Raw cryo- and negative stain micrographs of a native extract from C. thermophilum used to reconstruct oxo acid dehydrogenase complexes
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ABSTRACT:
SUBMITTER: Panagiotis L Kastritis
PROVIDER: EMPIAR-10625 | biostudies-other |
REPOSITORIES: biostudies-other
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| EMPIAR-11502 | biostudies-other
Project description:The nature of chemical bonds of ruthenium(Ru)-quinine(Q) complexes, mononuclear [Ru(trpy)(3,5-t-Bu(2)Q)(OH(2))](ClO(4))(2) (trpy = 2,2':6',2''-terpyridine, 3,5-di-tert-butyl-1,2-benzoquinone) (1), and binuclear [Ru(2)(btpyan)(3,6-di-Bu(2)Q)(2)(OH(2))](2+) (btpyan = 1,8-bis(2,2':6',2''-terpyrid-4'-yl)anthracene, 3,6-t-Bu(2)Q = 3,6-di-tert-butyl-1,2-benzoquinone) (2), has been investigated by broken-symmetry (BS) hybrid density functional (DFT) methods. BS DFT computations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(II)-Q complex is less stable than the open-shell structure (2bb) consisting of Ru(III) and semiquinone (SQ) radical fragments. These computations have also elucidated eight different electronic and spin structures of tetraradical intermediates that may be generated in the course of water splitting reaction. The Heisenberg spin Hamiltonian model for these species has been derived to elucidate six different effective exchange interactions (J) for four spin systems. Six J values have been determined using total energies of the eight (or seven) BS solutions for different spin configurations. The natural orbital analyses of these BS DFT solutions have also been performed in order to obtain natural orbitals and their occupation numbers, which are useful for the lucid understanding of the nature of chemical bonds of the Ru complexes. Implications of the computational results are discussed in relation to the proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems and the similarity between artificial and native water splitting systems.
| S-EPMC3465390 | biostudies-literature
Project description:BackgroundThe increasing number of novel approaches for large-scale, multi-dimensional imaging of cells has created an unprecedented opportunity to analyze plant morphogenesis. However, complex image processing, including identifying specific cells and quantitating parameters, and high running cost of some image analysis softwares remains challenging. Therefore, it is essential to develop an efficient method for identifying plant complex multicellularity in raw micrographs in plants.ResultsHere, we developed a high-efficiency procedure to characterize, segment, and quantify plant multicellularity in various raw images using the open-source software packages ImageJ and SR-Tesseler. This procedure allows for the rapid, accurate, automatic quantification of cell patterns and organization at different scales, from large tissues down to the cellular level. We validated our method using different images captured from Arabidopsis thaliana roots and seeds and Populus tremula stems, including fluorescently labeled images, Micro-CT scans, and dyed sections. Finally, we determined the area, centroid coordinate, perimeter, and Feret's diameter of the cells and harvested the cell distribution patterns from Voronoï diagrams by setting the threshold at localization density, mean distance, or area.ConclusionsThis procedure can be used to determine the character and organization of multicellular plant tissues at high efficiency, including precise parameter identification and polygon-based segmentation of plant cells.
| S-EPMC7390866 | biostudies-literature
Project description:Rhenium(V) oxo complexes of general formula [ReO(OMe)(N^N)Cl2], where N^N = 4,7-diphenyl-1,10-phenanthroline, 1, or 3,4,7,8-tetramethyl-1,10-phenanthroline, 2, effectively kill cancer cells by triggering necroptosis, a non-apoptotic form of cell death. Both complexes evoke necrosome (RIP1-RIP3)-dependent intracellular reactive oxygen species (ROS) production and propidium iodide uptake. The complexes also induce mitochondrial membrane potential depletion, a possible downstream effect of ROS production. Apparently, 1 and 2 are the first rhenium complexes to evoke cellular events consistent with programmed necrosis in cancer cells. Furthermore, 1 and 2 display low acute toxicity in C57BL/6 mice and reasonable stability in fresh human blood.
