Model r37 (blue) and r44 (orange) of G3:HER2_IV show similarity at the C-terminal region.

<p><b>(A)</b> Model overview <b>(B)</b> Hydrophobic interactions between F112 and a patch formed by F555 and V563 are conserved in both models. This works as an anchor that allows a pivoting to the correct pose. <b>(C)</b> The movement (indicated with an arrow) is facilitated by the additional hydrophobic contacts from I79 and F81 that slide around F555.</p

Comparison of simulations from different models of complex Efb-C:C3d.

<p><b>(A)</b> RMSD (Cα) from the respective initial structure for the highest ranking RosettaDock models of complex Efb-C:C3d as a function of simulation time; simulations were performed at 303 K; highlighted in black is the simulation starting from the experimental structure, and in blue and orange from two selected models (also shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006182#pcbi.1006182.g006" target="_blank">Fig 6</a>); in grey are shown all simulations starting from the 20 highest scoring models. <b>(B)</b> RMSD after 40 ns simulation plotted versus the RMSD deviation of the model from the crystal structure; simulations started from the RosettaDock models at two different temperatures; at the higher temperature (300 and 340K).</p

RMSD from the reference experimental structure as a function of time along simulations at 303 K for the models of Efb-C:C3d complex.

<p>Model r1 (blue) is close to the experimental structure and stays stable throughout the simulation. The trajectory starting from model r18 (orange) converges to the correct structure after about 30 ns.</p

Root-mean-square deviation from the position of Cα atoms in the respective models of G3:HER2_IV complex as a function of simulation time.

<p>While some models rapidly move away from the initial pose, others only deviate from the initial structure when temperature is increased. The only model that even after 20 ns simulation at a temperature of 390 K remains close to the initial structure is model r37, that is, the one closest to the correct structure.</p

RMSD (for Cα atoms) from the reference experimental structure as a function of time along simulations at 303 K for the G3:HER2_IV complex.

<p>Simulations starting from model r37 or from the experimental structure explore a narrow range of conformations close to the experimental structure. The simulation starting from model r44 converges to the correct structure after about 50 ns, suggesting that, despite the remarkable structural difference from the correct structure, model r44 is within the native basin of the free energy surface. All the other trajectories do not lead to the correct state after 32 ns simulation. A simulation started from the experimental structure is also shown: the RMSD fluctuates around 1 Å indicating high rigidity of the complex.</p

Summary of solution phase PLA for detection of IL8 proteins in PLA buffer or in 10% or 50% chicken serum.

<p>R² is the correlation coefficient of the fitting curve from 100 pM to 0.16 pM. Background Ct equals the average Ct from quadruplicates of sample in reactions with no spiked IL8. Background CV% is the coefficient of variation calculated from the background Ct values for all quadruplicates.</p><p>Summary of solution phase PLA for detection of IL8 proteins in PLA buffer or in 10% or 50% chicken serum.</p

SPR binding parameters for HER2 constructs binding to the DARPin G3 and trastuzumab.

<p>Note 1: The values given are the average values for three separate measurements and the uncertainties represent one standard deviation.</p>a<p>Note 2: About 30-fold higher affinities are obtained when avoiding random amine coupling of this very small DARPin [9,36], (Nagy-Davidescu and Plückthun, unpublished).</p

The computational model of the complex superimposed on the B and C chains of the X-ray crystal structure (BCxray).

<p>The G3 chains of the model and BCxray are in yellow and cyan, respectively, while the HER2 chains of the model and BCxray are shown in red and green, respectively.</p

Top ZRANKed docking solutions and their computed metrics shape complementarity (Sc) and interaction energy (IE).

a<p>This ZDOCK solution was selected as the optimal or preferred solution for the structural model of the G3 - HER2 complex.</p

Detection of HER2 proteins using immuno-RCA and <i>in</i><i>situ</i> PLA in fixed cells.

<p>(a) 5 nM pure G3-SNAP conjugates and 5 nM unpurified G3-SNAP conjugates were separately used in immune-RCA to detect HER2 proteins in HER2-positive (SK-OV-3) or -negative (BJhTERT) cells. Red dots represent RCA products arising from immuno-RCA reactions detected with fluorescence labeled complementary oligonucleotides. The numbers of RCA products per cell from those images are shown in bar charts (b). (c) Boxplots present the numbers of RCA products per cell when mixes of pure G3-SNAP conjugates (5 nM) and different amounts of unconjugated G3-SNAP (from 0 nM to 320 nM) were used to detect HER2 proteins via immuno-RCA in SK-OV-3 cells. (d) Boxplots reflect the number of RCA products per cell after <i>in</i><i>situ</i> PLA for detection of HER2 protein in SK-OV-3 cells, probed with pure probe conjugates (20 nM G3-SNAP conjugates and 20 nM 9.01-SNAP conjugates), mixed with different amounts of unconjugated DARPin binders (G3-SNAP and 9.03-SNAP at concentrations of 0 nM or 20 nM). The cell nuclei were counterstained with DAPI (blue).</p