A self-consistent approach for determining pairwise interactions that underlie channel activation.
A self-consistent approach for determining pairwise interactions that underlie channel activation.
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DOI：
10.1085/jgp.201411184
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发表时间：
2014-11
期刊：
影响因子：
--
通讯作者：
Chanda B
中科院分区：
文献类型：
--
作者：
Chowdhury S;Haehnel BM;Chanda B
净自由能测量可以与突变体循环分析相结合，以确定通道激活期间特定氨基酸对之间的相互作用能。信号蛋白如离子通道主要以两种功能形式存在，对应于活性和静息状态，由多个中间体连接。基于复杂的电生理实验的多参数动力学模型已经被设计来识别这些构象转变的分子相互作用。然而，这种方法是艰巨的，不适合大规模的相互作用途径的微扰分析。最近，我们描述了一种无模型的方法来获得电压和配体激活的离子通道的净活化自由能。在这里，我们扩展这种方法来估计成对的侧链，有助于门控转换的相互作用能。我们的方法，我们称之为广义的相互作用能量分析（GIA），结合了从电荷-电压曲线获得的中值电压估计与突变周期分析，以确定成对相互作用的强度。我们表明，对于一个系统与任意的门控方案，非加性的氨基酸对活化的净自由能的贡献可以计算在一个自洽的方式。通道激活的顺序和变构模型的数值分析也表明，这种方法可以测量充满活力的非加和性，即使当扰动影响多个过渡。为了证明这种方法的实验应用，我们重新评估了6个先前描述的长程相互作用者在振动钾通道的相互作用能。我们的方法提供了在电压和配体激活的离子通道中生成详细的相互作用能量图的能力，并且可以扩展到任何力驱动的系统，只要可以测量相关的“位移”。
Net free-energy measurements can be combined with mutant cycle analysis to determine interaction energies between specific amino acid pairs during channel activation. Signaling proteins such as ion channels largely exist in two functional forms, corresponding to the active and resting states, connected by multiple intermediates. Multiparametric kinetic models based on sophisticated electrophysiological experiments have been devised to identify molecular interactions of these conformational transitions. However, this approach is arduous and is not suitable for large-scale perturbation analysis of interaction pathways. Recently, we described a model-free method to obtain the net free energy of activation in voltage- and ligand-activated ion channels. Here we extend this approach to estimate pairwise interaction energies of side chains that contribute to gating transitions. Our approach, which we call generalized interaction-energy analysis (GIA), combines median voltage estimates obtained from charge-voltage curves with mutant cycle analysis to ascertain the strengths of pairwise interactions. We show that, for a system with an arbitrary gating scheme, the nonadditive contributions of amino acid pairs to the net free energy of activation can be computed in a self-consistent manner. Numerical analyses of sequential and allosteric models of channel activation also show that this approach can measure energetic nonadditivities even when perturbations affect multiple transitions. To demonstrate the experimental application of this method, we reevaluated the interaction energies of six previously described long-range interactors in the Shaker potassium channel. Our approach offers the ability to generate detailed interaction energy maps in voltage- and ligand-activated ion channels and can be extended to any force-driven system as long as associated “displacement” can be measured.
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影响因子：
16.2
作者：
Aggarwal, SK;MacKinnon, R
通讯作者：
MacKinnon, R
DOI：
10.1085/jgp.201210840
发表时间：
2012-12
期刊：
The Journal of general physiology
影响因子：
--
作者：
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通讯作者：
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DOI：
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发表时间：
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影响因子：
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作者：
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通讯作者：
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影响因子：
64.5
作者：
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通讯作者：
FERSHT, AR
DOI：
10.1073/pnas.1003609107
发表时间：
2010-11-02
影响因子：
11.1
作者：
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通讯作者：
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