The dependency of the optimal <i>w</i> values on the resolution of the matched EM maps.

<p>The full circles depict the results of self-matching (for systems listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003594#pone-0003594-t001" target="_blank">Table 1</a>). The hollow circles depict the results of matching of related EM maps (the average resolution is used here). The regression line (y = −0.0612x+3.7551; R² = 0.78) is based only on the full circles. The error bars reflect the range of the optimal <i>w</i>.</p

Examples of low-to-low resolution matching and docking.

<p>The top ranking matches are shown, obtained in <i>Fit</i>EM2EMin scans that employ <i>w</i> values calculated from the dependency graph in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003594#pone-0003594-g001" target="_blank">Figure 1</a>. EM envelopes are shown in yellow. The DifferenceGrid portions where object A protrudes out of object B are colored as object A, and vise versa for object B. The individual images were prepared with the software package Amira and are not to scale. Details for each row of pictures are listed from left to right. (A) Matching of two EM structures of the DnaB.DnaC complex (top and side views). Shown are the EM envelope of objects A (resolution 42.2 Å); the virtual atoms representation of object B (resolution 26 Å) in red within its EM envelope; the identity match (score 1963, ranked 1); match deviating by 6° (score 1352, ranked 4); match deviating by 12° (score 96, ranked 7). (B) The virtual atoms representations of GroES-ADP₇-GroEL-ATP₇ (blue) and GroEL-ATP₇ (red) within their EM envelopes; top and side views of the DifferenceGrid results. (C) Virtual atoms representations of AMPPNP-<i>T</i>ClpB (blue), ATP-<i>T</i>ClpB mutant (red) and ADP-<i>T</i>ClpB (cyan); top views of the DifferenceGrid results for the match of AMPPNP-<i>T</i>ClpB to ATP-<i>T</i>ClpB mutant and for the match of ATP-<i>T</i>ClpB mutant to ADP-<i>T</i>ClpB; sections through the side views of the DifferenceGrid results for the same matches. (D) Virtual atoms representations of the 80S ribosome (blue) and the 40S subunit (red); the top ranking match and the DifferenceGrid results. (E) Side and bottom views of the top ranking docking model between Kv4.2*-KChlP2 (blue) and the simulated map of β2₄ (red); changes in the complementarity score as function of ψ, the rotation angle about the 4-fold axis of the predicted complex.</p

Matching related EM maps.

a<p>The first structure in each pair is the stationary object A and the second structure is the moving object B.</p>b<p>Values are given for matching with the lowest density cutoff for object A and highest cutoff for object B (see text).</p

Benchmark of EM structures used in the optimization of <i>w</i>, the parameter that determines the width and shape of the surface layer of object A.

a<p>The resolution quoted here is the value in the EMDB; average resolution is given for the pairs of related structures.</p>b<p>R1 is the virtual atoms radius calculated with the central values of the <i>w</i> ranges in column 5.</p>c<p>R2 is the virtual atoms radius calculated with <i>w</i> values derived from the linear dependency of <i>w</i> on the resolution (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003594#pone-0003594-g001" target="_blank">Figure 1</a>).</p

Bioorganometallic Chemistry. 27. Synthetic, X‑ray Crystallographic, and Competitive Binding Studies in the Reactions of Nucleobases, Nucleosides, and Nucleotides with [Cp*Rh(H₂O)₃](OTf)_2, as a Function of pH, and the Utilization of Several Cp*Rh–DNA Base Complexes in Host–Guest Chemistry

The reactions of the air- and water-stable tris­(aqua) complex [Cp*Rh­(H₂O)₃]­(OTf)₂ (<b>1</b>; OTf = trifluoromethanesulfonate) with nucleobases and nucleosides that included 9-methyladenine (9-MA), 9-ethylguanine (9-EG), 9-methylhypoxanthine (9-MH), 9-ethylhypoxanthine (9-EH), 1-methylcytosine (1-MC), 1-methylthymine (1-MT), adenosine (Ado), and guanosine (Guo) provided new bonding modes, all as a function of pH. The 9-MA nucleobase provided a novel cyclic trimer, at pH 6, characteristic for all Ado complexes: [Cp*Rh­(μ₂-η¹(<i>N1</i>):η²(<i>N6</i>,<i>N7</i>)-9-MA/Ado)]₃(OTf)₃. The Cp*Rh­(9-EG) and Cp*Rh­(Guo) complexes showed N7 and 6-CO binding modes in water, [Cp*Rh­((η²(<i>N7</i>,<i>O6</i>)-9-EG/Guo)­(OH)]­(OTf), and no cyclic trimer products, due to a pronounced steric effect of the 2-amino group. This was shown convincingly by the results with 9-MH and 9-EH, which did form cyclic trimers at pH 6.1, [Cp*Rh­(μ₂-η¹(<i>N1</i>):η²(<i>N7</i>,<i>O6</i>)-9-MH/9-EH)]₃(OTf)₃, with a structure similar to that of 9-EG, but with no 2-amino group available. At pH 10.2, the p<i>K</i>_a of the 9-MH’s NH1 hydrogen dictated the structure, providing a μ-hydroxy dimer, <i>trans</i>-[Cp*Rh­(η¹(<i>N1</i>)-9-MH)­(μ-OH)]₂(OTf)₂, while in methanol the same reaction provided a mononuclear complex, [Cp*Rh­(η¹(<i>N7</i>)-9-MH)­(MeOH)₂]­(OTf)₂. The reaction of <b>1</b> and 1-MC, at pH 5.4, provided another μ-hydroxy dimer with intramolecular H bonding of the O and H atoms of the μ-OH groups (H-acceptor and H-donor, respectively), <i>trans</i>-[Cp*Rh­(η¹(<i>N3</i>)-1-MC)­(μ-OH)]₂(OTf)₂, while in acetone, the product was a monomeric complex, [(η⁵-Cp*Rh)­(η¹(<i>N3</i>)-1-MC)­(η²(<i>O2</i>,<i>N3</i>)-1-MC)]­(OTf)₂. The reaction of <b>1</b> and 1-MT at pH 10 showed the initial complex <b>1</b> being converted to its equilibrium complex, [(Cp*Rh)₂(μ-OH)₃]⁺, and this led to two components being formed. The anionic component was a linear [(η¹(<i>N3</i>)-MT)–Rh^I–(η¹(<i>N3</i>)-MT)]^<b>–</b> (12e Rh^I center) assembly, formed via a presumed reductive elimination of Cp*OH, and included an orthogonal array of two thymine planes. The cationic component was [(Cp*Rh)₂(μ-OH)₃]⁺, with its Cp* moiety being π–π stacked with thymine rings, as well as the π–π interactions of two thymine rings: {[Rh^I(η¹(<i>N3</i>)-1-MT)₂]₂[(Cp*Rh)₂(μ-OH)₃]₃}­OH. The competitive order of nucleoside reactivity was Ado ≫ Guo, while for the nucleotides it was GMP > AMP ≫ CMP ≈ TMP. Finally, we also discuss several examples of the utilization of these unique Cp*Rh–DNA base complexes, as aqueous hosts for molecular recognition of aromatic amino acids and as NMR shift reagents for many organic compounds

