title: Protein Domain-Swapping Can Be a Consequence of Functional Residues.
abstract: Monomer topology has been implicated in domain-swapping, a potential first step on the route to disease-causing protein aggregation. Despite having the same topology (β1-α1-β2-β3-β4-β5), the cysteine protease inhibitor stefin-B domain swaps more readily than a single-chain variant of the heterodimeric sweet protein monellin (scMn). Here, we computationally study the folding of stefin-B and scMn in order to understand the molecular basis for the difference in their domain-swapping propensities. In agreement with experiments, our structure-based simulations show that scMn folds cooperatively without the population of an intermediate while stefin-B populates an equilibrium intermediate state. Since the simulation intermediate has only one domain structured (β3-β4-β5), it can directly lead to domain-swapping. Using computational variants of stefin-B, we show that the population of this intermediate is caused by regions of stefin-B that have been implicated in protease inhibition. We also find that the protease-binding regions are located on two structural elements and localized in space. In contrast, the residues that contribute to the sweetness of monellin are not localized to a few structural elements but are distributed over the protein fold. We conclude that the distributed functional residues of monellin do not induce large local perturbations in the protein structure, eliminating the formation of folding intermediates and in turn domain-swapping. On the other hand, the localized protease-binding regions of stefin-B promote the formation of a folding intermediate which can lead to domain-swapping. Thus, domain-swapping can be a direct consequence of the constraints that function imposes on the protein structure.
authors.affiliation: Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India.
authors.forename: Nahren Manuel
authors.initials: NM
authors.lastname: Mascarenhas
authors.affiliation: Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India.
authors.forename: Shachi
authors.initials: S
authors.lastname: Gosavi
mesh_terms: D055313:Cystatin B / Q000737:chemistry* / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism; D000072417:Protein Domains; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D010940:Plant Proteins; C002541:monellin protein, Dioscoreophyllum cumminsii; D055313:Cystatin B