Catassembly

One important objective of molecular assembly research is to create highly complex functional molecular systems capable of responding, adapting, and evolving. Compared with living systems, the artificial systems are still rather primitive and are far away from realizing these features. Nature is by far the most important source of inspiration for designing and creating such systems. It has been shown that the assembly of many biological complexes is ‘’catalysed’’ by other molecules, such as molecular chaperones, rather than relying solely on self-assembly.

The concept of “catassembly”

Drawing inspiration from catalysis in chemistry, we pioneered the concept of “catassembly” as a new strategy towards the construction of complex assembly systems. It proposes to employ catassemblers (molecules or assemblies) act as “catalysts” for the assembly process. The catassemblers can accelerate the assembly and/or guide it towards a specific pathway, i.e., high efficiency and/or selectivity. Once the assembly is complete, the catassemblers are absent from the final product. The verb and adjective forms of catassembly are “catassemble” and “catassembled” (Fig.1).

Fig.1 Cartoons of the construction of a floating bridge that illustrate why catassembly is more efficient than self-assembly. Panels a to c represent a self-assembly process, which requires many hours to form a floating bridge. In contrast, with the assistance of porters and builders (corresponding to two kinds of catassemblers), a bridge can be built in 1 hour (panels d and e). After the first bridge is completed, the workers leave it and build other bridges somewhere else (panel f). The more complex the assembly, the more catassembly is required (panel g). To build a complex, multi-functional bridge requires the collaborative work of many workers (such as builders, sentries, transporters, coordinators etc.). Multiple catassemblers are required with varying participation timelines and functions for complex assembly systems.

The significance of catassembly in molecular assembly mirrors that of catalysis in chemical reactions. While simple assembly relies on spontaneous interactions among assembly units, achieving complex assemblies with multiple steps and pathways through spontaneous assembly alone is nearly impracticable. Therefore, assisted assembly strategies such as catassembly are indispensable. Indeed, the construction of intricate biological assemblies extensively employs catassembly strategies, leveraging the synergy of matter, energy, and information. Consequently, the concept and techniques of catassembly are poised to play a pivotal role in propelling artificial molecular assembly from simplicity to complexity.

Suggested models for catassembly

Fig. 2 Three possible models of artificial catassembly. (A) the catassembler act as a protective agent, stabilizing subunit A and accelerating its folding and assembly with subunit B. (B) The catassembler function as an activator. It activates subunit A by exposing the binding sites for subunit B, then the allosteric assembly of A and B releases the catassembler. (C) The catassembler needs to be activated by energy input, then functions as activator for the assembly of subunits A and B.

In the first suggested model (Fig. 2A), the catassembler can prevent subunits A from self-formation through irregular interactions, promoting A and B to bind accurately. Subunit B will replace the catassembler and release it from the complex. Catassemblers can act as activators for molecular assembly as the second model (Fig. 2B), The direct assembly of subunits A and B is hindered due to the concealment of their interaction sites. The introduction of a catassembler initiates the assembly process. The catassembler binds to subunit A in an allosteric manner, thereby exposing the binding sites on subunit A. Subsequently, the activated subunit A interacts with subunit B, forming the complex AB. The binding of A and B weakens the interactions between A and the catassembler, resulting in the release of the catassembler. The catassembler then proceeds to locate a new subunit A and starts a new cycle. Furthermore, catassembly can be powered by external energy as the third model. The energy inputs could be in the form of chemical energy, light, electrical energy, etc. Assuming a catassembler exists in a deactivated state, as shown in Fig. 2C, the energy input can activate the catassembler, initiating a catassembly cycle like Fig. 2B. After the assembly finishes, the deactivated catassembler is then released from the product and can be reactivated by further energy input.

It should be noted that catassemblers differ from co-assembly in that they do not become a part of the final product and can be reused, making catassembly more efficient. The leaving and recycling of catassemblers are crucial in this process. We proposed four possible leaving and recycling mechanisms for catassemblers. 1) The catassembler shares the binding site with other subunits and can be replaced by them at the end of the assembly process (Fig. 2A). 2) The completion of the assembly weakens the binding between the catassembler and the subunits, eventually causing the catassembler to detach (Fig. 2B). 3) The catassembler and final assembly product undergo phase separation (for instance, precipitation), with the product separated into another phase and the catassembler remaining with residual subunits. 4) The recycling of the catassembler is powered by energy input.

Catassembly and catalysis belong to a big family but may have some distinct principles based on the famous essay "More Is Different" by P. W. Anderson. Catassembly could be a much more complicated process based on noncovalent interactions, featuring synergistic multivalent and multicomponent interactions, and long-range feedback. These features are essential to construct hierarchical structures which can eventually emerge new properties and functions, which have yet to be the focus of chemical catalysis. Therefore, it could be highly desirable to make a great effort to develop and even establish fundamental principles, theoretical framework and characterization tools for catassembly. This approach may also initiate reforms in conventional catalysis theory and develop strategies integrating covalent synthesis and noncovalent assembly to construct complex molecular systems.

