Most proteins have evolved to spontaneously fold into native structure and specifically bind with their partners for the purpose of fulfilling biological functions. According to Darwin, protein sequences evolve through random mutations, and only the fittest survives. The understanding of how the evolutionary selection sculpts the interaction patterns for both biomolecular folding and binding is still challenging. In this study, we incorporated the constraint of functional binding into the selection fitness based on the principle of minimal frustration for the underlying biomolecular interactions. Thermodynamic stability and kinetic accessibility were derived and quantified from a global funneled energy landscape that satisfies the requirements of both the folding into the stable structure and binding with the specific partner. The evolution proceeds via a bowl-like evolution energy landscape in the sequence space with a closed-ring attractor at the bottom. The sequence space is increasingly reduced until this ring attractor is reached. The molecular-interaction patterns responsible for folding and binding are identified from the evolved sequences, respectively. The residual positions participating in the interactions responsible for folding are highly conserved and maintain the hydrophobic core under additional evolutionary constraints of functional binding. The positions responsible for binding constitute a distributed network via coupling conservations that determine the specificity of binding with the partner. This work unifies the principles of protein binding and evolution under minimal frustration and sheds light on the evolutionary design of proteins for functions.

大多数蛋白质已经进化为自发折叠成天然结构并与其伴侣特异性结合以实现生物学功能。根据达尔文的观点，蛋白质序列通过随机突变进化，只有适者生存。了解进化选择如何塑造生物分子折叠和结合的相互作用模式仍然具有挑战性。在这项研究中，我们基于潜在生物分子相互作用的最小挫败原则，将功能结合的约束纳入选择适合度中。热力学稳定性和动力学可及性是从全球漏斗能量景观中导出和量化的，满足折叠成稳定结构和与特定伙伴结合的要求。进化通过序列空间中的碗状进化能量景观进行，底部有一个闭环吸引子。序列空间逐渐减小，直到到达该环吸引子。分别从进化的序列中识别出负责折叠和结合的分子相互作用模式。参与负责折叠的相互作用的残余位置是高度保守的，并且在功能结合的额外进化限制下维持疏水核心。负责结合的位置通过耦合守恒构成了一个分布式网络，耦合守恒决定了与伙伴的结合的特异性。这项工作在最小的挫折下统一了蛋白质结合和进化的原理，并揭示了蛋白质功能的进化设计。