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Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks

Figure 1

Modeling proteins as spheres.

A: When structural information was available on PDB, we fit a sphere to the volume occupied by the α-carbon chain of the protein, with an initial volume of 0.5 nm and progressive increasing the volume by 0.025 nm until 100% of the α-carbons are contained within the sphere. We find that for most proteins the optimal sphere size contains 90% of α-carbons. B: The correlation between protein size (r, in nm) and chain length gives a power law (insert equation). Red: fitted line. Green: 95% confidence intervals. C: In general both globular and non-globular proteins follow the trend line. In some cases (rod shaped proteins or proteins that contain one or more clefts) protein size and chain-length are poorly correlated. (Labels: Protein Databank accession number).

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1003654.g001