生物识别网络的能量代价与优化设计
The energy cost and optimal design of networks for biological discrimination
摘要：
许多生物过程通过动力学校正机制区分正确和不正确的底物，该机制以较高的能量耗散为代价实现较低的误差。阐明物理化学约束的整体最小化的耗散和错误是很重要的理解酶的进化。在这里，我们从理论上确定了一个基本的错误成本约束，它严格限制了任何参数变化下的校对网络的性能，保持基板之间的速率歧视。结合是动力学控制的，即完全由潜在的自由能景观上的过渡态能量之间的差异决定。结合三个生物过程的重要性进行了分析。通过T7 DNA聚合酶的DNA复制被证明是接近优化的，即其动力学参数将其放置在误差成本界限的紧邻处。E.大肠杆菌也接近该界限，但由于需要反应速度，进一步优化受到阻碍。相反，E.大肠杆菌核糖体在高耗散状态下运作，可能是为了加速蛋白质的产生。总之，这些发现建立了一个基本的错误耗散关系的生物校对网络，并提供了一个理论框架，研究错误耗散权衡在其他系统与生物歧视。
英文摘要：
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify theoretically a fundamental error-cost bound which tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analyzed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized, i.e. its kinetic parameters place it in the immediate proximity of the error-cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound, but further optimization is prevented by the need for reaction speed. In contrast, E. coli ribosome operates in a high-dissipation regime, potentially in order to speed up protein production. Together, these findings establish a fundamental error-dissipation relation in biological proofreading networks and provide a theoretical framework for studying error-dissipation trade-off in other systems with biological discrimination.
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