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41.
T. Yu. Samgina V. A. Gorshkov Ye. A. Vorontsov K. A. Artemenko S. V. Ogourtsov R. A. Zubarev A. T. Lebedev 《Journal of Analytical Chemistry》2011,66(13):1298-1306
Amphibian skin secretion represents a cerain scientific interest as a source of biologically active natural peptides. In the
present research skin peptidome of wide-spread European frog Rana lessonae (Camerano, 1882) was studied for the first time ever. Peptide sequencing was accomplished with Fourier transform ion cyclotron
resonance mass spectrometer in collision-induced and electron capture dissociation modes. A portion of amphibian peptides
contains intramolecular C-terminal disulfide cycle which obstructs mass spectrometric sequencing. Two methods were utilized
to overcome this difficulty: reduction with dithiotreithol followed by thiol group alkylation and oxidation into sulfonic
acid groups with performic acid. Integrated approach employed in the present study allowed the identification of 49 peptides
(of 6 to 37 amino acid residues), including 19 novel species. 相似文献
42.
Artemenko KA Bergström Lind S Elfineh L Mayrhofer C Zubarev RA Bergquist J Pettersson U 《The Analyst》2011,136(9):1971-1978
Phosphorylation of protein tyrosine residues regulates many cell functions and has also been proved to be involved in oncogenesis. Thus, the identification of the phosphotyrosine (pTyr) proteome of cells is a very important task. Since tyrosine phosphorylation represents only around 1% of the total human phosphoproteome, the study of pTyr proteins is rather challenging. Here we report the optimization study of the phosphotyrosine proteome using K562 cells as a model system. A substantial segment of the phosphotyrosine proteome of K562 cells was characterized by immunoaffinity enrichment with 4G10 and PYKD1 antibodies followed by LC-MS/MS analysis. 480 non-redundant pTyr peptides corresponding to 342 pTyr proteins were found. 141 pTyr peptides were not described elsewhere. The mass spectrometry approach involving high-resolving FTMS analysis of precursor ions and subsequent detection of CID fragments in a linear ion trap was considered as optimal. For detection of low abundant pTyr peptides pooling of individual immunoaffinity enrichments for one LC-MS/MS analysis was crucial. The enrichment properties of the monoclonal PYKD1 antibody were presented for the first time, also in comparison to the 4G10 antibody. PYKD1 was found to be more effective for protein enrichment (1.2 and 5% efficiency at peptide and protein level correspondingly), while 4G10 showed better results when peptide enrichment was performed (15% efficiency versus 3.6% at protein level). Substantially different subsets of the phosphoproteome were enriched by these antibodies. This finding together with previous studies demonstrates that comprehensive pTyr proteome characterization by immunoprecipitation requires multiple antibodies to be used for the affinity enrichment. 相似文献
43.
44.
V. V. Skopetskii V. S. Deineka A. L. Artemenko 《Journal of Mathematical Sciences》1994,69(6):1430-1436
Convergence of the approximate solution is proved. Numerical solutions of some examples are given.Kiev University. Translated from Vychislitel'naya i Prikladnaya Matematika, No. 68, pp. 77–85, 1989. 相似文献
45.
46.
Investigation of mode coupling in a multimode superconducting cavity to store and extract UHF energy
S. N. Artemenko V. L. Kaminskii G. M. Samoilenko 《Radiophysics and Quantum Electronics》1990,33(7):644-650
Nuclear Physics Scientific Research Institute, Tomsk Polytechnical Institute. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 33, No. 7, pp. 868–875, July, 1990. 相似文献
47.
I. I. Artemenko A. A. Golovanov I. Yu. Kostyukov T. M. Kukushkina V. S. Lebedev E. N. Nerush A. S. Samsonov D. A. Serebryakov 《JETP Letters》2016,104(12):883-891
Studies of phenomena accompanying the interaction of superstrong electromagnetic fields with matter, in particular, the generation of an electron–positron plasma, acceleration of electrons and ions, and the generation of hard electromagnetic radiation are briefly reviewed. The possibility of using thin films to initiate quantum electrodynamics cascades in the field of converging laser pulses is analyzed. A model is developed to describe the formation of a plasma cavity behind a laser pulse in the transversely inhomogeneous plasma and the generation of betatron radiation by electrons accelerated in this cavity. Features of the generation of gamma radiation, as well as the effect of quantum electrodynamics effects on the acceleration of ions, at the interaction of intense laser pulses with solid targets are studied. 相似文献
48.
