Schematic view of Neighbor Overlap.

<p>In the depicted example nodes A (degree = 7) and B (degree = 5) have 3 common neighbors. According to the definitions in the text, NOcount  = 3, NOnorm = 3/5 and NOjaccard  = 1/3.</p

Enrichment of Neighbor Overlap in the yeast protein-protein interaction network – with and without complexes.

<p>Panel A shows the distribution of Neighbor Overlap using the NOnorm measure, for yeast (blue bars) versus control (red bars). Assessing the contribution of protein complexes to Neighbor Overlap was implemented by removing protein pairs that belong to the same complex from the original analysis (green bars). Panel B shows the yeast (blue bars) and control (red bars) NOnorm distributions on a collapsed version of the yeast interaction network. This was achieved by collapsing all proteins that are part of the same complex to a unified node and computing NOnorm values for the new network. To overcome difference in scale, the higher NOnorm bins are presented in the enlarged inserts. The figure shows that complexes contribute considerably to the NO enrichment, but even when complexes are removed the NO signal is strongly evident.</p

High Neighbor Overlap pairs have higher sequence similarity than low ones.

<p>The distribution of average sequence similarity for 1000 subsets (each of size 100) from the high (blue bars) and low (red bars) Neighbor Overlap groups are shown. These distributions indicate that high Neighbor Overlap pairs tend to have higher sequence similarity than low ones.</p

Neighbor Overlap in redundant gene pairs for Non-zero Neighbor Overlap pairs.

<p>Neighbor Overlap in redundant gene pairs for Non-zero Neighbor Overlap pairs.</p

GO annotation similarity for high and low Neighbor Overlap groups.

<p>The distributions in each panel represent the GO annotation similarity of 1000 subsets each of size 100) from the high (blue bars) and low (red bars) Neighbor Overlap groups. The distributions for the three ontologies: Biological Process (top), Molecular Function (middle) and Cellular Component (bottom) show a marked separation between their GO similarities for pairs with high and low NO values.</p

High Neighbor Overlap pairs have stronger genetic interactions than low ones.

<p>The distributions represent the average ε values of 1000 subsets (each of size 100) from the high (blue bars) and low (red bars) Neighbor Overlap groups. Clearly, the ε values are higher for the high than for the low group.</p

Non-zero Neighbor Overlap in redundant gene pairs.

<p>Non-zero Neighbor Overlap in redundant gene pairs.</p

MSPβ thermal stability monitored by DSF.

<p>Four representative experiments are shown, one for each MSPβ: Wild-type glycosylated, wild-type deglycosylated, glycosylated R689C, and deglycosylated R689C. The melting curves were measured by heating the samples at a rate of 2°C per minute (B). The T_m values were calculated as the maximum of the first derivative of the melting curves (A). The first derivative values (dF/dT) are normalized and given in %, where 100% corresponds to the highest peak of the entire experiment set. The fluorescence values are on an arbitrary scale (AU). <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027269#pone-0027269-t002" target="_blank">Table 2</a> provides the T_m values. The R689C variant melts at approximately 2.5 K lower temperature than the wild type for the deglycosylated protein and 1.6 K lower for the glycosylated form.</p

Side chain conformation of Arg689 in the MSPβ crystal and modeled structures.

<p>In the crystal structure (yellow), the side chain is involved in inter molecular crystal contacts, and in the modeled conformation (cyan) it forms an intra molecular salt bridge with Glu648 and a hydrogen bond with Gly649 backbone carbonyl. These interactions, if present or partly present in solution, may contribute the modest change in proteins stability introduced by the R689C substitution.</p

SPR equilibrium analysis of binding to immobilized binding to immobilized RON-Sema.

<p>(A) Wild-type and (B) R689C MSPβ. The inserts show the Scatchard plots.</p