Orthogonal Ubiquitin Transfer through Engineered E1-E2 Cascades for Protein Ubiquitination

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Highlights? Orthogonal ubiquitin (UB) transfer pathway to synthesize specific UB-E2 conjugates ? Phage display to engineer UB-E1 and UB-E2 interactions ? Engineered xUB-xE1 and xE1-xE2 pairs with no cross-reactivities with native enzymes     

The challenge to quantify proteins with charge trains due to isoforms or conformers

Single proteins separated by 2-DE often show multiple spots spreading along the first dimension. In many cases, such charge trains are explained by isoform differences or by putative post-translational modifications including phosphorylation, glycosylation and others. We now report that individual spots of such charge trains on 2-D gels in fact often represent the same protein, but, apparently due to conformational changes, segregate to different isoelectric points. If MS analysis reveals protein identity, we therefore suggest integrating all individual spots within a charge train for quantification. Especially in quality control of pharmaceutical proteins, the integration of the spot groups of all active contents is preferable in order to obtain reproducible and reasonable quantitative results. However, most commercial software packages for gel analysis integrate the signals spot-wise. We provide an improved quantification tool for proteins with charge train groups. This calculation can be implemented using the MATLAB software and the self-developed "Correct Integration Software System" or the commercial software package Delta2D.     

Synthesis, characterization and examination of Gd[DO3A-hexylamine]-functionalized silica nanoparticles as contrast agent for MRI-applications

Spherical, nonporous and monodisperse silica nanoparticles (NPs) with a diameter of about 100 nm were synthesized and covalently functionalized with lanthanoid(III) (Ln=Gd or Y) chelate complexes, which serve as contrast agents (CAs) for magnetic resonance imaging (MRI). The materials were fully characterized after each synthetic step by different analytical methods, such as dynamic light scattering, scanning electron microscopy, DRIFT and NMR spectroscopy, thermogravimetry and elemental analysis, as well as zetapotential measurements. High surface concentrations of Gd(III) complexes (up to 50 μmol g(-1)) were determined by ICP-AES and T(1)-measurements, respectively. MRI experiments show the typical concentration-dependent increase of the longitudinal relaxation rate. T(1)-weighted images of samples with more than 25 μg NPs per 100 μL agar display a clear contrast enhancement in the agar layer. The transverse relaxivities r(2) of the materials are significantly higher than r(2) of the corresponding free Gd(III) complexes in water and medium, whereas the longitudinal relaxivities r(1) are slightly increased. Due to the high loading of Gd(III) complexes, the relaxivities per particle are remarkably high (up to 2.78×10(5) mM(-1) s(-1) for r(1)). Thus, new hybrid materials, based on nonporous silica NPs with high local relaxivity values were synthesized, which can serve as very effective CAs for MRI.     

Peptide-antibody complex as handle for single-molecule cut & paste

Molecule-by-molecule arrangement of proteins, for example, in enzymatic networks of predefined composition and proximity, is a major goal that may be accomplished by the single-molecule cut-and-paste technique (SMC&P). For this purpose, co-expressed anchors and handles as protein tags should be employed. As a first step in this direction, the authors develop an SMC&P design which exploits an antibody-peptide complex as a molecular handle.     

Lyapunov Spectra for All Ten Symmetry Classes of Quasi-one-dimensional Disordered Systems of Non-interacting Fermions

A random phase property is proposed for products of random matrices drawn from any one of the classical groups associated with the ten Cartan symmetry classes of non-interacting disordered Fermion systems. It allows to calculate the Lyapunov spectrum explicitly in a perturbative regime. These results apply to quasi-one-dimensional random Dirac operators which can be constructed as representatives for each of the ten symmetry classes. For those symmetry classes that correspond to two-dimensional topological insulators or superconductors, the random Dirac operators describing the one-dimensional boundaries have vanishing Lyapunov exponents and almost surely an absolutely continuous spectrum, reflecting the gapless and conducting nature of the boundary degrees of freedom.     

Application of explicitly correlated coupled-cluster methods to molecules containing post-3d main group elements

A benchmark of explicitly correlated CCSD(T)-F12 methods for the dimers Ga₂, As₂, Br₂ and diatomic molecules AsN, BrO, HBr, GaF, GaCl, GaBr, AsF, AsCl, BrF, and BrCl is presented. Equilibrium distances, harmonic vibrational frequencies, and dissociation energies are compared with extensive conventional CCSD(T) calculations using a variety of orbital basis sets and different ansätze for the explicitly correlated wavefunctions. Correlation of the 3d electrons has a strong effect, in particular on the equilibrium distances, and it is shown that this can be recovered very efficiently by the explicit correlation treatment. It is found that CCSD(T)-F12 calculations with new F12-specific cc-pVnZ-F12 basis sets give comparable accuracy to standard CCSD(T) calculations with very much larger aug-cc-pwCV(n+2)Z basis sets. The effects of higher order valence electron correlation (up to CCSDTQP) are also investigated in conventional calculations and are found to be significant in some cases.     

Breakdown of Fermi liquid behavior near the hot spots in a two-dimensional model: A two-loop renormalization group analysis

Motivated by a recent experimental observation of a nodal liquid on both single crystals and thin films of Bi₂Sr₂CaCu₂O_8 + δ by Chatterjee et al. [Nature Phys. 6 (2010) 99], we perform a field-theoretical renormalization group (RG) analysis of a two-dimensional model such that only eight points located near the “hot spots” on the Fermi surface are retained, which are directly connected by spin density wave ordering wavevector. We derive RG equations up to two-loop order describing the flow of renormalized couplings, quasiparticle weight, several order-parameter response functions, and uniform spin and charge susceptibilities of the model. We find that while the order-parameter susceptibilities investigated here become non-divergent at two loops, the quasiparticle weight vanishes in the low-energy limit, indicating a breakdown of Fermi liquid behavior at this RG level. Moreover, both uniform spin and charge susceptibilities become suppressed in the scaling limit which indicate gap openings in both spin and charge excitation spectra of the model.     

Numerical simulation of organic binder decomposition and combined seepage- and diffusive transport of the gaseous reaction products through a porous green body during thermal debinding of ceramic parts.

This article presents a model which describes the chemical decomposition of organic binders, the combined Maxwell-Stefan and Knudsen diffusion and the seepage flow of multiple gaseous reaction products through a porous body and the implementation of the model into a finite element framework. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis and Crystal Structure of a Novel Heterocycle, 2-Oxa-4,7-Diazabicyclo[3.3.1]Non-3-Ene

Abstract  

The compound 5, containing the novel heterocycle 2-oxa-4,7-diazabicyclo[3.3.1]non-3-ene, has been obtained in a synthetic approach toward oxazoles and 1,3-diazepanes of natural product-like complexity from cyclization and rearrangement of δ-lactam cyanamides. When this procedure was applied to a silyl-protected N-((3S,4S,5S)-4,5-dihydroxy-2-oxopiperidin-3-yl)cyanamide (2b) formation of the novel heterobicyclic scaffold 5 was observed along with the expected oxazole (3b) and diazepane (4b) products. The crystal structures of 5 and diazepane 4b are described. Compound 5 crystallized from methanol in the monoclinic system, P2₁ space group with unit cell parameters a = 15.3402(9), b = 7.2717(4), c = 22.5803(13), β = 106.8620(10) and a cell volume of 2410.5(2) A³.