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     

Performance calculations of the X‐ray powder diffraction beamline at NSLS‐II

The X‐ray Powder Diffraction (XPD) beamline at the National Synchrotron Light Source II is a multi‐purpose high‐energy X‐ray diffraction beamline with high throughput and high resolution. The beamline uses a sagittally bent double‐Laue crystal monochromator to provide X‐rays over a large energy range (30–70 keV). In this paper the optical design and the calculated performance of the XPD beamline are presented. The damping wiggler source is simulated by the SRW code and a filter system is designed to optimize the photon flux as well as to reduce the heat load on the first optics. The final beamline performance under two operation modes is simulated using the SHADOW program. For the first time a multi‐lamellar model is introduced and implemented in the ray tracing of the bent Laue crystal monochromator. The optimization and the optical properties of the vertical focusing mirror are also discussed. Finally, the instrumental resolution function of the XPD beamline is described in an analytical method.     

The Vlasov–Poisson–Landau System in {\mathbb{R}^{3}_{x}}

For the Landau–Poisson system with Coulomb interaction in ${\mathbb{R}^{3}_{x}}$ R x 3 , we prove the global existence, uniqueness, and large time convergence rates to the Maxwellian equilibrium for solutions which start out sufficiently close.     

On the measurement of ¹⁵N-{¹H} nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression

Measurement of steady-state (15)N-{(1)H} nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008) 302-313; J. Am. Chem. Soc. 131 (2009) 6048-6049) reevaluated spin-dynamics during steady-state (or "saturated") and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state (15)N-{(1)H} NOE's without artifacts and with the highest possible accuracy.     

Study of variation of soil radon exhalation rate with meteorological parameters in Bakreswar–Tantloi geothermal region of West Bengal and Jharkhand,India

Radon gas is the predominant ionizing radiation on earth. Its occurrence is controlled by the presence of uranium in all types of rocks in the earthcrust, apart from local geological features and atmospheric factors which influence its release into the atmosphere. The present work deals with 24 h observation of the dependence of radon exhalation rate from soil on local meteorological parameters at four locations in Bakreswar–Tantloi geothermal region, located in the highly faulted Chhotanagpur Plateau of eastern India. This study is the primary step towards the determination of soil radon exhalation dynamics in this geothermal area.

     

Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: Modeling hydrophobic interactions

In an earlier article⁸ the need was demonstrated for atomic physicochemical properties for three dimensional structure directed quantitative structure-activity relationships, and it was shown how atomic parameters can be developed for successfully evaluating the molecular octanol-water partition coefficient, which is a measure of hydrophobicity. In this work we report more refined atomic values of octanol-water partition coefficients derived from nearly twice the number of compounds. Carbon, hydrogen, oxygen, nitrogen, sulfur and halogens are divided into 110 atom types of which 94 atomic values are evaluated from 830 molecules by least squares. These values gave a standard deviation of 0.470 and a correlation coefficient of 0.931. These parameters predicted the octanol-water partition coefficient of 125 compounds with a standard deviation of 0.520 and a correlation coefficient of 0.870. There is only a correlation coefficient of 0.432 between the atomic octanol-water partition coefficients and the atomic contributions to molar refractivity over the 93 atom types used for both the properties. This suggests that both parameters can be used simultaneously to model intermolecular interactions. We evaluated the CNDO/2 gross atomic charge distribution over several molecules to check the validity of our classification. We found that the charge density on the heteroatoms in conjugated systems is strongly affected by the presence of similar atoms in the conjugation which suggests it should be incorporated as a separate parameter in evaluating the partition coefficient.     

Bohmian picture of Rydberg atoms

Unlike the previous theoretical results based on standard quantum mechanics that established the nearly elliptical shapes for the centre-of-mass motion in Rydberg atoms using numerical simulations, we show analytically that the Bohmian trajectories in Rydberg atoms are nearly elliptical.     

Bicriterion differential games with qualitative outcomes

Combat games are studied as bicriterion differential games with qualitative outcomes determined by threshold values on the criterion functions. Survival and capture strategies of the players are defined using the notion of security levels. Closest approach survival strategies (CASS) and minimum risk capture strategies (MRCS) are important strategies for the players identified as solutions to four optimization problems involving security levels. These are used, in combination with the preference orderings of the qualitative outcomes by the players, to delineate the win regions and the secured draw and mutual kill regions for the players. It is shown that the secured draw regions and the secured mutual kill regions for the two players are not necessarily the same. Simple illustrative examples are given.This paper is based partially on research supported by the Council of Scientific and Industrial Research, India, through a Research Associateship Grant to the second author.     

Magnetic order in hedenbergite: CaFeSi2O6

Synthetic hedenbergite orders antiferromagnetically at 38 K although the principal interactions are ferromagnetic, between Fe²⁺ ions in the Ml chains of edge-sharing octahedra. The susceptibility follows a Curie-Weiss law above 100 K with θ = 35 K and p_eff = 4.98 μ_B. A fit of the 4.2 K Mossbauer spectrum yields a positive, near-axial electric field gradient and a hyperfine field of 18.8 T. The likely magnetic structure consists of ferromagnetic chains, each weakly coupled antiparallel to its four c-centred equivalents.