Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules

Rei Matsuoka, Atsushi Shimada, Yasuaki Komuro, Yuji Sugita, Daisuke Kohda

    Research output: Contribution to journalArticlepeer-review

    8 Citations (Scopus)

    Abstract

    Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.

    Original languageEnglish
    Pages (from-to)754-768
    Number of pages15
    JournalProtein Science
    Volume25
    Issue number3
    DOIs
    Publication statusPublished - Mar 2016

    All Science Journal Classification (ASJC) codes

    • Biochemistry
    • Molecular Biology

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