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Results for “ATOM complex”

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At least 19 recordsLinked to original sources

PubMed2026

Disruption of GxxxG motifs in pATOM36 impairs biogenesis of the mitochondrial protein translocase of the outer membrane in Trypanosoma brucei.

Mitochondrial biogenesis requires efficient import of cytosolically produced proteins and correct segregation of the mitochondrial genome during cytokinesis. In Trypanosoma brucei, a parasitic protozoan with a single mitochondrion harboring a single-unit mitochondrial genome, protein import across the outer membrane is mediated by the ATOM complex. An important, yet poorly understood role is played by the integral membrane protein pATOM36 of the outer mitochondrial membrane, which is essential for both ATOM complex assembly and mitochondrial DNA segregation. Here, we combined in vivo functional mutational analysis and structural modeling to investigate the function of pATOM36. AlphaFold3-based models predict five highly tilted helices forming a funnel-shaped cavity open toward the cytoplasm, reminiscent of membrane protein insertases. In the model, the protein is sealed towards the mitochondrial intermembrane space by tight helix packing, with conserved GxxxG motifs potentially facilitating these helix-helix interactions. Progressive replacement of these glycines by isoleucines does not affect protein production or correct localization but leads to defective ATOM complex biogenesis and arrest of growth, while mitochondrial DNA segregation is largely unaffected. Based on the predicted structure, these effects can be rationalized by hydrophobic bulking that interferes with associated electrostatic interactions. This hypothesis is supported by experimental mutational analysis of the respective electrostatic interactions in the presence of native GxxxG motifs. Together, our data support the hypothesis that pATOM36 functions as an outer mitochondrial insertase and arose by convergent evolution. The GxxxG motifs, also found in unrelated yeast and human outer membrane insertases, are crucial for protein activity.

Trypanosoma brucei brucei↗

PubMed2026

Bridging-driven condensation by eukaryotic SMC complexes is a conserved feature of genome organization.

The Structural Maintenance of Chromosome (SMC) protein family plays a central role in higher-order genome organization through ATP-dependent DNA loop extrusion by cohesin and condensin and other processes. Whether these activities fully account for the complexity of chromosome architecture remains unknown. Here, we uncover a conserved ATP-independent mechanism of chromatin condensation by SMC complexes, occurring via biomolecular condensation. Using single-molecule fluorescence imaging, we show that a variety of SMCs form dynamic DNA-bound condensates that exhibit key features of biomolecular condensates, including droplet coalescence, fluorescence recovery after photobleaching, and rapid exchange with free SMC complexes. Atomic force microscopy analysis of human cohesin-DNA assemblies reveals DNA-length-dependent clustering, providing evidence for bridging-driven condensation. Analyses of in vivo super-resolution imaging and high-throughput chromosome conformation capture (Hi-C) data indicate that these condensates form chromatin-associated clusters with multi-loop structures. Together, our results establish that SMC complexes employ ATP-independent phase condensation as well as ATP-dependent activities to shape genome architecture. This work reveals a broadly conserved principle of chromosomal organization across eukaryotes.

Chromosomal Proteins, Non-Histone↗

PubMed1979

Ionophore-mediated cation translocation in artificial systems. I. A23187-mediated calcium translocation.

The inophore A23187 stimulates the translocation of calcium from an aqueous Hepes buffer into an organic immiscible phase. At saturating calcium concentrations, 2 molecules of ionophore seem to complex each atom of calcium. Consistent with such a stoichiometric behaviour, the apparent ratio of calcium-ionophore association to dissociation rate constants increases as the concentration of ionophore is raised. As a result, at low calcium concentrations, the amount of translocated calcium increases as a power function of A23187 concentration. When allowance is made for such a phenomenon, the relation between calcium translocation and concentration is characterized by usual substrate-receptor binding kinetics.

Anti-Bacterial Agents↗

PubMedDate not supplied

[Effect of platinum and palladium compounds on mitochondrial enzymatic systems].

Effect of platinum and palladium complexes on respiration and ATPase activity in bovine heart tissue as well as on respiration of submitochondrial particles was studied. The highest inhibitory activity was exhibited by the complexes of platinum and palladium with pi-ligands in internal coorhdinational sphere such as ethylene-C H4, norbornadiene-C7H8 and allyl-C3H5. The electron density at the central atom of the complex was not responsible for the inhibitory affect of platinum and palladium on mitochondria.

Adenosine Triphosphatases↗

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↗

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↗

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↗

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↗

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↗

PubMed1978

Iron, an essential element for biosynthesis of aromatic compounds.

