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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Direct inference of protein-DNA interactions using compressed sensing methods
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Direct inference of protein-DNA interactions using compressed sensing methods

机译：使用压缩传感方法直接推断蛋白质-DNA相互作用

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摘要

Compressed sensing has revolutionized signal acquisition, by enabling complex signals to be measured with remarkable fidelity using a small number of so-called incoherent sensors. We show that molecular interactions, e.g., protein-DNA interactions, can be analyzed in a directly analogous manner and with similarly remarkable results. Specifically, mesoscopic molecular interactions act as incoherent sensors that measure the energies of microscopic interactions between atoms. We combine concepts from compressed sensing and statistical mechanics to determine the interatomic interaction energies of a molecular system exclusively from experimental measurements, resulting iti a "de novo" energy potential. In contrast, conventional methods for estimating energy potentials are based on theoretical models premised on a priori assumptions and extensive domain knowledge. We determine the de novo energy potential for pairwise interactions between protein and DNA atoms from (/) experimental measurements of the binding affinity of protein-DNA complexes and (//) crystal structures of the complexes. We show that the de novo energy potential can be used to predict the binding specificity of proteins to DNA with approximately 90% accuracy, compared to approximately 60% for the best performing alternative computational methods applied to this fundamental problem. This de novo potential method is directly extendable to other biomolecule interaction domains (enzymes and signaling molecule interactions) and to other classes of molecular interactions.
机译：压缩感测通过使用少量的所谓非相干传感器以非常高的保真度来测量复杂信号，彻底改变了信号采集。我们表明分子相互作用，例如蛋白质-DNA相互作用，可以以直接类似的方式进行分析，并具有相似的显着结果。具体而言，介观分子相互作用充当测量原子之间微观相互作用能的非相干传感器。我们将压缩感测和统计力学的概念结合起来，专门从实验测量结果确定分子系统的原子间相互作用能，从而产生“从头开始”的能量势。相反，用于估计能量势的常规方法基于以先验假设和广泛领域知识为前提的理论模型。我们从蛋白质/ DNA复合物的结合亲和力和//复合物的晶体结构的（/）实验测量值确定蛋白质和DNA原子之间成对相互作用的从头势能。我们表明，从头的能量潜力可用于预测蛋白质与DNA的结合特异性，准确性约为90％，相比之下，应用于该基本问题的最佳性能替代计算方法约为60％。这种从头方法可以直接扩展到其他生物分子相互作用域（酶和信号分子相互作用）和其他类型的分子相互作用。

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