Energetics of the presequence-binding poses in mitochondrial protein import through Tom20

Yasuaki Komuro, Naoyuki Miyashita, Takaharu Mori, Eiro Muneyuki, Takashi Saitoh, Daisuke Kohda, Yuji Sugita

    研究成果: Contribution to journalArticle査読

    10 被引用数 (Scopus)

    抄録

    Tom20 is located at the outer membrane of mitochondria and functions as a receptor for the N-terminal presequence of mitochondrial-precursor proteins. Recently, three atomic structures of the Tom20-presequence complex were determined using X-ray crystallography and classified into A-, M-, and Y-poses in terms of their presequence-binding modes. Combined with biochemical and NMR data, a dynamic-equilibrium model between the three poses has been proposed. To investigate this mechanism in further detail, we performed all-atom molecular dynamics (MD) simulations and replica-exchange MD (REMD) simulations of the Tom20-presequence complex in explicit water. In the REMD simulations, one major distribution and another minor one were observed in the converged free-energy landscape at 300 K. In the major distribution, structures similar to A- and M-poses exist, whereas those similar to Y-pose are located in the minor one, suggesting that A-pose in solution is more stable than Y-pose. A k-means clustering algorithm revealed a new pose not yet obtained by X-ray crystallography. This structure has double salt bridges between Arg14′ in the presequence and Glu78 or Glu79 in Tom20 and can explain the binding affinity of the complex in previous pull-down assay experiments. Structural clustering and analyses of contacts between Tom20 and the presequence suggest smooth conformational changes from Y- to A-poses through low activation barriers. M-pose lies between Y- and A-poses as a metastable state. The REMD simulations thus provide insights into the energetics of the multiple-binding forms and help to detail the progressive conformational states in the dynamic-equilibrium model based on the experimental data.

    本文言語英語
    ページ(範囲)2864-2871
    ページ数8
    ジャーナルJournal of Physical Chemistry B
    117
    10
    DOI
    出版ステータス出版済み - 3 14 2013

    All Science Journal Classification (ASJC) codes

    • 物理化学および理論化学
    • 表面、皮膜および薄膜
    • 材料化学

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