Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455-0215.
Department of Measurement and Information Systems, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25659-25667. doi: 10.1073/pnas.1902909116. Epub 2019 Nov 27.
Protein multivalency can provide increased affinity and specificity relative to monovalent counterparts, but these emergent biochemical properties and their mechanistic underpinnings are difficult to predict as a function of the biophysical properties of the multivalent binding partners. Here, we present a mathematical model that accurately simulates binding kinetics and equilibria of multivalent protein-protein interactions as a function of the kinetics of monomer-monomer binding, the structure and topology of the multidomain interacting partners, and the valency of each partner. These properties are all experimentally or computationally estimated a priori, including approximating topology with a worm-like chain model applicable to a variety of structurally disparate systems, thus making the model predictive without parameter fitting. We conceptualize multivalent binding as a protein-protein interaction network: ligand and receptor valencies determine the number of interacting species in the network, with monomer kinetics and structural properties dictating the dynamics of each species. As predicted by the model and validated by surface plasmon resonance experiments, multivalent interactions can generate several noncanonical macroscopic binding dynamics, including a transient burst of high-energy configurations during association, biphasic equilibria resulting from interligand competition at high concentrations, and multiexponential dissociation arising from differential lifetimes of distinct network species. The transient burst was only uncovered when extending our analysis to trivalent interactions due to the significantly larger network, and we were able to predictably tune burst magnitude by altering linker rigidity. This study elucidates mechanisms of multivalent binding and establishes a framework for model-guided analysis and engineering of such interactions.
蛋白质多价性相对于单价分子可以提供更高的亲和力和特异性，但这些新兴的生化特性及其潜在机制很难根据多价配体的物理化学性质来预测。在这里，我们提出了一个数学模型，可以准确地模拟多价蛋白-蛋白相互作用的结合动力学和平衡，作为单体-单体结合动力学、多结构域相互作用伙伴的结构和拓扑结构以及每个伙伴的价态的函数。这些性质都是通过实验或计算预先估计的，包括用适用于各种结构差异系统的蠕虫链模型来近似拓扑，从而使模型具有预测性而无需参数拟合。我们将多价结合概念化为蛋白质-蛋白质相互作用网络：配体和受体的价态决定了网络中相互作用的物种数量，单体动力学和结构特性决定了每个物种的动力学。正如模型所预测并通过表面等离子体共振实验验证的那样，多价相互作用可以产生几种非典型的宏观结合动力学，包括在结合过程中高能构象的短暂爆发、由于高浓度下配体间竞争导致的双相平衡以及由于不同网络物种的不同寿命导致的多指数解离。由于网络显著增大，只有在将我们的分析扩展到三价相互作用时，才能发现短暂爆发，并且我们能够通过改变连接体的刚性来可预测地调节爆发幅度。这项研究阐明了多价结合的机制，并为这种相互作用的模型指导分析和工程奠定了框架。
