Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

<p>Abstract</p> <p>Background</p> <p>Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.</p> <p>Methods</p> <p>We generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.</p> <p>Results and conclusion</p> <p>We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as <it>fpair </it>and propose to use it for evaluation of the accuracy of multiple protein docking.</p

A latitude-dependent wind model for Mira's cometary head

We present a 3D numerical simulation of the recently discovered cometary structure produced as Mira travels through the galactic ISM. In our simulation, we consider that Mira ejects a steady, latitude-dependent wind, which interacts with a homogeneous, streaming environment. The axisymmetry of the problem is broken by the lack of alignment between the direction of the relative motion of the environment and the polar axis of the latitude-dependent wind. With this model, we are able to produce a cometary head with a ``double bow shock'' which agrees well with the structure of the head of Mira's comet. We therefore conclude that a time-dependence in the ejected wind is not required for reproducing the observed double bow shock.Comment: 4 pages, 4 figures, accepted for publication in ApJ

Typical Mexican agroindustrial residues as supports for solid-state fermentation

Biological wastes contain several reusable substances of high value such as soluble sugars and fiber. Direct disposal of such wastes to soil or landfill causes serious environmental problems. Thus, the development of potential value-added processes for these wastes is highly attractive. These biological wastes can be used as support-substrates in Solid-State Fermentation (SSF) to produce industrially relevant metabolites with great economical advantage. In addition, it is an environment friendly method of waste management. In this study were analyzed six different Mexican agro industrial residues to evaluate their suitability as support-substrate in SSF, between physicochemical properties that have included Water Absorption Index (WAI), Critical Moisture Point (CHP) and Packing Density (PD). The selection of an appropriate solid substrate plays an important role in the development of an efficient SSF process. The results provided important knowledge about the characteristics of these materials revealing their potential for use in fermentation processes.(undefined

A model of Mira's cometary head/tail entering the Local Bubble

We model the cometary structure around Mira as the interaction of an AGB wind from Mira A, and a streaming environment. Our simulations introduce the following new element: we assume that after 200 kyr of evolution in a dense environment Mira entered the Local Bubble (low density coronal gas). As Mira enters the bubble, the head of the comet expands quite rapidly, while the tail remains well collimated for a 100 kyr timescale. The result is a broad-head/narrow-tail structure that resembles the observed morphology of Mira's comet. The simulations were carried out with our new adaptive grid code WALICXE, which is described in detail.Comment: 12 pages, 8 figures (4 in color). Accepted for publication in The Astrophysical Journa

Zn-Cr layered double hydroxides for photocatalytic transformation of CO2 under visible light irradiation: the effect of the metal ratio and interlayer anion

Carbon dioxide is the main gas responsible for the greenhouse effect. Over the last few years, the research focus of many studies has been to transform CO2 into valuable products (CO, HCOOH, HCHO, CH3OH and CH4), since it would contribute to mitigating global warming and environmental pollution. Layered double hydroxides (LDHs) are two-dimensional materials with high CO2 adsorption capacity and compositional flexibility with potential catalytic properties to be applied in CO2 reduction processes. Herein, Zn-Cr LDH-based materials with different metal ratio and interlayer anions, i.e., chloride (Cl−), graphene quantum dots (GQDs), sodium dodecyl sulfate (SDS) and sodium deoxycholate (SDC), have been prepared by a co-precipitation method and characterized by different techniques. The influence of the interlayer inorganic and organic anions and the metal ratio on the application of Zn-Cr LDHs as catalysts for the photocatalytic CO2 reduction reaction under visible light irradiation is unprecedentedly reported. The catalytic tests have been carried out with Ru(bpy)32+ as photosensitizer (PS) and triethanolamine as sacrificial electron donor (ED) at λ = 450 nm. All LDHs materials exhibited good photocatalytic activity towards CO. Among them, LDH3-SDC showed the best catalytic performance, achieving 10,977 µmol CO g−1 at 24 h under visible light irradiation with a CO selectivity of 88%. This study provides pertinent findings about the modified physicochemical features of Zn-Cr LDHs, such as particle size, surface area and the nature of the interlayer anion, and how they influence the catalytic activity in CO2 photoreduction

