Comment on "Ab initio calculations of the lattice parameter and elastic stiffness coefficients of bcc Fe with solutes" Comp. Mat. Sci. v.126 pp.503-513 (2017)

In a recent paper, the authors propose to separately calculate the volumetric and chemical contributions to the elastic stiffness coefficients of systems containing solutes, as it is "computationally more efficient". We show that this is not the case and further that their methodology and hence their results are incorrect. There is no short cut for performing the desired calculations, if done rigorously, as we show in our 2012 work

Variations in the 6.2 μ\mum emission profile in starburst-dominated galaxies: a signature of polycyclic aromatic nitrogen heterocycles (PANHs)?

Analyses of the polycyclic aromatic hydrocarbon (PAH) feature profiles, especially the 6.2 $\mu$m feature, could indicate the presence of nitrogen incorporated in their aromatic rings. In this work, 155 predominantly starburst-dominated galaxies (including HII regions and Seyferts, for example), extracted from the Spitzer/IRS ATLAS project (Hern\'an-Caballero & Hatziminaoglou 2011), have their 6.2 $\mu$m profiles fitted allowing their separation into the Peeters' A, B and C classes (Peeters et al. 2002). 67% of these galaxies were classified as class A, 31% were as class B and 2% as class C. Currently class A sources, corresponding to a central wavelength near 6.22 $\mu$m, seem only to be explained by polycyclic aromatic nitrogen heterocycles (PANH, Hudgins et al. 2005), whereas class B may represent a mix between PAHs and PANHs emissions or different PANH structures or ionization states. Therefore, these spectra suggest a significant presence of PANHs in the interstellar medium (ISM) of these galaxies that could be related to their starburst-dominated emission. These results also suggest that PANHs constitute another reservoir of nitrogen in the Universe, in addition to the nitrogen in the gas phase and ices of the ISM

Prediction of NOD tertiary structure.

<p>(<b>A</b>) NOD protein sequence annotated with the secondary structure elements predicted by the QUARK and LOMETS web-services. (<b>B</b>) The three-dimensional model of NOD was constructed using QUARK and LOMETS, with the positive amino acids which replacement with Alanines affect RNA-binding are shown in red letters (A) or in red sticks (B). β-sheets are shown in green, long α-helix is shown in yellow. The picture was prepared using PyMOL (<a href="http://www.pymol.org" target="_blank">www.pymol.org</a>). (<b>C</b>) Circular dichroism far UV-light spectra of NOD and its mutant with the deleted α-helix (NOD-dα). Fluorescence intensity is given in relative units. (<b>D</b>) The hydrodynamic radius of the NOD-dα mutant as free protein particles or in complex with U1 snRNA, determined by DLS.</p

Structural characteristics of the predicted domains of Atcoilin.

<p>(<b>A</b>) Circular dichroism far UV-light spectra of the wt Atcoilin and its isolated domains. (<b>B</b>) Tryptophan fluorescence spectra of the wt Atcoilin and its isolated domains. Fluorescence intensity is given in relative units.</p

Plant Coilin: Structural Characteristics and RNA-Binding Properties

<div><p>Cajal bodies (CBs) are dynamic subnuclear compartments involved in the biogenesis of ribonucleoproteins. Coilin is a major structural scaffolding protein necessary for CB formation, composition and activity. The predicted secondary structure of <em>Arabidopsis thaliana</em> coilin (Atcoilin) suggests that the protein is composed of three main domains. Analysis of the physical properties of deletion mutants indicates that Atcoilin might consist of an N-terminal globular domain, a central highly disordered domain and a C-terminal domain containing a presumable Tudor-like structure adjacent to a disordered C terminus. Despite the low homology in amino acid sequences, a similar type of domain organization is likely shared by human and animal coilin proteins and coilin-like proteins of various plant species. Atcoilin is able to bind RNA effectively and in a non-specific manner. This activity is provided by three RNA-binding sites: two sets of basic amino acids in the N-terminal domain and one set in the central domain. Interaction with RNA induces the multimerization of the Atcoilin molecule, a consequence of the structural alterations in the N-terminal domain. The interaction with RNA and subsequent multimerization may facilitate coilin’s function as a scaffolding protein. A model of the N-terminal domain is also proposed.</p> </div

Effect of U1 snRNA on Atcoilin multimerization.

<p>(<b>A</b>) Effect of U1 snRNA on the structure and packing density of Atcoilin and its RNA-binding domains, determined via tryptophan fluorescence, the intensity of which is given in relative units. (<b>B</b>), (<b>C</b>), The hydrodynamic radii of (<b>B</b>) coilin and (<b>C</b>) NOD as free proteins or in complex with U1 snRNA, as elucidated by the DLS method. (<b>D</b>) Atomic-force microscopy of coilin as a free protein (left panels) or in complex with U1 snRNA (right panels). The topographic images of the particles were obtained on the AFM microscope (Nanoscope III) using a contact mode discontinuous with the sample surface. Indicated frame sizes are 1.5×1.5 and 0.6×0.6 µm.</p

Content of secondary structure elements in the coilin molecule^*.

*<p>- Determination of the content of β-structure elements (in contrast to α-elements) by algorhithms calculating the data achieved from circular dichroism is not very precise and can fall far from true. Besides, the inaccurate increase of β-elements drives to inaccurate decrease of non-structured elements within the protein. That is why the calculated amount of β-elements should be validated by the form of spectre curve and overall signal intensity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053571#pone.0053571-Sreerama1" target="_blank">[30]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053571#pone.0053571-Johnson1" target="_blank">[32]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053571#pone.0053571-Uversky1" target="_blank">[33]</a>.</p

Influence of U1 snRNA on coilin structure.

<p>Influence of U1 snRNA on coilin structure.</p

Amino acid sequence analysis and predicted domain organization of <i>Arabidopsis thaliana</i>

<p><b>coilin.</b> (<b>A</b>) Schematic representation of functional sites and regions that have been identified within the coilin protein molecule. (<b>B</b>) The predicted domain organization of <i>Arabidopsis thaliana</i> coilin, as elucidated by the bioinformatic tools FoldIndex and DISOPRED.</p

Atcoilin mutants and their RNA binding capacities.

<p>(<b>A</b>) Schematic representation of Atcoilin and its mutants. The indicated protein regions and motifs are according to MyHits Motif Search, and the domain predictions are according to FoldIndex and DisoPred. The substitution mutations (R and K to A) are indicated by white boxes and the RNA-binding pattern and apparent <i>Kd</i> value for each mutant is indicated. (<b>B</b>) RNA binding capacity of Atcoilin and its isolated domains, as determined using EMSA. Increasing amounts of protein (protein:RNA ratios indicated above each lane) were incubated with 0.1 µg of RNA in RNA binding buffer (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053571#s2" target="_blank">Materials and Methods</a>) and loaded onto 2% non-denaturing Tris-acetate agarose gels. The rightmost lane contains RNA without protein.</p