Homogeneous preparations of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [7-phospho-2-keto-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate lyase (pyruvate phosphorylating), EC 4.1.2.15] isolated as the enzyme-phosphoenolpyruvate complex from Escherichia coli are shown by atomic absorption analysis to contain approximately one mole of iron per mole of native enzyme. No cobalt was found, in contrast to suggestions of earlier workers. Pure enzyme preparations show a unique absorption maximum around 350 nm with an epsilon value of about 3500 M-1cm-1. The 350-nm band as well as the enzyme activity is lost when the enzyme is denatured with guanidine-hydrochloride, or when phosphoenolpyruvate, the first substrate to bind to the enzyme, is totally removed from the enzyme by incubation with an excess of erythrose 4-phosphate, the second substrate to bind to the enzyme. The iron remains bound to the enzyme when phosphoenolpyruvate is removed from the enzyme-phosphoenolpyruvate complex.

3-Deoxy-7-Phosphoheptulonate Synthase↗

PubMed1979

A chemical mechanism for tissue staining by osmium tetroxide-ferrocyanide mixtures.

The presence of Fe(CN)6(-4) provides sequential, one-electron reduction pathways for OSO4. An equilibrium is established containing OSO4, Fe(CN)6(-4), Fe(CN)6(-3), OSO2(OH)4(-4), and labile cyano-bridged OS-Fe species containing Os in nominal oxidation states of VIII, VII, and VI. These osmium complexes are chelated by appropriately placed donor atoms in the macromolecular tissue matrix, and chelation facilitates the reduction of osmium in situ to lower oxidation states (predominantly IV) that are relatively nonlabile. The greater reactivity and concentration of the Os(VII and VI) intermediates in this system leads to more Os deposition than OsO4 alone; the chelation is responsible for the immobilization of Os and the observed staining pattern in electron micrographs. Chemical data from model systems and electron micrographs of tissue are presented in support of this mechanism.

Animals↗

PubMedDate not supplied

[Inhibition of membrane-bound adenosine triphosphatase by platinum and palladium salts].

Inhibition capacity of platinum and palladium complexes is studied on membrane-bound ADTP. The degree of inhibition of the enzyme activity is determined by the nature of the central atom and by the electron density on it, as well as by the ligand donor-acceptor capacity, by its mobility. The configuration of the complex and the charge of complex ion are of importance. The acidoligands studied according to their inhibition effect can be arranged in the following line: NO2, Cl, Br, SCN, I, which is true both for platinum and palladium compounds. For palladium complexes this line coincides with the location of ligands according to their ability to draw off the electron density from the central atom while in case of platinum complexes it has an opposite course of relationship for platinum and palladium complexes, points to a different mechanism of their interaction with the enzyme.

Adenosine Triphosphatases↗

PubMed1979

Differential effects of metal ions on Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase and stoichiometric incorporation of HCO3- into a cobalt(III)--enzyme complex.

Mg2+ or Mn2+ ions supported both the carboxylase and oxygenase activities of the Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase. For the carboxylase reaction, Mn2+ supported 25% of the maximum activity obtained with Mg2+; oxygenase activity, however, was twice as great with Mn2+ as compared to that with Mg2+. A further differential effect was obtained with Co2+. Co2+ did not support carboxylase activity and, in fact, was a strong inhibitor of Mg2+-dependent carboxylase activity, with a Ki of 10 microM. Co2+ did, however, support oxygenase activity, eliciting about 40% of the Mg2+-dependent oxygenase activity. No other divalent cations supported either activity. With high concentrations of Mg2+ or Mn2+, maximum carboxylase activity was seen after a 5-min activation period; activity decreased to about half of maximum after 30-min activation. A similar time dependence of activation was observed with Mn2+-dependent oxygenase activity but was not seen for Mg2+- or Co2+-dependent activity. Both carboxylase and oxygenase activities were inactivated by the oxidation of Co2+ to Co(III) with the resultant formation of a stable Co(III)--enzyme complex. In the presence of HCO3- (CO2), Co(III) modification was stoichiometric, with two cobalt atoms bound per enzyme dimer. Carbon dioxide was also incorporated into this Co(III)--enzyme complex, but only one molecule per enzyme dimer was bound, indicative of half-the-sites activity. These results thus indicate that there are substantial differences in the metal ion sites of the carboxylase and oxygenase activities of R, rubrum ribulosebisphosphate carboxylase/oxygenase.

Bicarbonates↗

PubMed1975

Intramolecular arsanilazotyrosine-248-Zn complex of carboxypeptidase A: a monitor of catalytic events.

