Additional file 1 of Putative causal relations among gut flora, serums metabolites and arrhythmia: a Mendelian randomization study

Additional file 1: Supplementary Table 1. 2,232 SNPs in the gut flora were identified as Final IV

Native mass spectrometric analysis of Shank1 PDZ protein with peptide dendrimers in 1:1 mixture.

<p>(A) Deconvoluted native mass spectrum of Shank1 PDZ protein without ligands, 130 μM in 150 mM ammonium acetate. (B-D) Deconvoluted mass spectra of Shank1 PDZ protein and peptide ligands <b>p1</b>, <b>p2</b> and <b>p3</b> mixed at 1:1 ratio (B, C and D are for <b>p1</b>, <b>p2</b> and <b>p3</b> respectively). In all three spectra, protein−peptide complexes with 1:1 stoichiometry were observed (indicated by the arrows). [Shank1 PDZ] = [peptide] = 65 μM.</p

Additional file 1: of Relationship between serum uric acid level and mild cognitive impairment in Chinese community elderly

Appendix Tables (appendix Table S1 and S2). Multiple linear and logistic regression of SUA level for MMSE score and MCI prevalence for participants without cerebral vascular disease or without kidney diseases. We ascertained the association of SUA level with MMSE score and MCI prevalence in the sensitivity analysis (Appendix Table S1 and S2). When participants with cerebral vascular disease (n = 267, 12.7%) and kidney disease (n = 105, 5.0%) were excluded, the βs and ORs were similar with that in the Table 4 (all participants). (DOC 62 kb

Versatile Site-Selective Protein Reaction Guided by WW Domain–Peptide Motif Interaction

A short, flexible, and unstructured peptide tag that has versatile and facile use in protein labeling applications is highly desirable. Here, we report an 11-residue peptide tag with an internal cysteine (a W-tag, derived from a Comm PY peptide motif that is known to bind with Nedd4 WW3* domain) that can be installed at different regions of the target protein without compromising its covalent reactivity with the reactive label (a 35-residue synthetic Nedd4 WW3* domain derivative). This versatility is explained by the unique structural features of the reaction. NMR analysis reveals that both the W-tag peptide and reactive Nedd4 WW3* protein are unstructured before they encounter each other. The binding interaction of the two induces noticeable structural changes and promotes global folding. Consequently, the reactive cysteine residue at W-tag and the electrophilic chloroacetyl group at Nedd4 WW3* domain are positioned to be in close proximity, inducing an intermolecular covalent cross-linking. The covalent linkage in turn stabilizes the folding of the protein complex. This unique multistep mechanism renders this labeling reaction amenable to different sites of the proteins of interest: installation of the tag at N- and C-termini, in the flexible linker region, in the loop region, and the extracellular terminus of target proteins exhibited comparable reactivity. This work therefore represents the first proximity-induced cysteine reaction based on the unique binding features of WW domains that demonstrates unprecedented versatility

Additional file 1: of Endogenous BDNF augments NMDA receptor phosphorylation in the spinal cord via PLCÎł, PKC, and PI3K/Akt pathways during colitis

Supplemental data. (PDF 18 kb

Native mass spectrometric analysis of Shank1 PDZ protein with peptide dendrimer in 4:1 mixture.

<p>(A) Deconvoluted native mass spectrum of Shank1 PDZ protein without ligands, 91 μM in 150 mM ammonium acetate. (B-D) Deconvoluted mass spectra of Shank1 PDZ protein and peptide ligands <b>p1</b>, <b>p2</b> and <b>p3</b> mixed at 4:1 ratio (B, C and D are for <b>p1</b>, <b>p2</b> and <b>p3</b> respectively). Similarly, only protein−peptide complexes with 1:1 stoichiometry were observed (indicated by the solid line arrows). [Shank1 PDZ] = 45 μM; [peptide] = 11 μM. The peak at 13757 (indicated by * in the spectra) is from an impurity protein that co-purified with Shank1 PDZ protein in this batch. The protein peaks at around 14900 is from the Shank PDZ protein with the first methionine removed and the peak at around 15076 is from the Shank PDZ protein with the first methionine; both peaks are present in the spectrum of protein itself, so they are not relevant to the protein−peptide complex.</p

CART analyses of the relationships between biome and environmental factors along the gradients of precipitation and temperature in the Hulunbuir grasslands.

<p>The key environmental factors were screened in panels A (AGB), B (BGB) and C (R/S). Branches are labeled with criteria used to segregate data. Values in terminal nodes represent mean vegetation biomass of sites grouped within the cluster. n = number of plots in the category. The below corresponding panels were structural complexity (cp value) of trees. All designations are the same as those in the footnotes below <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102344#pone-0102344-t001" target="_blank">Table 1</a>.</p

Isothermal titration calorimetry results and the curving fitting between peptide ligands and Shank1 PDZ protein.

<p>(A) The titration of ligands <b>p1</b>, <b>p2</b> and <b>p3</b> to Shank1 PDZ protein (A1, A2 and A3 are for <b>p1</b>, <b>p2</b> and <b>p3</b> respectively). (A1) [<b>p1</b>] = 4 mM, [Shank1 PDZ] = 400 μM; (A2) [<b>p2</b>] = 326 μM, [Shank1 PDZ] = 43 μM; (A3) [<b>p3</b>] = 354 μM, [Shank1 PDZ] = 35 μM. For the binding pair <b>p1</b> ligand and Shank1 PDZ, the affinity was very low so that protein concentration was adjusted higher to get accuracy affinity data. (B)The titration of diluted <b>p2</b>, <b>p3</b> and dimeric peptide with changed linker length to Shank1 PDZ protein. (B1) [<b>p2</b>] = 194 μM, [Shank1 PDZ] = 0.018 μM; (B2) [<b>p3</b>] = 160 μM, [Shank1 PDZ] = 16 μM; (B3) [dimeric peptide BM(PEG)₃] = 600 μM, [Shank1 PDZ] = 53 μM.</p

Standardized direct effect, indirect effect and total effect of critical environmental factors on aboveground biomass (AGB), belowground biomass (BGB) and root to shoot ratio (R/S).

<p>Note: The “**” represented the significant. All designations are the same as those in the footnotes below <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102344#pone-0102344-t001" target="_blank">Table 1</a>.</p

Frequency distribution curves of the AGB, BGB and R/S; the samples were collected across the Hulunbuir grasslands.

<p>All designations are the same as those in the footnotes below <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102344#pone-0102344-t001" target="_blank">Table 1</a>.</p