Increase in Treg cells in isolated splenocytes of TPC-treated CIA mice.

<p>[A] The data are presented as percentage of Treg cells -CD4⁺CD25⁺FOXP3⁺ expansion in isolated splenocytes of tuftsin- phosphorylcholine (TPC), PBS, tuftsin (T), phosphoryl choline (PC), and untreated CIA mice (n = 10). Values are the mean ± SD, <i>P</i> < 0.001. [B] Representative flow cytometry analyses of Treg cells -CD4⁺CD25⁺FOXP3⁺ (gated on CD4⁺) in isolated splenocytes derived from CIA mice treated with TPC, PBS, T and PC and untreated CIA mice. [C] The data are presented as percentage of Tregs -CD4⁺CD25⁺FOXP3⁺ neuropilin-1⁺ (NPN1⁺⁾ expansion in isolated splenocytes of TPC and PBS treated mice (n = 10). Values are the mean ± SD, <i>P</i> < 0.001. [D] Representative flow cytometry analyses of Tregs -CD4⁺CD25⁺FOXP3⁺ neuropilin-1⁺ NPN1⁺ (gated on CD4⁺FOXP3⁺) in splenocytes derived from the TPC and PBS treated mice <i>P</i> < 0.001.</p

The effect of TPC on arthritis scores in DBA/1J CIA mice.

<p>The data are presented as arthritis score of s.c. treated CIA mice, measured from day (0) (disease induction) until day 35 mean ± SD. Tuftsin-phosphorylcholine (TPC) (n = 10), PBS (n = 10), tuftsin (T) (n = 10), phosphorylcholine (PC) (n = 10), untreated (n = 10). Values are mean ± SD. ***<i>P</i> < 0.001.</p

B10 regulatory cells increase in isolated splenocytes of TPC-treated CIA mice.

<p>[A] The data are presented as percentage of Breg cells–IL-10⁺CD5⁺CD1d⁺ increase in isolated splenocytes derived from tuftsin- phosphorylcholine (TPC), PBS, tuftsin (T), phosphorylcholine (PC), and untreated CIA mice (n = 10). Values are mean ± SD, <i>P</i> < 0.001. [B] Representative flow cytometry analyses of Breg cells–IL-10⁺CD5⁺CD1d⁺ (gated on IL-10⁺) in isolated splenocytes derived from CIA mice treated with TPC, PBS, T, and PC, as well as untreated CIA mice.</p

Histological analysis.

<p>Representative arthritic paws from each study group of CIA mice were removed and stained with H&E. Magnification presented × 100.</p

Cytokine expression in polarized RAW cells macrophages.

<p>In vitro analyses of <b>concentrations</b> of the pro-inflammatory cytokines IL-6, TNF-α, and the anti-inflammatory cytokine IL-10 in the culture fluids of M1 polarized RAW cells macrophages incubated with tuftsin-phosphoryl choline (TPC), tuftsin (T) and phosphorylcholine (PC). The data are presented as concentration in pg/ml. Values are the mean±SD, <i>P</i> < 0.001. [A] In vitro analyses of the pro-inflammatory cytokine IL-6 concentration. [B] In vitro analyses of the pro-inflammatory cytokine TNF-α concentration. [C] In vitro analyses of the anti-inflammatory cytokine IL-10 concentration. [D] TPC manipulate the shift from M1 toward M2 via neuropilin receptor. M1 RAW macrophages were incubated with neuropilin inhibitor EG00229, before adding TPC, T, and PC. The data are presented as mean ± SD of three repeated experiments (<i>P</i> < 0.001). [E] The effect of TPC on neuropilin mRNA expression in RAW cells by RT-PCR. The data are presented as mean ± SD of three repeated experiments. [F] Model structure of the TCP neuropilin complex. Tuftsin is shown as a stick diagram with carbon, nitrogen and oxygen atoms in green, blue and red, respectively. The surface of neuropilin is shown, colored by the electrostatic potential, blue for positive, red for negative and white for neutral. The surface was made transparent to show the binding of TPC residue R in a deep cavity and the bifurcated hydrogen bond between R and neuropilin residue D320.</p