分子组装研究的一个重要目标，是构建能够响应、适应和演化的高度复杂功能分子体系。与生命体系相比，人工体系仍然相当原始，距离实现这些特征还很遥远。自然界迄今仍是设计和构建此类体系最重要的灵感来源。研究表明，许多生物复合体的组装是由分子伴侣等其他分子“催化”的，而不是仅仅依赖自组装。

“催组装”的概念

受化学中催化思想的启发，我们率先提出“催组装”（catassembly）概念，作为构建复杂组装体系的新策略。该概念提出使用催组装体（分子或组装体）作为组装过程的“催化剂”。催组装体能够加速组装和/或引导组装进入特定路径，即提高效率和/或选择性。一旦组装完成，催组装体不会出现在最终产物中。catassembly 的动词和形容词形式分别为 “catassemble” 和 “catassembled”（图 1）。

图 1. 浮桥建造的卡通示意，用于说明为什么催组装比自组装更高效。a 到 c 表示自组装过程，需要许多小时才能形成一座浮桥。相比之下，在搬运者和建造者（对应两类催组装体）的帮助下，一座桥可以在 1 小时内建成（d 和 e）。第一座桥完成后，工人离开并在其他地方建造新的桥（f）。组装越复杂，越需要催组装（g）。建造复杂的多功能桥需要许多工人（如建造者、哨兵、运输者、协调者等）协同工作。复杂组装体系需要多个催组装体，它们具有不同的参与时间线和功能。

催组装在分子组装中的意义类似于催化在化学反应中的意义。简单组装依赖组装单元之间的自发相互作用，而仅通过自发组装实现具有多步骤和多路径的复杂组装几乎不可行。因此，催组装等辅助组装策略不可或缺。事实上，复杂生物组装体的构建广泛采用催组装策略，并利用物质、能量和信息的协同作用。因此，催组装的概念和技术有望在推动人工分子组装从简单走向复杂的过程中发挥关键作用。

催组装的建议模型

图 2. 人工催组装的三种可能模型。(A) 催组装体作为保护剂，稳定亚基 A，并加速其折叠以及与亚基 B 的组装。(B) 催组装体作为激活剂发挥作用。它通过暴露亚基 B 的结合位点来激活亚基 A，随后 A 和 B 的变构组装释放催组装体。(C) 催组装体需要通过能量输入被激活，随后作为亚基 A 和 B 组装的激活剂发挥作用。

在第一个建议模型中（图 2A），催组装体可以防止亚基 A 通过不规则相互作用发生自形成，从而促进 A 和 B 准确结合。亚基 B 将取代催组装体，并将其从复合物中释放出来。在第二个模型中（图 2B），催组装体可以作为分子组装的激活剂。由于相互作用位点被隐藏，亚基 A 和 B 的直接组装受到阻碍。催组装体的引入启动组装过程。催组装体以变构方式结合亚基 A，从而暴露亚基 A 上的结合位点。随后，被激活的亚基 A 与亚基 B 相互作用，形成复合物 AB。A 和 B 的结合削弱了 A 与催组装体之间的相互作用，从而导致催组装体释放。随后，催组装体继续寻找新的亚基 A，并开始新的循环。此外，在第三个模型中，催组装可以由外部能量驱动。能量输入可以是化学能、光能、电能等形式。假设催组装体如图 2C 所示处于失活状态，能量输入可以激活催组装体，并启动类似图 2B 的催组装循环。组装完成后，失活的催组装体从产物中释放，并可通过进一步能量输入重新激活。

需要指出的是，催组装体不同于共组装，因为它们不会成为最终产物的一部分，并且可以被重复利用，从而使催组装更高效。催组装体的离去和循环利用在这一过程中至关重要。我们提出了催组装体离去和循环利用的四种可能机制。1) 催组装体与其他亚基共享结合位点，并可在组装过程结束时被其他亚基取代（图 2A）。2) 组装完成削弱催组装体与亚基之间的结合，最终导致催组装体脱离（图 2B）。3) 催组装体与最终组装产物发生相分离（例如沉淀），产物进入另一相，而催组装体与剩余亚基留在原相中。4) 催组装体的循环利用由能量输入驱动。

催组装和催化属于一个大家族，但基于 P. W. Anderson 著名文章 “More Is Different” 的观点，它们可能具有一些不同的原则。催组装可能是一个更加复杂的过程，基于非共价相互作用，并具有协同多价和多组分相互作用以及长程反馈等特征。这些特征对于构建层级结构至关重要，而层级结构最终能够涌现新的性质和功能，但这些尚未成为化学催化关注的重点。因此，非常有必要大力发展甚至建立催组装的基本原理、理论框架和表征工具。这一方法也可能推动传统催化理论的革新，并发展整合共价合成与非共价组装的策略，以构建复杂分子体系。