能量涨落塑造非特异性生物分子相互作用的自由能
Energy fluctuations shape free energy of nonspecific biomolecular interactions
摘要：
了解生物分子识别的设计原理是分子生物学的一个关键问题。然而，生物分子的巨大复杂性和多样性阻碍了获得蛋白质-蛋白质、蛋白质-DNA和蛋白质-RNA结合的自由能的预测能力的努力。在这里，使用德里达模型的一个变体，我们预测，对于一大类生物分子相互作用，它是可以准确地估计的相对自由能结合的基础上，其能量谱的波动特性，即使是有限数量的能级是已知的。我们发现，具有较宽的结合能谱的系统的自由能几乎肯定比具有较窄的能谱的系统的自由能低。我们的预测意味着，低亲和力结合分数，通常浪费在蛋白质-蛋白质和蛋白质-DNA对接算法，可以有效地利用计算的自由能。使用Andre等人的蛋白质相互作用的Rosetta对接模拟结果，Proc. Natl. Acad. Sci. U.S.A. 105，16148（2008），我们证明了我们预测的力量。
英文摘要：
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of protein-protein, protein-DNA, and protein-RNA binding. Here, using a variant of the Derrida model, we predict that for a large class of biomolecular interactions, it is possible to accurately estimate the relative free energy of binding based on the fluctuation properties of their energy spectra, even if a finite number of the energy levels is known. We show that the free energy of the system possessing a wider binding energy spectrum is almost surely lower compared with the system possessing a narrower energy spectrum. Our predictions imply that low-affinity binding scores, usually wasted in protein-protein and protein-DNA docking algorithms, can be efficiently utilized to compute the free energy. Using the results of Rosetta docking simulations of protein-protein interactions from Andre et al., Proc. Natl. Acad. Sci. U.S.A. 105, 16148 (2008), we demonstrate the power of our predictions.
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