Fig. 1

Rational design of domain swapping in MNEI. a Schematic representation of domain swapping. The hinge loop, connecting the exchangeable domains, adopts an extended conformation in the swapped dimer. Each monomer-like half of the swapped dimer, formed by contributions from the two polypeptide chains (or protomers), is referred to as a “functional unit”. The proximal arrangement of the polypeptide chains in the domain-swapped conformation may lead to the formation of a novel intermolecular interface (secondary interface), which is not found in the monomeric structure. The secondary interface is shown in the cartoon as a set of new interactions established between the two polypeptide chains in the region of crossover. b Structure of the domain-swapped dimer of stefin B (PDB ID: 2OCT) is shown. The two polypeptide chains contributing to the dimer are shown in purple and orange. Sub-domains β1-α1-loopA-β2 and β3-loop2-β4-loop3-β5 are exchanged between the two protomers. Loop1 (green) containing the QVVAG stretch acts as the hinge loop. c Structural superposition of MNEI (PDB ID: 1IV7, blue) and stefin B monomer (PDB ID: 4N6V, orange) is shown. d Structure-based sequence alignment of residues 7–98 of Stefin B with the full sequence of MNEI (1–97) is shown. The MNEI variants designed in this study are also shown in the alignment. The secondary structures are indicated above the alignment in gray. The loop sequences are colored as green: loop1, blue: loop2, and red: loop3