Additional file 2 of DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Parameter values. Reaction rates that were obtained by our automated database search for different metabolic systems. (XLSX 510 kb

Additional file 1 of RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

Output files. Each output format of the following RDF resources: i) the CHEBI database, ii) Reactome (Biopax level 3) database, iii) UniProt database, iv) SAPP. (1,572 kb

Comparison of functional and taxonomic profiles of the Altered Schaedler Flora from the intestine of a NOD mouse model [13].

<p>A) Alignment vs assembly functional profiling; x-axis, direct genome alignment; y-axis, <i>de novo</i> assembly. Taxonomic profiles of mRNA reads obtained by direct genome mapping (B) and by using the <i>de novo</i> assembly method (C). Sample labels were taken from Xiong et al.</p

Metabolic pathways mapping of <i>Lachnospiraceae</i> and <i>Erysipelotrichaceae</i> expression profiles.

<p>Relative contribution of each family (green <i>Lachnospiraceae</i>, red <i>Erysipelotrichaceae</i>) are color scaled. Line-width indicates the total amount of reads mapped to the corresponding KEGG ortholog (log scaled).</p

Metatranscriptome analysis workflow.

<p>Details of the programs used are described in the methods section.</p

Distribution of COG functional categories of the mouse cecal metatranscriptome.

<p>Distribution of COG functional categories of the mouse cecal metatranscriptome.</p

Similarity score distributions of predicted Mouse and Human microbial community proteins to known proteins.

<p>Translated proteins were aligned to the NCBI nr protein database and binned according to their SRV score. The SRV score represents the bit-score of the best hit divided by the maximum obtainable bit-score [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146423#pone.0146423.ref061" target="_blank">61</a>].</p

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

<div><p>D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.</p></div

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access - Fig 3

<p>An examples of AQUA-DUCT results of tracking of water molecule passing during 50 ns of MD simulations through active site of: (A) hDAAO, (B) Y55A hDAAO, (C) Y55AL56T hDAAO.</p> <p>Protein shown as cartoon, active site object as orange wireframe, Y224, Y55 and Y314 as red, blue and yellow sticks, respectively. The inlets of water molecules entering/leaving the protein scope shown as small spheres.</p

Geometry of main entities allowing entry to the active site of hDAAO.

<p>(A) tunnels represented by mesh, residues dividing tunnels by sticks, protein by cartoon, cofactor FAD is shown in black (wireframe), (B) (protein rotated approximately 30°), tunnels identified in single frame, tunnels represented by balls, protein by the solvent accessible surface. (C) tunnels and inlets of water molecules identified in entire MD simulation, tunnels represented by lines, water inlets by small spheres, protein by the solvent accessible surface. Tunnels calculated by CAVER, water inlets by AQUA-DUCT, picture prepared by PyMOL.</p