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Significance Theoretical and experimental efforts during the last two decades have revealed many important features of protein folding. However, these efforts have largely focused on single-domain proteins, and additional methods and concepts have been awaited to understand the rich variety of multidomain proteins. To understand the relationship between the topology and folding pathways of multidomain proteins, we developed an Ising-like structure-based model. Our simulated results showed that a dominant pathway is selected in an example protein, dihydrofolate reductase (DHFR), which prevents the rapid decrease in conformation entropy during the course of folding. However, in its circular permutant, for which the topological complexity of wild-type DHFR is resolved, two pathways coexist, resulting in a complex folding behavior.

Folding pathway of a multidomain protein depends on its topology of domain connectivity