Coupling protein complex analysis to peptide based proteomics

Proteolysis is a central component of most proteomics methods. Unfortunately much of the information relating to the structural diversity of proteins is lost during digestion. This paper describes a method in which the native proteome of yeast was subjected to preliminary fractionation by size exclusion chromatography (SEC) prior to trypsin digestion of SEC fractions and reversed phase chromatography-mass spectral analysis to identify tryptic peptides thus generated. Through this approach proteins associated with other proteins in high molecular mass complexes were recognized and identified. A focus of this work was on the identification of Hub proteins that associate with multiple interaction partners. A critical component of this strategy is to choose methods and conditions that maximize retention of native structure during the various stages of analysis prior to proteolysis, especially during cell lysis. Maximum survival of protein complexes during lysis was obtained with the French press and bead-beater methods of cell disruption at approximately pH 8 with 200 mM NaCl in the lysis buffer. Structure retention was favored by higher ionic strength, suggesting that hydrophobic effects are important in maintaining the structure of protein complexes. Recovery of protein complexes declined substantially with storage at any temperature, but storage at -20°C was best when low temperature storage was necessary. Slightly lower recovery was obtained with storage at -80°C while lowest recovery was achieved at 4°C. It was concluded that initial fractionation of native proteins in cell lysates by SEC prior to RPC-MS/MS of tryptic digests can be used to recognize and identify proteins in complexes along with their interaction partners in known protein complexes.     

Prior exposure to an attenuated <Emphasis Type="Italic">Listeria</Emphasis> vaccine does not reduce immunogenicity: pre-clinical assessment of the efficacy of a <Emphasis Type="Italic">Listeria</Emphasis>vaccine in the induction of immune responses against HIV

Background  

We have evaluated an attenuated Listeria monocytogenes (Lm) candidate vaccine vector in nonhuman primates using a delivery regimen relying solely on oral vaccination. We sought to determine the impact of prior Lm vector exposure on the development of new immune responses against HIV antigens.     

Study of radiation background at the north crossing point of the BEPCⅡ in collision mode

Understanding the radiation background at the north crossing point (NCP) in the tunnel of BEPCII is crucial for the performance safety of the High Purity Germanium (HPGe) detector, and in turn of great significance for long-term stable running of the energy measurement system. Therefore, as the first step, a NaI(Tl) detector is constructed to continuously measure the radiation level of photons as background for future experiments. Furthermore, gamma and neutron dosimeters are utilized to explore the radiation distribution in the vicinity of the NCP where the HPGe detector will be located. Synthesizing all obtained information, the shielding for neutron irradiation is studied based on model-dependent theoretical analysis.     

A delay-dependent model with HIV drug resistance during therapy

The use of combination antiretroviral therapy has proven remarkably effective in controlling HIV disease progression and prolonging survival. However, the emergence of drug resistance can occur. It is necessary that we gain a greater understanding of the evolution of drug resistance. Here, we consider an HIV viral dynamical model with general form of target cell density, drug resistance and intracellular delay incorporating antiretroviral therapy. The model includes two strains: wild-type and drug-resistant. The basic reproductive ratio for each strain is obtained for the existence of steady states. Qualitative analysis of the model such as the well-posedness of the solutions and the equilibrium stability is provided. Global asymptotic stability of the disease-free and drug-resistant steady states is shown by constructing Lyapunov functions. Furthermore, sufficient conditions related to the properties of the target cell density are obtained for the local asymptotic stability of the positive steady state. Numerical simulations are conducted to study the impact of target cell density and intracellular delay focusing on the stability of the positive steady state. The occurrence of Hopf bifurcation of periodic solutions is shown to depend on the target cell density.     

Completions of fans

In a finite-dimensional real vector space furnished with a rational structure with respect to a subfield of the field of real numbers, every (simplicial) rational semifan is contained in a complete (simplicial) rational semifan. In this paper this result is proved constructively on use of techniques from polyhedral geometry.     

