Murugan Rajamanickam, Muñoz Victor
Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India.
Department of Bioengineering, School of Engineering, University of California Merced, California 95343, United States.
J Phys Chem B. 2025 Jul 31;129(30):7753-7765. doi: 10.1021/acs.jpcb.5c04019. Epub 2025 Jul 18.
Certain biomolecular functions require the accurate choreographing of binding events among several partners. Some examples are enzymatic reactions involving multiple sequential steps, or the DNA search for the target site performed by transcription factors. Such molecular oscillatory machines need a core protein oscillator that alternates between conformational substates to coordinate sequential binding events to partners. A productive oscillatory cycle of such a system requires the exchange between the two binding-competent conformations to occur quickly while the oscillator resides in both states for sufficient time as to facilitate binding to each target and thus ensure the right sequence of steps. The efficiency of these machines is determined by the number of productive cycles generated per unit of time. However, it is currently unclear whether achieving this type of binding choreography is feasible without coupling the process to an additional energy source. Here we investigate theoretically the technical requirements for designing the core oscillator of these machines. We looked at the oscillatory binding patterns emerging from the thermal fluctuations of a protein domain that is flexible or marginally stable, and which (un)folds in either two-state or downhill fashion. We find that the downhill scenario speeds the transition between conformational alternants, but makes the residence times in the binding-competent substates fleeting. The two-state scenario provides ample time for binding in either substate, but makes the transitions too slow and memoryless, and hence decorrelated. That is, neither a pure downhill nor a pure two-state folding protein domain can operate as an effective core oscillator. However, we do find that the oscillator can be remarkably efficient if it can interconvert between downhill and two-state scenarios in response to subtle changes in environment at an inherently high rate. We contend that such alternating downhill vs two-state interconversions might constitute an important natural design principle to attain optimal coordination of multistep processes without the need for additional energy inputs. That mechanism is consistent with what is known of how transcription factors perform their genome target searches. We further note that the oscillatory machine model outlined in this work makes predictions that are in close agreement with the experimental turnover rate of the multienzymatic pyruvate dehydrogenase complex, a paradigm of oscillatory behavior. Our observations support the significance of the downhill vs two-state conversion mechanism and its usefulness as tool for predicting or designing oscillatory machines.
某些生物分子功能需要精确编排几个分子间的结合事件。一些例子包括涉及多个连续步骤的酶促反应，或转录因子对目标位点的DNA搜索。这种分子振荡机器需要一个核心蛋白振荡器，它在构象亚态之间交替，以协调与分子伴侣的连续结合事件。这样一个系统的有效振荡周期要求在振荡器处于两种状态足够长的时间以便促进与每个靶点的结合从而确保正确的步骤顺序时，两种具有结合能力的构象之间的交换能够快速发生。这些机器的效率由每单位时间产生的有效周期数决定。然而，目前尚不清楚在不将该过程与额外能量源耦合的情况下实现这种类型的结合编排是否可行。在这里，我们从理论上研究设计这些机器核心振荡器的技术要求。我们研究了由一个灵活或接近稳定的蛋白质结构域的热涨落产生的振荡结合模式，该结构域以两态或下坡方式（去）折叠。我们发现下坡模式加快了构象交替之间的转变，但使在具有结合能力的亚态中的停留时间短暂。两态模式在任一亚态中都提供了充足的结合时间，但使转变过于缓慢且无记忆性，因此不相关。也就是说，单纯的下坡或单纯的两态折叠蛋白质结构域都不能作为有效的核心振荡器。然而，我们确实发现，如果振荡器能够以固有高频率响应环境中的细微变化在下坡和两态模式之间相互转换，那么它可以非常高效。我们认为，这种交替的下坡与两态相互转换可能构成一种重要的自然设计原则，以实现多步过程的最佳协调而无需额外的能量输入。该机制与已知的转录因子如何进行基因组靶点搜索是一致的。我们进一步指出，本文概述的振荡机器模型所做的预测与多酶丙酮酸脱氢酶复合物的实验周转速率密切一致，丙酮酸脱氢酶复合物是振荡行为的一个范例。我们的观察结果支持了下坡与两态转换机制的重要性及其作为预测或设计振荡机器工具的有用性。
