Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules.

ABSTRACT: Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference state associated to the null interaction case. Despite their significant effectiveness, the physical interpretation of knowledge-based potentials has been repeatedly questioned, with no consensus on the choice of the reference state. Here we use the fact that the Flory theorem, originally derived for chains in a dense polymer melt, holds also for chain fragments within the core of globular proteins, if the average over buried fragments collected from different non-redundant native structures is considered. After verifying that the ensuing

SUBMITTER: Zamuner S 

PROVIDER: S-EPMC8794220 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature