Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

ABSTRACT: Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabo

SUBMITTER: Yu I 

PROVIDER: S-EPMC5089862 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature