Additional file 1: Table S1. of Infant and young child feeding practices differ by ethnicity of Vietnamese mothers

Type of foods consumed by 6–23-month-old children. (PDF 128 kb

Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail

<div><p>Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors.</p></div

A and B) Selective constraints imposed upon MAPKs (foreground) that most contribute to sequence divergence from CMGC Kinases (background).

<p>Representative alignment of MAPKs is shown. Residues identified via CHAIN as distinctive of MAPKs are shown with black dots above each aligned column. The height of the red histograms above each corresponding column shows the degree of divergence of the MAPK foreground sequence from the CMGC counterparts (background). The residue frequency in the foreground is shown directly below the display alignment in positive integer tenths (i.e. 6 corresponds to 60–70% of weighted foreground sequences). The number of residues aligned in the foreground and weighted foreground frequency is shown near the “foreground” and wt_res_freqs designation, respectively. In particular, the weighted frequency was automatically done by the sampler to adjust to the overrepresentation of selected subfamilies in the alignment. The number of residues in the background and the weighted frequency is shown below in pink, respectively. Residues with strongest constraints are colored accordingly with residues of similar biochemical properties having similar color. Notable secondary structural locations are indicated above the histograms, and general numbering scheme is shown at the bottom with designated family numbering for reference. In Fig. 2B, the C-tail starts after the conserved HPY motif of the kinase domain.</p

Cross correlation map of Cα-Cα displacement of ERK2 in A) D-Domain/D-Peptide Bound Form with C-tail, B) D-Domain Peptide Unbound (Apo) Form with C-tail, C) D-Domain Peptide Bound Form without C-tail, and D) D-domain Peptide Unbound (Apo) Form without C-tail.

<p>Cross correlation map of Cα-Cα displacement of ERK2 in A) D-Domain/D-Peptide Bound Form with C-tail, B) D-Domain Peptide Unbound (Apo) Form with C-tail, C) D-Domain Peptide Bound Form without C-tail, and D) D-domain Peptide Unbound (Apo) Form without C-tail.</p

Structural location of conserved interactions between the αE-helix, the flanking C-tail, and the CD (Common Docking Site) region.

<p>A) Key conserved interactions in MAPKs, using a p38α as a representative model (PDBID: 4LOO), with cyan sticks representation denoting MAPK specific residues. Brown segment denotes the C-tail. B) Display set of sequence constraints imposed upon JNK C-terminal segment. General labelling schemes follow that of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#pone.0119636.g002" target="_blank">Fig. 2</a>; the background corresponds to MAPK alignment while foreground corresponds to JNK alignment with number of sequences in alignment shown, respectively. The numbering schemes are shown at the bottom for each representative family. C) Divergent interaction of JNK in the analogous regions (PDBID: 1JNK) with JNK specific residues at the interface identified via the samplers. JNK-specific residues are shown in light orange, MAPK specific residues are shown in cyan, and JNK Insert is shown in light pink. D) Structural alignment of JNK’s C-tail (in brown) with a canonical p38α MAPK C-tail (in orange).</p

Structural delineation of MAPK specific residues (PDBID: 2OKR).

<p>Key structural regions being discussed in the text is highlighted, namely, the L16 helix and loop, D-domain/D-peptide docking site, CD (Common Docking site), αE and αC helices. Cyan sticks presentation denotes MAPK-specific residues identified via CHAIN (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#sec014" target="_blank">Methods</a>) and displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#pone.0119636.g002" target="_blank">Fig. 2A</a> alignment.</p

Root Means Square Fluctuation (RMSF) plot of A) ERK2 and B) P38α.

<p>Root Means Square Fluctuation (RMSF) plot of A) ERK2 and B) P38α.</p

Interactions between the conserved acidic and associated residues in the L16 3/10 Helix.

<p>Residue coloring scheme is similar to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#pone.0119636.g003" target="_blank">Fig. 3</a> (i.e. cyan sticks representation denotes MAPK specific residues and light orange/tan sticks denotes subfamily (e.g. JNK) specific residues). A) Interactions of the MAPK specific salt bridge in the apo, unphosphorylated p38α (PDBID: 1P38). B) Interactions of the corresponding region in phosphorylated, apo form of p38α (PDBID: 3PY3). C) Interactions of the salt bridge in ATP analog bound, dually phosphorylated state in p38γ (PDBID: 1CM8). D) Interactions in apo, unphosphorylated ERK5 (PDBID: 4IC8). E) Interactions in ATP analogue bound, unphosphorylated ERK5 (PDBID: 4IC7). F) Interactions in phosphorylated, ATP bound ERK2 (PDBID: 2ERK). G) Disengagement of canonical salt bridge in apo ERK2 (PDBID: 4GSB), where the side chains of E332^ERK2 and D334^ERK2 are disordered.</p

Interactions of MAPK β4-β5 Insert, αC-helix, and L16 helix.

<p>A) Structural alignment of MAPK β4-β5 loop with representative canonical CMGC kinase, where orange denotes Casen Kinase II (CK2) (PDBID: 1JWH), green denotes cyclin dependent kinase (CDK) (PDBID: 1QMZ), and blue denotes MAPK with insert colored in cyan with rectangle representation (PDBID: 4LOO). B) Conserved MAPK-specific interactions in p38α, with MAPK specific residues shown in cyan (PDBID: 4LOO). C) ERK5 variations in the equivalent region, where discussed interactions are shown (PDBID: 4IC7).</p

Display set showing selective sequence constraints imposed upon ERK5 and p38α flanking C-terminal segment.

<p>Top alignment shows ERK5 display (foreground) set with labels accordingly explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#pone.0119636.g002" target="_blank">Fig. 2</a>; boxed sequence motifs denote discussed positions in the text. The middle alignment shows p38α (foreground) display set with labels similar to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119636#pone.0119636.g002" target="_blank">Fig. 2</a>, and boxed sequence motifs denote discussed positions in the text. The background sequence at bottom corresponds to related MAPK sequences that belong to families outside of ERK5 and p38α, respectively.</p