Comparison of Backbone Dynamics of Monomeric and Domain-Swapped Stefin A

Boštjan Japelj, Jonathan P. Waltho, Roman Jerala

    Research output: Contribution to journalArticlepeer-review

    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 15N 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 α-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 Β-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 Β-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. © 2004 Wiley-Liss, Inc.
    Original languageEnglish
    Pages (from-to)500-512
    Number of pages12
    JournalProteins: Structure, Function and Bioinformatics
    Volume54
    Issue number3
    DOIs
    Publication statusPublished - 15 Feb 2004

    Keywords

    • Chemical exchange
    • Diffusion
    • Domain swapping
    • NMR spectroscopy
    • Order parameter
    • Relaxation

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