Detecting substeps in the rotary motors of FoF1-ATP synthase by Hidden Markov Models
Detecting substeps in the rotary motors of FoF1-ATP synthase by Hidden Markov Models
复制标题
通过隐马尔可夫模型检测 FoF1-ATP 合酶旋转电机的子步骤
DOI：
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发表时间：
2007
期刊：
影响因子：
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通讯作者：
M. Börsch
中科院分区：
文献类型：
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作者：
N. Zarrabi;M. Düser;Rolf Reuter;Stanley D. Dunn;J. Wrachtrup;M. Börsch
FoF1-ATP 合酶是为活细胞提供“化学能量货币”三磷酸腺苷 ATP 的酶。 ATP 的形成是通过酶内亚基的逐步内旋转来完成的。我们通过单分子荧光共振能量转移（FRET）方法使用两个专门附着在酶上的荧光团来监测亚基旋转。为了确定 ATP 合酶电机旋转运动的步长，我们模拟了自由扩散酶的共焦单分子 FRET 数据，并开发了基于“隐马尔可夫模型”(HMM) 的步长查找算法。 HMM 能够找到三级系统和五级系统的邻近因子 P，并揭示模拟旋转运动的停留时间。为了识别系统中隐藏状态的数量，计算应用于每组模拟数据的一系列单状态到八状态 HMM 的似然参数。因此，定义了实验单分子 FRET 数据的基本先决条件，允许区分 ATP 合酶质子驱动 Fo 电机的 120o 步进模式或 36o 子步旋转模式。
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. We monitor subunit rotation by a single-molecule fluorescence resonance energy transfer (FRET) approach using two fluorophores specifically attached to the enzyme. To identify the stepsize of rotary movements by the motors of ATP synthase we simulated the confocal single-molecule FRET data of freely diffusing enzymes and developed a step finder algorithm based on 'Hidden Markov Models' (HMM). The HMM is able to find the proximity factors, P, for a three-level system and for a five-level system, and to unravel the dwell times of the simulated rotary movements. To identify the number of hidden states in the system, a likelihood parameter is calculated for the series of one-state to eight-state HMMs applied to each set of simulated data. Thereby, the basic prerequisites for the experimental single-molecule FRET data are defined that allow for discrimination between a 120o stepping mode or a 36o substep rotation mode for the proton-driven Fo motor of ATP synthase.
DOI：
10.1073/pnas.92.24.10964
发表时间：
1995-11-21
影响因子：
11.1
作者：
DUNCAN, TM;BULYGIN, VV;CROSS, RL
通讯作者：
CROSS, RL