihydroxybenzamide (MDHB). The spectral signatures of the enterobactin and MDHB complexes are virtually identical and differ from those of the catechol complex in ways that reflect the influence of the amide group on the electronic structure. Excitation in either the visible charge-transfer bands or the near-ultraviolet pi-pi* bands enhances Raman bands associated with benzene ring modes, although the relative enhancements differ markedly in the two regions. The data stronly support a structural model in which iron is bound exclusively to the phenolate oxygen atoms in all three complexes.

Benzamides↗
PubMed1978

Use of the sulphite adduct of nicotinamide-adenine dinucleotide to study ionizations and the kinetics of lactate dehydrogenase and malate dehydrogenase.

1. The formation of the non-enzymic adduct of NAD(+) and sulphite was investigated. In agreement with others we conclude that the dianion of sulphite adds to NAD(+). 2. The formation of ternary complexes of either lactate dehydrogenase or malate dehydrogenase with NAD(+) and sulphite was investigated. The u.v. spectrum of the NAD-sulphite adduct was the same whether free or enzyme-bound at either pH6 or pH8. This suggests that the free and enzyme-bound adducts have a similar electronic structure. 3. The effect of pH on the concentration of NAD-sulphite bound to both enzymes was measured in a new titration apparatus. Unlike the non-enzymic adduct (where the stability change with pH simply reflects HSO(3) (-)=SO(3) (2-)+H(+)), the enzyme-bound adduct showed a bell-shaped pH-stability curve, which indicated that an enzyme side chain of pK=6.2 must be protonated for the complex to form. Since the adduct does not bind to the enzyme when histidine-195 of lactate dehydrogenase is ethoxycarbonylated we conclude that the protein group involved is histidine-195. 4. The pH-dependence of the formation of a ternary complex of lactate dehydrogenase, NAD(+) and oxalate suggested that an enzyme group is protonated when this complex forms. 5. The rate at which NAD(+) binds to lactate dehydrogenase and malate dehydrogenase was measured by trapping the enzyme-bound NAD(+) by rapid reaction with sulphite. The rate of NAD(+) dissociation from the enzymes was calculated from the bimolecular association kinetic constant and from the equilibrium binding constant and was in both cases much faster than the forward V(max.). No kinetic evidence was found that suggested that there were interactions between protein subunits on binding NAD(+).

Histidine↗
PubMed1976

Observations and interpretation of x-ray absorption edges in iron compounds and proteins.

X-ray absorption spectra near the Kalpha edge have been measured in various iron group compounds using the intense synchrotron radiation at the Stanford Synchrotron Research Project. In the cubic compounds KMF3 where M = Mn+2, Fe+2, Co+2, Ni+2, and Zn+2, well resolved lines were observed and assigned to the 1s leads to 3d, 1s leads to 4s, and 1s leads to 4p transitions. The observed energies agreed rather well with the spectroscopic energy levels of the Z + 1 ion and the intensities are shown to agree with those expected on the basis of one electron transitions of the form Z 1s2dn(L,S) leads to (Z + 1)1s2dnn'l'(L",S). The energies of the intense 1s leads to 4p transition increase by about 5 V going from KFeF3 to K2NaFeF6, but only by about 1 V from K4Fe(CN)6 to K3Fe(CN)6. The transitions confirm that upon oxidation of the hexacyanides the iron electronic structure barely changes. In the iron sulfur protein rubredoxin, where the iron is bound to a tetrahedron of sulfurs, the 1s leads to 3d transition was about seven times more intense than the same transition in an octahedrally coordinated compound. These intensities parallel those observed in the d-d transitions of optical spectra, because in both types of spectra the intensities depend upon 4p admixture. In the heme protein cytochrome c, upon oxidation the 1s leads to 4p transition shifts only about 1 V to higher energies similar to the iron hexacyanides. These results are discussed in terms of covalent bonding.

Cytochrome c Group↗
PubMedDate not supplied

The orientation of the electric field gradient tensor in CO-liganded myoglobin.

The EFG-tensor at the position of the Fe-atom of CO-liganded sperm whale myoglobin has been investigated by nuclear gamma-resonance absorption experiments on single crystals. In addition the temperature dependence of the quadrupole splitting of the 14.4 keV level of the iron nucleus was measured. An unambiguous solution for the magnitude and the orientation of the field gradient tensor could only be obtained with the assumption that a C2-axis perpendicular to the haem plane is one principal axis of the electric field gradient tensor. Within this solution the electronic structure of the iron is described by a singlet ground state with Nz = 0.75 and the largest EFG component perpendicular to the haem plane.

Animals↗