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マイクロ秒から秒の原子折り畳み時間の計算式推定

Upendra Adhikari1, Barmak Mostofian1, Jeremy Copperman1

  • 1Department of Biomedical Engineering, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.

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この研究では,GPUコンピューティングによる加重アンサンブル (WE) 戦略を使用してタンパク質の折り畳みをシミュレートし,マイクロ秒からミリ秒までの折り畳み時間の分析を可能にします. このアプローチはタンパク質の折りたたみのような希少な出来事を 統計的に偏見のない見積もりで提供します

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科学分野:

  • コンピュータ生物学
  • バイオ物理学
  • 分子力学

背景:

  • 室温での原子タンパク質の折り畳みをシミュレートすることは,従来の分子動力学 (MD) でマイクロ秒に制限されています.
  • GPUコンピューティングの進歩は,より長い時間スケールのシミュレーションの可能性を提供します.

研究 の 目的:

  • GPUコンピューティングと組み合わせた加重アンサンブル (WE) 戦略を使用して,原子型タンパク質システムの折り畳みを報告する.
  • タンパク質の折りたたみのような希少なイベントの速度定数の統計的に偏らない推定を可能にします.

主な方法:

  • GPUで加速されたMDシミュレーションで加重アンサンブル (WE) 戦略を使用した.
  • 無偏見な見積もりのために,剪定と複製を用いた軌道セグメントの組織化された集合.
  • 折り畳み時間を分析 WE確率フルスと歴史拡張マルコフ解析

主要な成果:

  • マイクロ秒からミリ秒までの折りたたみ時間を有する 暗黙的に溶解されたタンパク質の折りたたみを成功裏にシミュレートした.
  • 異なる粘度でNTL9 (0. 8~9μs,0. 2~2μs) とプロテインG (3~200μs) を試験した.
  • WEシミュレーションは折り畳み時間,不確実性,およびアンサンブル特性を提供し,プロテインGの従来のMDよりも少ない計算を必要とする.

結論:

  • GPUコンピューティングによるWE戦略は,より長い時間スケールでタンパク質の折り畳みをシミュレートすることが可能である.
  • この方法は,折り畳み時間および不確実性を含む運動量に関する統計的に偏らない推定を可能にします.
  • この発見は,精密な運動推定のための力場と溶媒モデルの使用と校正の実現可能性を示唆している.