Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts

Description

Ikram Mahmoudi, Chloé Quignot, Carla Martins, and Jessica Andreani compare how protein-RNA contact points change across related structures. Predicting these interfaces matters, since the contacts drive many cell processes, yet experiments are slow and the complexes are flexible. The team built a data set of 2,022 pairs of structurally matching interfaces and checked which contacts survive between relatives.

Distance-based contacts were conserved about 73 percent of the time on average, and greasy contacts about 68 percent. That held even for distant relatives sharing under 20 percent sequence identity. Hydrogen bonds, salt bridges, and stacking contacts, by contrast, shifted freely even between close relatives. Nearly half of the lost contacts came from a few residues dropping out of the interface entirely. The authors also mapped how lost polar contacts get replaced or compensated. The findings can guide prediction tools that borrow evolutionary signals for protein-RNA modeling.

Catalog record

Source: https://europepmc.org/articles/PMC11642956