EnzymAgglo - Multiscale model-based investigation of functional enzyme and protein agglomerates for biotechnological applications.Part 2: From structure to function

近年来，基于模型的对多酶系统和蛋白质团聚过程的结构定义的理解，以及它们与功能（如活性）的关系，受到了越来越多的关注。随着近年来新的多尺度建模方法和计算能力的提高（特别是gpu），对这种大分子现象的详细研究和预测成为可能。为了实现这一目标，我们在项目的第一阶段开发了一个普遍适用的多尺度模型框架，称为“分子离散元方法（MDEM）”。具体来说，它侧重于这种系统的结构发展取决于工艺条件。它适用于大分子尺度（ms和µm），将在项目第一期的剩余时间内完成。与传统的MD相比，MDEM框架在模拟时间和/或尺度方面的速度提高了5到7个数量级，因此可以研究生物学和技术上有趣的结构现象。同时，它通过考虑特性的各向异性，保留了中尺度上必要的细节。虽然在项目的第一个阶段，该框架是使用多酶丙酮酸脱氢酶复合物（PDC）作为模型系统建立的，但它已经从其他SPP项目合作伙伴那里得到了非常积极的反馈，可以应用于许多其他过程和现象（例如，油水界面的蛋白质吸收）。已经开始并计划加强初步合作。项目第二阶段的重点将放在从结构确定功能方面扩展MDEM方法；增加规模和时间尺度；与SPP项目伙伴合作，将已开发的框架应用于新流程。为了实现这些目标，MDEM框架将与人口平衡建模相结合（例如，用于实验验证和参数研究）。此外，蛋白质-蛋白质和蛋白质-界面的相互作用将被改进和扩展，以涵盖密度效应（分子拥挤；扩散限制）和多个伙伴的竞争性相互作用。将MDEM与计算流体动力学/有限体积计算方法（包括空间分解的酶反应和代谢物扩散动力学）耦合，完成从结构到功能的推导。为了实现更高规模的模型（称为“MDEM-2”）并向工艺规模推进，将进行进一步的抽象：将稳定连接的单元（例如PDC的催化核心）抽象为一个颗粒，并使用MDEM的数据进行参数化。催化活性多酶系统的实验反馈将在内部获得，而与SPP项目合作伙伴的广泛合作正在开发和进行中，允许在各种工艺参数上改进和验证MDEM（-2）方法。

The model based understanding of the structure defining processes of multi-enzymatic systems and protein agglomeration, as well as their relation to function (e.g., activity) has received increasing interest in recent years. With new multi-scaled modeling approaches and increased computational capabilities in recent years (especially GPUs), the detailed investigation and prediction of such macromolecular phenomena comes into reach. To achieve this, we developed a generally applicable multi-scale model framework, termed “Molecular discrete element method (MDEM)”, during the first project phase.Specifically, it focuses on the structural development of such systems depending on process conditions. It applies on the macro-molecular scale (ms and µm) and will be finalized in the remaining time of the first period of the project. The MDEM framework allows investigations of biologically and technically interesting structural phenomena due to its speedup of 5 to 7 orders of magnitude with respect to simulation time and/or scale in comparison to traditional MD. At the same time, it retains the necessary detail on the meso-scale through anisotropic consideration of properties. While, during the first project phase, the framework was established using the multi-enzymatic pyruvate dehydrogenase complex (PDC) as a model system, it has received very positive feedback from other SPP project partners for applications to numerous other processes and phenomena (e.g., protein absorption at the oil-water interface). Initial collaborations have been initiated and are planned to be intensified. The focus of the second project phase will lie on expansion of the MDEM approach with respect to the determination of function from structure; increased size and time scales; and application of developed framework to new processes in collaboration with SPP project partners. To achieve these goals, the MDEM framework will be coupled to population balance modeling (e.g., for experimental validation and parameter studies). Further, protein-protein and protein-interface interaction will be refined and extended to cover density effects (molecular crowding; diffusion limitation), and competetive interaction of multiple partners. Deduction from structure to function will be done by coupling MDEM to computational fluid dynamics / finite volume computation method, including spatially resolved enzymatic reaction and metabolite diffusion kinetics. A further abstraction will take place to enable higher-scale model (termed “MDEM-2”) and push towards the process scale: Stably connected units (e.g., the catalytic core of PDC) are abstracted as one particle and parameterized using the data from MDEM. Experimental feedback for catalytically active multi-enzymatic systems will be obtained in-house, while extensive collaborations with SPP project partners are developing and ongoing, allowing to refine and verify the MDEM(-2) approach on wide variety of process parameters.