Wetterhall M Shevchenko G Artemenko K Sjödin MO Bergquist J 《Analytical and bioanalytical chemistry》2011,400(9):2827-2836
In this study, a temperature-induced phase fractionation known as cloud-point extraction (CPE) with the non-ionic surfactant
Triton X-114 was used to simultaneously extract, concentrate, and fractionate hydrophobic and hydrophilic proteins from mouse
brain tissue. Two bottom-up proteomic techniques were used to comprehensively identify the extracted proteins. The first “shotgun”-based
approach included tryptic digestion of the proteins followed by reversed-phase nanoliquid chromatography (RP-nanoLC) in combination
with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). In the second approach, the extracted intact proteins
were first separated by one-dimensional (1D) gel electrophoresis and then in-gel digested with trypsin and analyzed with nanoLC-MS/MS.
In total, 1,825 proteins were unambiguously identified and the percentage of membrane proteins was 26% which is at the reported
genome expression levels of 20–30%. The protein overlap between the two approaches was high. The majority (77%) of the identifications
in the first approach was also found by the second method. The protein overlap between the CPE-extracted hydrophilic and hydrophobic
fractions was rather small (16–23%) for both methods, which indicates a good phase separation. A quantitative evaluation of
the CPE with iTRAQ labeling and nanoLC-ESI-MS/MS analysis gave iTRAQ ratios at the expected levels and an overall variation
of the entire method at 17–31%. The results indicate very reproducible sample preparation and analysis methods that readily
can be applied on large-scale sample sets. 相似文献
49.
Samgina TY Vorontsov EA Gorshkov VA Artemenko KA Nifant'ev IE Kanawati B Schmitt-Kopplin P Zubarev RA Lebedev AT 《Journal of the American Society for Mass Spectrometry》2011,22(12):2246-2255
Mass spectrometry faces considerable difficulties in de novo sequencing of long non-tryptic peptides with S–S bonds. Long
disulfide-containing peptides brevinins 1E and 2Ec from frog Rana ridibunda were reduced and alkylated with nine novel and three known derivatizing agents. Eight of the novel reagents are maleimide
derivatives. Modified samples were subjected to MS/MS studies on FT-ICR and Orbitrap mass spectrometers using CAD/HCD or ECD/ETD
techniques. Procedures, fragmentation patterns, and sequence coverage for two peptides modified with 12 tags are described.
ECD/ETD and CAD fragmentation revealed complementary sequence information. Higher-energy collisionally activated dissociation
(HCD) sufficiently enhanced y-ions formation for brevinin 1E, but not for brevinin 2Ec. Some novel tags [N-benzylmaleimide, N-(2,6-dimethylphenyl)maleimide] along with known N-phenylmaleimide and iodoacetic acid showed high total sequence coverage taking into account combined ETD and HCD fragmentation.
Moreover, modification of long (34 residues) brevinin 2Ec with N-benzylmaleimide or N-(2,6-dimethylphenyl)maleimide yielded high sequence coverage and full C-terminal sequence determination with ECD alone. 相似文献
50.
We examine the relative efficiencies of three- algorithms for performing Brownian Dynamics simulations without many-body hydrodynamics. We compare the conventional Brownian Dynamics algorithm of Ermak (CBD), Smart Monte Carlo (SMC) which incorporates Boltzmann sampling into essentially a CBD procedure, and the Stochastic Runge Kutta (SRK) method. We show, using the repulsive potential φ(r) = ε(σ/r) n , where n = 36 and 72, that the SRK algorithm gives the most accurate short-time dynamics for the mean-square displacements. The SRK algorithm static and dynamical properties converge better with a reducing time step to the exact values, than those generated by the CBD algorithm; giving efficiency gains typically of a factor of 3–4. Both CBD and SMC have the incorrect sign for the first correction term to the mean square displacement in a time step, whereas the SRK algorithm gives essentially the exact solution to order Δt 2, where Δt is the simulation time step. In fact, these correction terms are almost equal and opposite in sign. Expressions for these terms were derived in terms of the average interaction energy per particle. The force, shear and bulk stress autocorrelation functions were calculated. The average energy per particle and time correlation functions at short time have values in excess of the exact values, while the corresponding quantities for SRK are below this. This difference in behaviour can be traced back to the extent of compliance of the particle trajectories with the exact expansion of the Smoluchowski equation. The accuracy, at a given value of the time step, of the stochastic algorithms can significantly depend on the form of the interaction potential between particles. It is also demonstrated that the long time limits of various correlation functions are fairly insensitive to a particular scheme (SRK or CBD) used in the simulations. All the correlation functions have a stretched exponential region at intermediate to long times, and the values of the exponents on density and force law steepness have been determined. 相似文献