Abstract
Protein structure networks (PSNs) have long been used to provide a
coarse yet meaningful representation of protein structure, dynamics, and
internal communication pathways. An important question is what criteria
should be applied to construct the network so that to include relevant
interresidue contacts while avoiding unnecessary connections. To address
this issue we systematically considered varying residue distance cutoff
length and the probability threshold for contact formation to construct
PSNs based on atomistic molecular dynamics in order to assess the amount
of mutual information within the resulting representations. We found
that the minimum in mutual information is universally achieved at the
cutoff length of 5 Å, irrespective of the applied contact formation
probability threshold in all considered, distinct proteins. Assuming
that the optimal PSNs should be characterised by the least amount of
redundancy, which corresponds to the minimum in mutual information, this
finding suggests an objective criterion for cutoff distance and supports
the existing preference towards its customary selection around 5 Å
length, typically based to date on heuristic criteria.