In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non-native interactions.

ABSTRACT: We examine the influence of cellular interactions in all-atom models of a section of the Homo sapiens cytoplasm on the early folding events of the three-helix bundle protein B (PB). While genetically engineered PB is known to fold in dilute water box simulations in three microseconds, the three initially unfolded PB copies in our two cytoplasm models using a similar force field did not reach the native state during 30-microsecond simulations. We did however capture the formation of all three helices in a compact native-like topology. Folding in vivo is delayed because intramolecular contact formation within PB is in direct competition with intermolecular contacts between PB and surrounding macromolecules. In extreme cases, intermolecular beta-sheets are formed. Interactions with other macr

SUBMITTER: Russell PPS 

PROVIDER: S-EPMC10578126 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature