Type 2 asparaginase loop models.

<p>Modeled structures of the Taspase1 loop homologous regions in other type 2 asparaginases generated with YASARA. The loop of human Taspase1 (template PDB 2a8i; 25 modeled amino acids) is predicted as predominantly helical, while for human glycosylasparaginase (template PDB 1apy; 20 modeled aa), human asparaginase (template PDB 4pvs; 14 modeled aa), plant asparaginase (template PDB 2gez; 33 modeled aa), <i>E</i>. <i>coli</i> asparaginase (template PDB 2zal; 17 modeled aa), and <i>F</i>. <i>meningosepticum</i> glycosylasparaginase (template PDB 1ayy; 10 modeled aa) mainly random coil elements are predicted. The modeled loop regions are highlighted in red; the active site (corresponding to Thr234 in Taspase1) is highlighted in green.</p

Chemical shift difference analysis of the long Taspase1 loop.

<p>Analysis of the chemical shift differences with respect to random coil values for H_α, C_α, and C_β shifts of the Taspase1 loop. Helices according to the secondary structure prediction are depicted on top. Note that stretches of negative H_α and C_β values, as well as positive C_α values indicate a helical conformation of the respective amino acids.</p

Secondary structure predictions of Taspase1 loop.

<p>Primary sequence based secondary structure predictions of the loop region Gly178-Asp233 of Taspase1, which is missing in the crystal structure of active Taspase1 (PDB 2a8j). The algorithms predict a stretch of helices between Asn185 and Ser223. For the YASARA model and the JNet prediction, cylinders represent helical areas, lines represent random coil and loops are represented as curves. Confidence (conf) values range from 0 (uncertain) to 9 (confident). Residues predicted as buried by sol25 and sol0 are labeled (B).</p

Spectroscopic analysis and MD simulation of the Taspase1 loop at the C-terminus of the α-subunit.

<p>(a) CD spectra of the long (G178-D233; red) and the short Taspase1 loop (P183-S222; black) show a helical structure for both peptides. (b) CD spectrum based secondary structure deconvolution using CDSSTR confirms a higher helical content (green) in the long loop compared to the short loop. Numbers are given in percent. (c) Three 10 ns molecular dynamics simulations were performed in YASARA starting with a linear loop peptide. For each amino acid, the time of the respective amino acid in helix, sheet, turn or random coil conformation is plotted. (d) Representative snapshots of the simulations indicate the formation of helices, especially around Arg190.</p

Additional file 1: Figure S1. of NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase

Sequence alignment of NmPin from N. maritimus with various homologues from other phyla to investigate a potential conservation of the positively charged lysine patch of NmPin. Representatives were found by BLAST search. Each group was separately aligned to NmPin (green). Lysines of the patch (K5, K7, K31, K34, K37, K47, K48, K90) are labelled in dark blue and Arg or positively charged residues which are in close proximity to the conserved position are labelled in light blue. The positively charged patch on the surface of NmPin might be conserved also in other members of the TACK phylum. (PDF 464 kb