title: Comparison of backbone dynamics of monomeric and domain-swapped stefin A.
abstract: Three-dimensional domain swapping has been observed in increasing number of proteins and has been implicated in the initial stages of protein aggregation, including that of the cystatins. Stefin A folds as a monomer under native conditions, while under some denaturing conditions domain-swapped dimer is formed. We have determined the backbone dynamics of the monomeric and domain-swapped dimeric forms of stefin A by (15)N relaxation using a model-free approach. The overall correlation times of the molecules were determined to be 4.6 +/- 0.1 ns and 9.2 +/- 0.2 ns for the monomer and the dimer, respectively. In the monomer, decreased order parameters indicate an increased mobility for the N-terminal trunk, the first and the second binding loops. At the opposite side of the molecule, the loop connecting the alpha-helix with strand B, the beginning of strand B and the loop connecting strands C and D show increased localized mobility. In the domain-swapped dimer, a distinctive feature of the structure is the concatenation of strands B and C into a single long beta-strand. The newly formed linker region between strands B and C, which substitutes for the first binding loop in the monomer, has order parameters typical for the remainder of the beta-strands. Thus, the interaction between subunits that occurs on domain-swapping has consequences for the dynamics of the protein at long-range from the site of conformational change, where an increased rigidity in the newly formed linker region is accompanied by an increased mobility of loops remote from that site.
authors.affiliation: Laboratory of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
authors.forename: Bostjan
authors.initials: B
authors.lastname: Japelj
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Waltho
authors.forename: Roman
authors.initials: R
authors.lastname: Jerala
mesh_terms: D016880:Anisotropy; D055312:Cystatin A; D015891:Cystatins / Q000737:chemistry* / Q000378:metabolism*; D004058:Diffusion; D019281:Dimerization; D006801:Humans; D006859:Hydrogen / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012399:Rotation
chemical_list: D055312:Cystatin A; D015891:Cystatins; D006859:Hydrogen; C026407:CSTA protein, human