Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces

Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc

The 400d Galaxy Cluster Survey Weak Lensing Programme: I: MMT/Megacam Analysis of CL0030+2618 at z=0.50

The mass function of galaxy clusters at high redshifts is a particularly useful probe to learn about the history of structure formation and constrain cosmological parameters. We aim at deriving reliable masses for a high-redshift, high-luminosity sample of clusters of galaxies selected from the 400d survey of X-ray selected clusters. Here, we will focus on a particular object, CL0030+2618 at z=0.50 Using deep imaging in three passbands with the MEGACAM instrument at MMT, we show that MEGACAM is well-suited for measuring gravitational shear. We detect the weak lensing signal of CL0030+2618 at 5.8 sigma significance, using the aperture mass technique. Furthermore, we find significant tangential alignment of galaxies out to ~10 arcmin or >2r_200 distance from the cluster centre. The weak lensing centre of CL0030+2618 agrees with several X-ray measurements and the position of the brightest cluster galaxy. Finally, we infer a weak lensing virial mass of M_200=7.5 10^{14} M_sun for CL0030+2618. Despite complications by a tentative foreground galaxy group in the line of sight, the X-ray and weak lensing estimates for CL0030+2618 are in remarkable agreement. This study paves the way for the largest weak lensing survey of high-redshift galaxy clusters to date.Comment: 32 pages, 24 figures, submitted to Astronomy & Astrophysics; fixed some LaTeX issues, now 30 pages v3: Improved version accepted by Astronomy & Astrophysic

Planck intermediate results. XXIII. Galactic plane emission components derived from Planck with ancillary data

Planck data when combined with ancillary data provide a unique opportunity to separate the diffuse emission components of the inner Galaxy. The purpose of the paper is to elucidate the morphology of the various emission components in the strong star-formation region lying inside the solar radius and to clarify the relationship between the various components. The region of the Galactic plane covered is l = 300° → 0° → 60° wherestar-formation is highest and the emission is strong enough to make meaningful component separation. The latitude widths in this longitude range lie between 1° and 2°, which correspond to FWHM z-widths of 100−200 pc at a typical distance of 6 kpc. The four emission components studied here are synchrotron, free-free, anomalous microwave emission (AME), and thermal (vibrational) dust emission. These components are identified by constructing spectral energy distributions (SEDs) at positions along the Galactic plane using the wide frequency coverage of Planck (28.4−857 GHz) in combination with low-frequency radio data at 0.408−2.3 GHz plus WMAP data at 23−94 GHz, along with far-infrared (FIR) data from COBE-DIRBE and IRAS. The free-free component is determined from radio recombination line (RRL) data. AME is found to be comparable in brightness to the free-free emission on the Galactic plane in the frequency range 20−40 GHz with a width in latitude similar to that of the thermal dust; it comprises 45 ± 1% of the total 28.4 GHz emission in the longitude range l = 300° → 0° → 60°. The free-free component is the narrowest, reflecting the fact that it is produced by current star-formation as traced by the narrow distribution of OB stars. It is the dominant emission on the plane between 60 and 100 GHz. RRLs from this ionized gas are used to assess its distance, leading to a free-free z-width of FWHM ≈ 100 pc. The narrow synchrotron component has a low-frequency brightness spectral index β_(synch) ≈ −2.7 that is similar to the broad synchrotron component indicating that they are both populated by the cosmic ray electrons of the same spectral index. The width of this narrow synchrotron component is significantly larger than that of the other three components, suggesting that it is generated in an assembly of older supernova remnants that have expanded to sizes of order 150 pc in 3 × 10^5 yr; pulsars of a similar age have a similar spread in latitude. The thermal dust is identified in the SEDs with average parameters of T_(dust) = 20.4 ± 0.4 K, β_(FIR) = 1.94 ± 0.03 (> 353 GHz), and β_(mm) = 1.67 ± 0.02 (< 353 GHz). The latitude distributions of gamma-rays, CO, and the emission in high-frequency Planck bands have similar widths, showing that they are all indicators of the total gaseous matter on the plane in the inner Galaxy

3D Cosmic Shear: Cosmology from CFHTLenS

This paper presents the first application of 3D cosmic shear to a wide-field weak lensing survey. 3D cosmic shear is a technique that analyses weak lensing in three dimensions using a spherical harmonic approach, and does not bin data in the redshift direction. This is applied to CFHTLenS, a 154 square degree imaging survey with a median redshift of 0.7 and an effective number density of 11 galaxies per square arcminute usable for weak lensing. To account for survey masks we apply a 3D pseudo-Cl approach on weak lensing data, and to avoid uncertainties in the highly non-linear regime, we separately analyse radial wave numbers k<=1.5h/Mpc and k<=5.0h/Mpc, and angular wavenumbers l~400-5000. We show how one can recover 2D and tomographic power spectra from the full 3D cosmic shear power spectra and present a measurement of the 2D cosmic shear power spectrum, and measurements of a set of 2-bin and 6-bin cosmic shear tomographic power spectra; in doing so we find that using the 3D power in the calculation of such 2D and tomographic power spectra from data naturally accounts for a minimum scale in the matter power spectrum. We use 3D cosmic shear to constrain cosmologies with parameters OmegaM, OmegaB, sigma8, h, ns, w0, wa. For a non-evolving dark energy equation of state, and assuming a flat cosmology, lensing combined with WMAP7 results in h=0.78+/-0.12, OmegaM=0.252+/-0.079, sigma8=0.88+/-0.23 and w=-1.16+/-0.38 using only scales k<=1.5h/Mpc. We also present results of lensing combined with first year Planck results, where we find no tension with the results from this analysis, but we also find no significant improvement over the Planck results alone. We find evidence of a suppression of power compared to LCDM on small scales 1.5 < k < 5.0 h/Mpc in the lensing data, which is consistent with predictions of the effect of baryonic feedback on the matter power spectrum.Comment: Full journal article here http://mnras.oxfordjournals.org/content/442/2/1326.full.pdf+htm

Studies of aging and HV break down problems during development and operation of MSGC and GEM detectors for the Inner Tracking System of HERA-B

The results of five years of development of the inner tracking system of the HERA-B experiment and first experience from the data taking period of the year 2000 are reported. The system contains 184 chambers, covering a sensitive area of about 20 * 20 cm2 each. The detector is based on microstrip gas counters (MSGCs) with diamond like coated (DLC) glass wafers and gas electron multipliers (GEMs). The main problems in the development phase were gas discharges in intense hadron beams and aging in a high radiation dose environment. The observation of gas discharges which damage the electrode structure of the MSGC led to the addition of the GEM as a first amplification step. Spurious sparking at the GEM cannot be avoided completely. It does not affect the GEM itself but can produce secondary damage of the MSGC if the electric field between the GEM and the MSGC is above a threshold depending on operation conditions. We observed that aging does not only depend on the dose but also on the spot size of the irradiated area. Ar-DME mixtures had to be abandoned whereas a mixture of 70% Ar and 30% CO2 showed no serious aging effects up to about 40 mC/cm deposited charge on the anodes. X-ray measurements indicate that the DLC of the MSGC is deteriorated by the gas amplification process. As a consequence, long term gain variations are expected. The Inner Tracker has successfully participated in the data taking at HERA-B during summer 2000.Comment: 29 pages, 22 figure