Experimental and Computational Study on the Anti-Markovnikov Hydrofunctionalization of Olefins Using Glycine-Extended AQ-Auxiliaries

Two similar tridentate directing groups derived from glycine and 8-aminoquinoline were shown to enable the palladium-catalyzed anti-Markovnikov hydrofunctionalization of 4-pentenylamine with drastically different efficiencies. A computational investigation into the origin of the reactivity difference between these isomeric, carbonyl-transposed auxiliaries suggests that protonation state, thus charge of the substrate-metal complex prior to nucleopalladation is key. These investigations have culminated in a directing group design that can undergo Pd-catalyzed hydrofunctionalization under relatively mild conditions, as low as room temperature.     

Stress effects on the anisotropic thermal expansions of “martensitic” A15 compounds

Precision capacitance dilatometry provides a sensitive measure of the thermal strain developed in a sample undergoing a structural distortion with its varying temperature. The A15 structure compounds, V₃Si and Nb₃Sn, are well known to undergo distortion from their cubic structures at room temperature to tetragonal structures (c/a > 1 for V₃Si and c/a < 1 for Nb₃Sn) at low temperatures. In the past, highly anomalous thermal expansion behaviour recorded for these materials has been attributed to a strongly anharmonic lattice potential manifesting itself in unusually high, and strongly temperature-dependent, Grüneisen parameters. Further studies on polycrystalline material revealed this anomalous expansion to be highly anisotropic at temperatures for which, according to conventional diffraction data, the materials are cubic. This behaviour was linked to control of sample morphology by a residual stress field resulting from sample preparation.

More recent experiments, in which the transformation morphology has been controlled by the application of external stresses to single crystal V₃Si and polycrystalline samples of Nb₃Sn and Nb₃(Sn_1-x Sb _x ), have confirmed the occurrence of significant anisotropy in the thermal strain in the cubic phase, well above the structural transformation.

We link this departure from cubic symmetry with the well-known soft-mode character of these materials and the associated “central peak” scattering which is also observed well above the transformation temperature. We are led to propose that the “central peak” is the precursor to a Bragg reflection for the transformation structure. This coincidence between “central peak” scattering and the reciprocal lattice for the transformed phase in Ti-Ni has been termed a “ghost lattice”.     

Die Korrektur des Bildes der Anger-Kamera (Teil II)

Ausgehend von der im ersten Teil begründeten Notwendigkeit, die mit der Szintillationskamera Impulsverteilung korrigieren zu müssen, wird in der vorliegenden Arbeit der Programmablanfplan für diese Korrekturrechnung mit Hilfe der elektronischen Datenverarbeitung (R 300) erläutert. Im gegenwärtigen Stadium der Entwicklung eines umfangreichen Konzepts zum Einsatz der EDV für die Szintigraphie – an der alle Nuklearmedizinischen Abteilungen der DDR beteiligt sind – erfolgt bei den Autoren die Ein- und ausgabe der Daten über Lochstreifen. Die Wirkung der Korrekturrechnung wird am homogenen Phantom selbst und an einer Pankreasunfersuchung demonstriert.     

The NMR Coupling Constants,and Conformational and Structural Properties of Flexible Aldopyranosyl Rings: α- and β-D-Idopyranose

ABSTRACT

The flexible ring structures of α- and β-D-idopyranose have been investigated by conformational analysis using structures generated by MacroModel and GMMX search protocols. The lowest energy structures found during the conformer search for the ⁴ C ₁, ¹ C ₄, ^O S ₂ and the ³ S ₁ structures were then examined by AM1 and Gaussian ab initio methods at the HF/6-311G** and HF/6-31+G* levels. The B _2,5 conformer found for β-D-idopyranose at 14 kJ/mol by GMMX and 29.5 kJ/mol for α-D-idopyranose by MacroModel would not contribute to Boltzmann-averaged ¹H NMR coupling constants. The Merck MMFF force field tends to overweight the ¹ C ₄ structures, making these the lowest energy conformers for both anomers. Boltzmann-averaged coupling constants are heavily weighted by this structure in the MMFF search conformer ensemble. Averaged proton coupling constants determined using MMFF fit very well for α-D-idopyranose compared to the observed values, but fit poorly for the β-anomer. Ab initio results place the ¹ C ₄ conformer at lowest energy for the α-anomer and place the ⁴ C ₁ conformer at lowest energy for the β-anomer. The GMMX and MM3* force fields find the ⁴ C ₁ conformer to have the lowest energies for both anomers.