A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms.

ABSTRACT: Protein homodimers have been classified as three-state or two-state dimers depending on whether a folded monomer forms before association, but the details of the folding-binding mechanisms are poorly understood. Kinetic transition networks of conformational states have provided insight into the folding mechanisms of monomeric proteins, but extending such a network to two protein chains is challenging as all the relative positions and orientations of the chains need to be included, greatly increasing the number of degrees of freedom. Here, we present a simplification of the problem by grouping all states of the two chains into two layers: a dissociated and an associated layer. We combined our two-layer approach with the Wako-Saito-Muñoz-Eaton method and used Transition Path Theory to invest

SUBMITTER: Gyorffy D 

PROVIDER: S-EPMC10741920 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature