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Domain swapping: a mathematical model for quantitative assessment of structural effects
Irena Roterman1, Katarzyna Stapor2, Dawid Dułak3
1Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Krakow, Poland.
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.
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