Katharina Dorothea Dalton
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PROVIDER: S-EPMC524613 | biostudies-literature | 2004 Oct
REPOSITORIES: biostudies-literature
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Project description:The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS2 nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing the amino acid isomers. This ultra-confined nanopore system is further used to detect the phosphorylation of individual amino acids, demonstrating its capability for reading post-translational modifications. Our study suggests that a sub-nanometer engineered pore has the potential to be applied in future chemical recognition and de novo protein sequencing at the single-molecule level.
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Project description:A high throughput single-molecule method for identifying peptides and sequencing proteins based on nanopores could reduce costs and increase speeds of sequencing, allow the fabrication of portable home-diagnostic devices, and permit the characterization of low abundance proteins and heterogeneity in post-translational modifications. Here we engineer the size of Fragaceatoxin C (FraC) biological nanopore to allow the analysis of a wide range of peptide lengths. Ionic blockades through engineered nanopores distinguish a variety of peptides, including two peptides differing only by the substitution of alanine with glutamate. We also find that at pH 3.8 the depth of the peptide current blockades scales with the mass of the peptides irrespectively of the chemical composition of the analyte. Hence, this work shows that FraC nanopores allow direct readout of the mass of single peptide in solution, which is a crucial step towards the developing of a real-time and single-molecule protein sequencing device.
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Project description:Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis.
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Project description:The dataset depicted in this article related to our earlier article entitled "Phytofabrication and encapsulated of silver nanoparticles from Gloriosa Superba" (Saradha Devi et al., 2017) [1], which reports the characteristic features (UV Visible spectra, FTIR, SEM, TEM, DLS, Zeta potential and XRD analysis) of the Gloriosa superba biosynthesised silver nanoparticles (AgNPs). In this context, the present dataset was provided to identify the antioxidant, antitumor and apoptotic (in DLA cells) properties with the synthesized AgNPs. The result enlightens the AgNPs exhibits antitumor, apoptotic activity in DLA cells and antioxidant properties. The results of the in vivo experiments increased life span of liver cells in DLA induced tumour mice and not showed any histopathological variations between control and DLA induced mice animals. The HPTLC examination of the Gloriosa superba (L.) seed extract infers the presence of colchicines derivatives as a major alkaloid sources.
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Project description:The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to Ttotal = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.
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Project description:Hepatic microsomal glucose-6-phosphatase activity was rendered extremely unstable by a variety of techniques: (a) incubation at pH 5.0; (b) extraction of the microsomal fraction in the presence of 1% Lubrol; (c) various purification procedures. These techniques all result in the removal of a 21 kDa polypeptide from the fraction containing glucose-6-phosphatase activity. The 21 kDa protein was purified to apparent homogeneity by solubilization in the detergent Lubrol 12A-9 and chromatography on Fractogel TSK DEAE-650(S) and centrifugation at 105 000 g. The 21 kDa protein stabilizes glucose-6-phosphatase activity, whereas other purified hepatic microsomal proteins do not. The 21 kDa protein appears to be a potential regulator of glucose-6-phosphatase activity.
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Project description:Addition of lutropin (luteinizing hormone, 'LH') and 3-isobutyl-1-methylxanthine to tumour Leydig cells stimulated phosphorylation of five proteins, of 17 000, 22 000, 24 000, 33 000 and 57 000 Da. Phosphorylation of these proteins coincided with increased pregnenolone production. Phosphorylation of a 33 000-Da protein was lutropin-dependent in Leydig cells isolated from a Leydig-cell tumour, from immature testes or from mature testes. In tumour Leydig cells this protein was present in the small ribosomal subunit. Incubation of tumour Leydig cells with either cycloheximide or puromycin inhibited both basal and lutropin-dependent pregnenolone production, by approx. 90% and 98% respectively. In contrast, basal pregnenolone production in Leydig cells from immature and mature testes was insensitive to cycloheximide or puromycin. Cycloheximide or puromycin increased phosphorylation of the 33 000-Da phosphoprotein by approx. 130% and 80% respectively (effect of lutropin/3-isobutyl-1-methylxanthine on phosphorylation: 100%). The molecular mass, the subcellular localization and the sensitivity to phosphorylation in the presence of inhibitors of protein synthesis indicate that the 33 000-Da protein could be similar to ribosomal protein S6.
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Project description:The 160 and 150 kDa proteins of sarcoplasmic reticulum (SR) are phosphorylated endogenously. The phosphorylation of both proteins has a marked requirement for Ca2+. Half-maximal and maximal phosphorylation was obtained at about 1 nM- and 1 microM-Ca2+ respectively, and a Hill coefficient of about 0.5 was calculated. The phosphorylation is also dependent on NaF as an inhibitor of the SR phosphoprotein phosphatase. The phosphorylation of these proteins is very rapid, and maximal phosphorylation is achieved in less than 15 s. The phosphorylation of the 160 kDa and 150 kDa polypeptides is completely inhibited by 5 mM-MgCl2 and by 75 microM-LaCl3, by very low concentrations of different detergents, and by preincubation of the SR for 2 min at 60 degrees C. The inhibition by Mg2+ is due to stimulation of ATP hydrolysis, thereby decreasing ATP concentration. Different phosphorylated peptides were obtained by digestion with protease V8 of the 160 kDa and 150 kDa protein bands, suggesting that the 160 kDa and 150 kDa proteins are distinct. The two phosphorylated proteins are present in different fractions and preparations of SR, with or without [3H]PN200-110 binding capacity. These and other results suggest that the phosphorylated SR proteins are distinct from the alpha 1 and alpha 2 subunits of the voltage-gated Ca2+ channel of the T-system membranes. Different inhibitors and activators of protein kinase C and calmodulin-dependent protein kinase have no effect on the endogenous phosphorylation of both polypeptides, suggesting that the phosphorylation is regulated solely by Ca2+. A possible regulatory function for this phosphorylation system is described in the accompanying paper [Gechtman. Orr & Shoshan-Barmatz (1991) Biochem. J. 276.97-102].
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Project description:Two new species of two genera of the family Ancorabolidae, Ceratonotus elongatussp. n. and Dendropsyllus californiensissp. n., found at 1642 m and 1759 m depth, respectively, in the Southern Trough of Guaymas Basin, are described. Ceratonotus elongatussp. n. was attributed to that genus by a series of character states of which the lack of dendroid dorsal processes on the P6-bearing somite and the presence of such processes on the first abdominal somite were definitive. This species was observed to be very close to Ceratonotus thistlei Conroy-Dalton, 2003 from the San Diego Trough, and can be separated by a number of traits of which the elongated sensilla-bearing dorsal tubercles on the second abdominal somite in the new species was definitive. Dendropsyllus californiensissp. n. has been placed within that genus given the presence of four geniculate setae on P1EXP2 and one seta on P1ENP2, one inner seta on P3EXP3, and lack of inner armature on P4EXP3. Dendropsyllus californiensissp. n. appears to be more closely related to Dendropsyllus thomasi Conroy-Dalton, 2003 and Dendropsyllus magellanicus (George & Schminke, 1998) on account of the spinulose nature of the basis of the maxilliped, the two-segmented P4ENP, and the fused condition of the P5 baseoendopod and exopod, and seems to be even more closely related to Dendropsyllus thomasi by the degree of development of the lateroventral processes of the cephalothorax. Dendropsyllus californiensissp. n. can be separated from its congeners by the relative length of the first antennulary segment, relative length of the caudal rami, and by the armature formula of P3ENP2.
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Project description:Over time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of Pyrococcus furious, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of P. furiosus. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes.
2022-08-08 | PXD035847 | Pride