| S-EPMC4702498 | biostudies-literature
Project description:The reaction between Mo(O)(CHAro)(ORF6)2(PMe3) (Aro = ortho-methoxyphenyl, ORF6 = OCMe(CF3)2) and 2 equiv of LiOHMT (OHMT = O-2,6-(2,4,6-Me3C6H2)2C6H3) leads to Mo(O)(CHAro)(OHMT)2, an X-ray structure of which shows it to be a trigonal bipyramidal anti benzylidene complex in which the o-methoxy oxygen is coordinated to the metal trans to the apical oxo ligand. Addition of 1 equiv of water (in THF) to the benzylidyne complex, Mo(CArp)(OR)3(THF)2 (Arp = para-methoxyphenyl, OR = ORF6 or OC(CF3)3 (ORF9)) leads to formation of {Mo(CArp)(OR)2(μ-OH)(THF)}2(μ-THF) complexes. Addition of 1 equiv of a phosphine (L) to Mo(CArp)(ORF9)3(THF)2 in THF, followed by addition of 1 equiv of water, all at room temperature, yields Mo(O)(CHArp)(ORF9)2(L) complexes in good yields for several phosphines (e.g., PMe2Ph (69% by NMR), PMePh2 (59%), PEt3 (69%), or P( i-Pr)3 (65%)). The reaction between Mo(O)(CHArp)(ORF9)2(PEt3) and 2 equiv of LiOHMT proceeds smoothly at 90 °C in toluene to give Mo(O)(CHArp)(OHMT)2, a four-coordinate syn alkylidene complex. Mo(O)(CHArp)(OHMT)2 reacts with ethylene (1 atm in C6D6) to give (in solution) a mixture of Mo(O)(CHArp)(OHMT)2, Mo(O)(CH2)(OHMT)2, and an unsubstituted square pyramidal metallacyclobutane complex, Mo(O)(CH2CH2CH2)(OHMT)2, along with ethylene and ArpCH═CH2. Mo(O)(CHArp)(OHMT)2 also reacts with 2,3-dicarbomethoxynorbornadiene to yield syn and anti isomers of the "first-insertion" products that contain a cis C═C bond.
| S-EPMC6341480 | biostudies-literature
Project description:By using the data of the DFT quantum chemical calculation in the OPBE/TZVP and B3PW91/TZVP levels, the possibility of the existence of a manganese(VI) heteroligand complex containing porphyrazine or its tetra[benzo] derivative (phthalocyanine) and two oxygen (O2-) ligands, which is still unknown for this element, is shown. The parameters of the molecular structure, multiplicity of the ground state, NBO analysis data and standard thermodynamic parameters (enthalpy ΔH0f, entropy S0f and Gibbs's energy ΔG0f of formation) of each of these metal macrocyclic compounds are presented. Additionally, it is noted that, based on the totality of structural data obtained by the above versions of the DFT method, the existence of a similar complex of manganese with di[benzo] derivative of porhyrazine and two oxygen (O2-) ligands seems doubtful.
| S-EPMC10059719 | biostudies-literature
Project description:Oxo-ester mediated native chemical ligation (OMNCL) is a variation of the more general native chemical ligation (NCL) reaction that is widely employed for chemoselective ligation of peptide fragments. While OMNCL has been used for a variety of peptide ligations and for biomolecular modification of surfaces, it is typically practiced under harsh conditions that are unsuitable for use in a biological context. In this report we describe the use of OMNCL for polymer hydrogel formation, in-vitro cell encapsulation, and in-vivo implantation. Multivalent polymer precursors containing N-hydroxysuccinimide (NHS) activated oxo-esters and N-cysteine (N-Cys) endgroups were chemically synthesized from branched poly(ethylene glycol) (PEG). Hydrogels formed rapidly at physiologic pH upon mixing of aqueous solutions of NHS and N-Cys functionalized PEGs. Quantitative 1H NMR experiments showed that the reaction proceeds through an OMNCL pathway involving thiol capture to form a thioester intermediate, followed by an S-to-N acyl rearrangement to yield an amide cross-link. pH and temperature were found to influence gelation rate, allowing tailoring of gelation times from a few seconds to a few minutes. OMNCL hydrogels initially swelled before contracting to reach an equilibrium increase in relative wet weight of 0%. This unique behavior impacted the gel stiffness and was attributed to latent formation of disulfide cross-links between network-bound Cys residues. OMNCL hydrogels were adhesive to hydrated tissue, generating a lap shear adhesion strength of 46 kPa. Cells encapsulated in OMNCL hydrogels maintained high viability, and in-situ formation of OMNCL hydrogel by subcutaneous injection in mice generated a minimal acute inflammatory response. OMNCL represents a promising strategy for chemical cross-linking of hydrogels in a biological context and is an attractive candidate for in-vivo applications such as wound healing, tissue repair, drug delivery, and tissue engineering.
| S-EPMC3719992 | biostudies-literature
Project description:A direct oxo-ester peptide ligation method has been developed. Through the use of an activated C-terminal para nitrophenyl ester (1), it is possible to achieve direct cysteine ligations (1 + 2 --> 4). Peptide substrates incorporating bulky C-terminal amino acids (1) can be accommodated with high reaction efficiency.
| S-EPMC2645925 | biostudies-literature
Project description:Crop genetic diversity uncovers metabolites, elements and decentralized networks associated with high plant biomass yields in maize (Zea mays L.)
| PRJEB45810 | ENA