MOESM2 of Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

Additional file 2. OMPLA multiple sequence alignment file

<i>[I_uni,I_ave]</i> Plot for 1TGQ Calculated Using the QUEEN Program [36]

<p>Long-range restraints (blue filled circles) and the 1TGQ_sim restraints (red filled circles) are indicated. Restraints that are among the 30 most unique and most important (those above the dashed gray line) and that involve residues in either the α2 or β3 region (cf. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-g001" target="_blank">Figure 1</a>A) are indicated by black boxes.</p

Sequence and Structure Ensembles of Two DLC2A Structures

<div><p>(A) The sequence of human DLC2A (hDLC2A) (AA).</p><p>(B) The sequence of mouse DLC2A (mDLC2A) proceeded by an eight-residue His-tag (AA). The secondary structure as predicted using PSIPRED [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-b033" target="_blank">33</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-b050" target="_blank">50</a>] (Pred) and the confidence of this prediction (Conf) are shown above the sequences. The secondary structure as observed in the ensembles (Obs) is indicated below the sequences. Except for the His-Tag, the mouse and human sequences differ at three positions (indicated in bold).</p><p>(C) Ribbon diagram of the structure ensemble of mDLC2A (PDB entry 1Y4O). The residues of the His-tag have been omitted for clarity.</p><p>(D) Ribbon diagram of the structure ensemble of hDLC2A (PDB entry 1TGQ).</p><p>(E) The refined average structure of the ensemble calculated using the reconstructed 1TGQ dataset, as discussed in the text. Secondary structure is indicated using colors: helices are shown in blue and purple, strands are shown in red and orange. A numbering scheme for the secondary structure elements is indicated between the two sequences.</p></div

Structure Quality <i>Z</i>-Scores for a Large Set of Recent NMR Structures

<p>The quality scores of 620 NMR ensembles released from the PDB after January 1, 2003, are shown. For comparison, the dataset is separated in structures solved as part of structural genomics projects (orange) and structures originating from individual research groups (green). For each quality indicator, the average <i>Z</i>-score is indicated with a filled black circle. The black horizontal markers indicate (from top to bottom) the 90th, 75th, 50th (the median), 25th, and 10th percentiles of the data points for each quality indicator. The distribution of the outliers outside the markers is indicated using colored data points. The quality scores of the original and refined 1TGQ ensemble (cf. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-t001" target="_blank">Table 1</a>) are indicated by red and blue crosses, respectively. The backbone normality score of 1TGQ is identical for the original and refined ensemble.</p

Examples of Observed Structural Anomalies

<div><p>(A) An arginine side chain protruding the hydrophobic core of the second PDZ domain of PTP-Bas [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-b039" target="_blank">39</a>].</p><p>(B) The corresponding arginine in the highly homologous second PDZ domain of PTP-BL [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-b037" target="_blank">37</a>] is solvent exposed.</p><p>(C) The C-terminal region of DR1885 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020009#pcbi-0020009-b042" target="_blank">42</a>] (residues 120 to 149 are color-coded from yellow to red) forms a knot-like structure in the apo-form of DR1885.</p><p>(D) In the copper bound form of DR1885, the C-terminus wraps around the protein, instead of traversing through it. For each of the four structure ensembles, only the first, and presumably best, model is shown.</p></div

These 24 structure observablesto have been used to characterize the protein structure space.

<p>These 24 structure observablesto have been used to characterize the protein structure space.</p

Projection of the dynasome onto descriptors 1 and 2.

<p>Each point represents one protein. <b>a)</b> Protein dynamics as described by dynasome descriptors 1 and 2. The axes labels indicate which dynamics properties are mainly described by the respective descriptor. The inset focuses on the lower left region. <b>b)</b> same projection as in <b>a)</b>, colored according to SCOP structure classes (see legend). Ellipses indicate the distributions of structure classes; Large thin ellipses denote standard deviations of the distributions, small thick ellipses the standard deviations of their mean.</p

Eigenvalue spectrum of the collective dynamics descriptors

<p>Eigenvalues are given as fractions of the sum of all eigenvalues. The inset shows the cumulative distribution.</p

Distribution of proteins in <i>structure</i> space.

<p>Each point represents one protein. <b>a)</b> Protein structures as described by eigenvectors 1 and 2. In plot <b>a)</b> the same proteins as in Fig. 3 are labelled. <b>b)</b> same projection as in <b>a)</b>, but colored according to SCOP structure classes (see legend). Distributions of SCOP classes are described by their standard deviations (thin large ellipses) as well as the standard deviation of their respective means (thick small ellipses).</p

These 34 dynamics observables to have been used to characterize the dynasome.

<p>These 34 dynamics observables to have been used to characterize the dynasome.</p