Entropy‐based distance cutoff for protein internal contact networks

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 characterized 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.

Phosphate-binding protein-loaded iron oxide particles: adsorption performance for phosphorus removal and recovery from water

“…Atom–atom contacts between H 2 PO 4 − and PBP were then analyzed using a contact distance criterion of 5.0 Å, which is the default for PyContact for protein structure networks. 62,63 Atom–atom contacts were accumulated over residues to obtain P i -amino acid contact data. Amino acids with a total contact lifetime of more than 250 ns are plotted in Fig.…”

Connected Component Analysis of Dynamical Perturbation Contact Networks

“…From this list, the atomic contact matrix A ij , with elements a ij = 1 if atoms i and j are in contact or a ij = 0 in the opposite case, is constructed. Here, the distance cutoff value of 5 Å was used to define when two atoms are set to be in contact, consistently with the previous analyses. , In fact, the 5 Å cutoff value is considered to be a robust choice for protein structure networks, as documented in the literature. , …”

“… 8 , 27 In fact, the 5 Å cutoff value is considered to be a robust choice for protein structure networks, as documented in the literature. 66 , 67 …”