Fructo-oligosaccharides (FOS) production by fungal submerged culture using aguamiel as a low-cost by-product

Supplementary data to this article can be found online at https:// doi.org/10.1016/j.lwt.2018.12.020.Fructooligosaccharides (FOS) are important ingredients in the functional food industry because they have different biological properties such as decrease level of triglycerides, cholesterol and phospholipids and stimulate growth of probiotics for enhancement of microflora in large intestine. However, current strategies for the FOS production through simple and economical bioprocess has been necessary. The aim of this work was evaluated the capacity of three fungal strains (Aspergillus niger GH1, Aspergillus niger PSH and Aspergillus oryzae DIA-MF) to produce fructooligosaccharides (FOS) using aguamiel from Agave salmiana as an economical substrate. In addition, Czapek Dox medium supplemented with sucrose as carbon source was used as a control medium for the FOS production. A. oryzae DIA-MF was a fungi producer of FOS using aguamiel or Czapek Dox medium as substrate at 24?h of fermentation. However, the yield of FOS was increased two folds (20.30?g/L), with a productivity of 0.84?g FOS/l.h when aguamiel was used as substrate. On the other hand, A. niger GH1 and A. niger PSH showing only hydrolytic activity on sucrose under the studied conditions. In conclusion, this study shown excellent compatibility of A. oryzae DIA-MF using aguamiel as an economical substrate for the FOS production under a simple bioprocess.Authors thank all technical support and comments made by Dra. Adriana C. Flores-Gallegos and Dra. Abril Flores-Maltos. Authors thank National Council for Science and Technology (CONACYT) of Mexico by the financial support through the project No. CB-2011-C01-167764. Author D. B. Muñiz-Márquez also thank CONACYT for the financial support during her postgraduate program (Doctorate) in Food Science and Technology offered by the University Autonomous of Coahuila, Mexico.info:eu-repo/semantics/publishedVersio

Winds from clu\sters with non-uniform stellar distributions

We present analytic and numerical models of the `cluster wind' resulting from the multiple interactions of the winds ejected by the stars of a dense cluster of massive stars. We consider the case in which the distribution of stars (i.e., the number of stars per unit volume) within the cluster is spherically symmetric, has a power-law radial dependence, and drops discontinuously to zero at the outer radius of the cluster. We carry out comparisons between an analytic model (in which the stars are considered in terms of a spatially continuous injection of mass and energy) and 3D gasdynamic simulations (in which we include 100 stars with identical winds, located in 3D space by statistically sampling the stellar distribution function). From the analytic model, we find that for stellar distributions with steep enough radial dependencies the cluster wind flow develops a very high central density and a non-zero central velocity, and for steeper dependencies it becomes fully supersonic throughout the volume of the cluster (these properties are partially reproduced by the 3D numerical simulations). Therefore, the wind solutions obtained for stratified clusters can differ dramatically from the case of a homogeneous stellar distribution (which produces a cluster wind with zero central velocity, and a fully subsonic flow within the cluster radius). Finally, from our numerical simulations we compute predictions of X-ray emission maps and luminosities, which can be directly compared with observations of cluster wind flows.Comment: 10 pages, 11 figures. MNRAS - Accepted 2007 June 29. Received 2007 June 28; in original form 2007 May 2

3D numerical model of the Omega Nebula (M17): simulated thermal X-ray emission

We present 3D hydrodynamical simulations of the superbubble M17, also known as the Omega nebula, carried out with the adaptive grid code yguazu'-a, which includes radiative cooling. The superbubble is modelled considering the winds of 11 individual stars from the open cluster inside the nebula (NGC 6618), for which there are estimates of the mass loss rates and terminal velocities based on their spectral types. These stars are located inside a dense interstellar medium, and they are bounded by two dense molecular clouds. We carried out three numerical models of this scenario, considering different line of sight positions of the stars (the position in the plane of the sky is known, thus fixed). Synthetic thermal X-ray emission maps are calculated from the numerical models and compared with ROSAT observations of this astrophysical object. Our models reproduce successfully both the observed X-ray morphology and the total X-ray luminosity, without taking into account thermal conduction effects.Comment: 8 pages, 6 figures, accepted for publication in MNRA