THERMODYNAMIC AND KINETIC ASPECTS OF THE FOLDING AND SELFASSEMBLY OF PROTEINS

Abstract

The acquisition of the spatial structure of proteins may be described as a hierarchical condensation reaction. Starting from next-neighbor interac tions (involved in secondary structure formation), the native tertiary and quaternary structure are generated by the merging and docking of domains and subunits. The overall kinetics of the folding and assembly of multi subunit oligomeric proteins consist of consecutive unimolecular and bimo lecular steps which may be distinguished by concentration-dependent recon stitution experiments. In order to reach the native state, both folding and association must be tuned such that the formation of the correct subunit recognition sites precedes association. Beyond a limiting concentration, "wrong aggregation” (in vitro) or precipitation of "inclusion bodies" (in overexpressing strains of bacteria) are found to outrun proper structure formation. Other variables determining the yield and rate of in vitro reconstitution are the temperature, pH, ionic strength and specific ligands. Apart from the physi co-chemical parameters, folding in vivo may be affected by codon usage, amino-acid pools and genome organization.