Ion mobility mass spectrometry uncovers the impact of the patterning of oppositely charged residues on the conformational distributions of intrinsically disordered proteins

The global dimensions and amplitudes of conformational fluctuations of intrinsically disordered proteins are governed, in part, by the linear segregation versus clustering of oppositely charged residues within the primary sequence. Ion mobility-mass spectrometry (IM-MS) affords unique advantages for probing the conformational consequences of the linear patterning of oppositely charged residues because it measures and separates proteins electrosprayed from solution on the basis of charge and shape. Here, we use IM-MS to measure the conformational consequences of charge patterning on the C-terminal intrinsically disordered region (p27 IDR) of the cell cycle inhibitory protein p27Kip1. We report the range of charge states and accompanying collisional cross section distributions for wild-type p27 IDR and two variants with identical amino acid compositions, κ14 and κ56, distinguished by the extent of linear mixing versus segregation of oppositely charged residues. Wild-type p27 IDR (κ31) and κ14, where the oppositely charged residues are more evenly distributed, exhibit a broad distribution of charge states. This is concordant with high degrees of conformational heterogeneity in solution. By contrast, κ56 with linear segregation of oppositely charged residues leads to limited conformational heterogeneity and a narrow distribution of charged states. Gas-phase molecular dynamics simulations demonstrate that the interplay between chain solvation and intrachain interactions (self-solvation) leads to conformational distributions that are modulated by salt concentration, with the wild-type sequence showing the most sensitivity to changes in salt concentration. These results suggest that the charge patterning within the wild-type p27 IDR may be optimized to sample both highly solvated and self-solvated conformational states

Novel LRBA Mutation and Possible Germinal Mosaicism in a Slavic Family

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Thermodynamic driving force in the formation of hexagonal-diamond Si and Ge nanowires

The metastable hexagonal-diamond phase of Si and Ge (and of SiGe alloys) displays superior optical properties with respect to the cubic-diamond one. Based on first-principle calculations we show that the surface energy of the typical facets exposed in Si and Ge nanowires is lower in the hexagonal-diamond phase than in the cubic one. By exploiting a synergic approach based also on a recent state-of-the-art interatomic potential and on a simple geometrical model, we investigate the relative stability of nanowires in the two phases up to few tens of nm in radius, highlighting the surface-related driving force and discussing its relevance in recent experiments. We also explore the stability of Si and Ge core-shell nanowires with hexagonal cores (made of GaP for Si nanowires, of GaAs for Ge nanowires). In this case, the stability of the hexagonal shell over the cubic one is also favored by the energy cost associated with the interface linking the two phases. Interestingly, our calculations indicate a critical radius of the hexagonal shell much lower than the one reported in recent experiments, indicating the presence of a large kinetic barrier allowing for the enlargement of the wire in a metastable phase

Effects of lattice parameter manipulations on electronic and optical properties of BaSi2

We present comprehensive experimental and theoretical investigation on a band-gap engineering and modification in optical properties of BaSi2 – a new and very promising material for solar cell fabrication. BaSi2 thin films have been synthesized by molecular beam epitaxy with various deposition rates of Si and Ba. Changes in their band gaps and shifts in absorption edges with respect to alteration in the a lattice parameter have been investigated by optical measurements. It is possible to shrink a by about 0.003 nm (or 0.3%), while the other lattice parameters are locked by the epitaxial relationship with a Si(111) substrate, that leads to the gap reduction from 1.28 eV to 1.20 eV. By means of ab initio calculations we explore a possibility to manipulate bandgap values in BaSi2 along with the corresponding shift in the absorption edge by changing its a, b and c lattice parameters. It is revealed that an increase in any of the lattice parameters provides band-gap enlargement while the opposite trend is observed when decreasing the lattice parameters. Numerically uniaxial lattice strain of 3% can provide variations in the band gap up to 0.1 eV. We also discuss possible reasons for a variation and applicability of the band-gap engineering in BaSi2 by strain

Electronic structure and optical properties of Ca2Si films grown on silicon different oriented substrates and calculated from first principles

The work considered the growth, optical properties and emerging interband transitions in Ca2Si films grown on silicon substrates with (111), (001), and (110) orientations at two temperatures (250 °C and 300 °C) using the sacrificial-template method. The optimum temperature for MBE single-phase growth of Ca2Si is 250 °C. Calculations of optical functions from the transmission and reflection spectra were carried out within the framework of a two-layer model and by the Kramers–Kronig method. It is shown that the main peaks in the experimental reflection spectra and the optical conductivity calculated according to Kramers–Kronig are in good agreement with each other. Comparison of ab initio calculations of the energy band structure and optical properties of a Ca2Si single crystal and two-dimensional Ca2Si layers with experimental data in the region of high-energy transitions showed good coincidence

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011