Sparse networks of conformational fluctuations communicate signals within proteins.

ABSTRACT: To respond to environmental cues, proteins must amplify angstrom-scale signals across nanometers in the presence of thermal fluctuations. A prevailing view is that thermal fluctuations attenuate (1-7) signal-bearing coherent motions (8-11), yet numerous experiments correlate signaling state with fluctuations themselves (12-36). Here, we show that residue-level fluctuations encode "geometric bits" that are communicated within a sparse 3D network of shared entropy. We demonstrate this by developing an open-source framework that discovers shared entropy networks by inferring discrete residue conformations from molecular dynamics simulations of protein structure and finding maximum-likelihood tree distributions with minimal assumptions, enabling multiscale conformational entropy calculation wi

SUBMITTER: Trenfield K 

PROVIDER: S-EPMC12154606 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature