Domain swapping: a mathematical model for quantitative assessment of structural effects

Abstract

The domain‐swapping mechanism involves the exchange of structural elements within a secondary or supersecondary structure between two (or more) proteins. The present paper proposes to interpret the domain‐swapping mechanism using a model that assesses the structure of proteins (and complexes) based on building the structure of a common hydrophobic core in a micelle‐like arrangement (a central hydrophobic core with a polar shell in contact with polar water), which has a considerable impact on the stabilisation of the domain structure built by domain swapping. Domains with a hydrophobicity system that is incompatible with the micelle‐like structure have also been identified. This incompatibility is the form of structural codes related to biological function.

Keywords

• domain swapping
• hydrophobicity
• micelle‐like
• protein structure