Abstract
Domain swapping is the process by which two or more identical proteins exchange structural elements or “domains.” Monellin and stefin-B (a cystatin) have very similar structures but entirely different functions. They also have very different domain-swapping propensities. We show using structure-based models (SBMs) and MD simulations, that these propensities can be determined by the position and the chemistry of functional residues in the proteins. Thus, domain-swapping, often a first step in disease-causing aggregation, can be a byproduct of the need to conserve function in the protein. We also show that SBMs and MD simulations can be used to predict mutations which introduce domain-swapping into a non-domain-swapping protein (monellin).
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