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

    研究成果: ジャーナルへの寄稿記事

    7 引用 (Scopus)

    抄録

    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.

    元の言語英語
    ページ(範囲)754-768
    ページ数15
    ジャーナルProtein Science
    25
    発行部数3
    DOI
    出版物ステータス出版済み - 3 1 2016

    Fingerprint

    Spatial distribution
    Crystals
    Molecules
    Proteins
    Electrons
    Carrier concentration
    Spatial Analysis
    X-Ray Diffraction
    Peptides
    Fusion reactions
    X ray diffraction
    Processing

    All Science Journal Classification (ASJC) codes

    • Biochemistry
    • Molecular Biology

    これを引用

    Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules. / Matsuoka, Rei; Shimada, Atsushi; Komuro, Yasuaki; Sugita, Yuji; Kohda, Daisuke.

    :: Protein Science, 巻 25, 番号 3, 01.03.2016, p. 754-768.

    研究成果: ジャーナルへの寄稿記事

    @article{b34fa4d8f38f4d6f82e6da575cc4de66,
    title = "Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules",
    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.",
    author = "Rei Matsuoka and Atsushi Shimada and Yasuaki Komuro and Yuji Sugita and Daisuke Kohda",
    year = "2016",
    month = "3",
    day = "1",
    doi = "10.1002/pro.2867",
    language = "English",
    volume = "25",
    pages = "754--768",
    journal = "Protein Science",
    issn = "0961-8368",
    publisher = "Cold Spring Harbor Laboratory Press",
    number = "3",

    }

    TY - JOUR

    T1 - Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules

    AU - Matsuoka, Rei

    AU - Shimada, Atsushi

    AU - Komuro, Yasuaki

    AU - Sugita, Yuji

    AU - Kohda, Daisuke

    PY - 2016/3/1

    Y1 - 2016/3/1

    N2 - 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.

    AB - 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.

    UR - http://www.scopus.com/inward/record.url?scp=84959018150&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=84959018150&partnerID=8YFLogxK

    U2 - 10.1002/pro.2867

    DO - 10.1002/pro.2867

    M3 - Article

    C2 - 26694222

    AN - SCOPUS:84959018150

    VL - 25

    SP - 754

    EP - 768

    JO - Protein Science

    JF - Protein Science

    SN - 0961-8368

    IS - 3

    ER -