The intensely chromophoric intramolecular coordination complex formed between arsanilazotyrosine-248 and the active site zinc atom of azocarboxypeptidase A (Johansen, J. T. & Vallee, B. L. (1971) Proc. Nat. Acad. Sci. USA 68, 2532-2535) is a spectrokinetic probe of catalytic events. The interconversion of the azoTyr-248-Zn complex and its constituents is measured by stopped-flow pH and temperature-jump methods. The rate of interconversion, 64,000 sec-1, is orders of magnitude faster than that of the catalytic step itself (about 0.01-100 sec-1). Rapidly turned over peptide and ester substrates disrupt the azoTyr-248-Zn complex before hydrolysis occurs. As a consequence, formation of azoTyr-248, substrate binding, and catalysis can all be monitored while catalysis is actually in progress. The results of these dynamic studies specify a course of catalytic events, different from those postulated based on x-ray structure analysis. If azoTyr-248 is displaced, the direction is opposite to the inward movement postulated on the basis of x-ray studies and is not unique to induction by substrates, since rapid changes in pH also result in analogous spectral changes. AzoTyr-248 carboxypeptidase has all the features which are essential for mechanistic studies: (1) It is enzymatically active; (2) the spectra of the metal complex differ characteristically from those of its constituents; (3) it responds dynamically to environmental factors; and (4) the response time of the probe itself is much more rapid than is required for the measurement of the catalytic step. These combined kinetic and spectral properties of the metal complex render it a powerful spectrokinetic probe to visualize and discern microscopic details of the catalytic process.

Arsenicals↗

PubMed1975

Mandelate racemase from Pseudomonas putida. Magnetic resonance and kinetic studies of the mechanism of catalysis.

The interactions of mandelate racemase with divalent metal ion, substrate, and competitive inhibitors were investigated. The enzyme was found by electron paramagnetic resonance (EPR) to bind 0.9 Mn2+ ion per subunit with a dissociation constant of 8 muM, in agreement with its kinetically determined activator constant. Also, six additional Mn2+ ions were found to bind to the enzyme, much more weakly, with a dissociation constant of 1.5 mM. Binding to the enzyme at the tight site enhances the effect of Mn2+ on the longitudinal relaxation rate (1/T1p) of water protons by a factor of 11.9 at 24.3 MHz. From the frequency dependence of 1/T1p, it was determined that there are similar to 3 water ligands on enzyme-bound Mn2+ which exchange at a rate larger than or equal to 10-7 sec-1. The correlation time for enzyme-bound Mn2+-water interaction is frequency-dependent, indicating it to be dominated by the electron spin relaxation time of Mn2+. Formation of the ternary enzyme-Mn2+-mandelate complex decreases the number of fast exchanging water ligands by similar to 1, but does not affect tau-c, suggesting the displacement or occlusion of a water ligand. The competitive inhibitors D,L-alpha-phenylglycerate and salicylate produce little or no change in the enzyme-Mn2+-H2O interaction, but ternary complexes are detected indirectly by changes in the dissociation constant of the enzyme-Mn2+ complex and by mutual competition experiments. In all cases the dissociation constants of substrates and competitive inhibitors from ternary complexes determined by magnetic resonance titrations agree with K-M and K-i values determined kinetically and therefore reflect kinetically active complexes. From the paramagnetic effects of Mn2+ on 1/T1 and 1/T2 of the 13C-enriched carbons of 1-[13C]-D,L-mandelate and 2-[13C]-D,L-mandelate, Mn2+ to carboxylate carbon and Mn2+ to carbinol carbon distances of 2.93 plus or minus 0.04 and 2.71 plus or minus 0.04 A, respectively, were calculated, indicating bidentate chelation in the binary Mn2+-mandelate complex. In the active ternary complex of enzyme, Mn2+, and D,L-mandelate, these distances increase to 5.5 plus or minus 0.2 and 7.2 plus or minus 0.2 A, respectively, indicating the presence of at least 98.9% of a second sphere complex in which Mn2+, and C1 and C2 carbon atoms are in a linear array. The water relaxation data suggest that a water ligand is immobilized between the enzyme-bound Mn2+ and the carboxylate of the bound substrate. This intervening water ligand may polarize or protonate the carboxyl group. From 1/T2p the rate of dissociation of the substrate from this ternary complex (larger than or equal to 5.6 times 10-4 sec-1) is at least 52 times greater than the maximal turnover number of the enzyme (1070 sec-1), indicating that the complex detected by nuclear magnetic resonance (NMR) is kinetically competent to participate in catalysis. Relationships among the microscopic rate constants are considered.

Binding, Competitive↗

PubMed2025

RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.

RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficiency and mRNA localization. Additionally, rG4s of long noncoding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, the atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We studied the folding of the r(GGGA)3GGG and r(GGGUUA)3GGG (TERRA) sequences into parallel-stranded rG4 using all-atom enhanced-sampling molecular dynamics simulations, applying well-tempered metadynamics coupled with solute tempering. The obtained folding pathways suggest that RNA initially adopts a compacted coil-like ensemble characterized by dynamic guanine stacking and pairing. The three-quartet rG4 gradually forms from this compacted coil ensemble via diverse routes involving strand rearrangements and guanine incorporations. While the folding mechanism is multipathway, various two-quartet rG4 structures appear to be a common transitory ensemble along most routes. Thus, the process seems more complex than previously predicted, as G-hairpins or G-triplexes do not act as distinct intermediates, even though some are occasionally sampled. We also discuss the challenges of applying enhanced sampling methodologies to such a multidimensional free-energy surface and address the force-field limitations.

G-Quadruplexes↗