The Role of 'Dynamics Motifs' in Modulating Specificity in PDZ Domains

PDZ结构域是人类蛋白质组中最丰富的蛋白质之一，对正常细胞生理学至关重要。毫不奇怪，序列或表达中的错误导致从罕见的Usher综合征到结肠癌的许多疾病状态。然而，我们很难理解PDZ结构域驱动的混杂蛋白质-蛋白质相互作用，并且仍然没有明确的分子机制来详细描述PDZ结构域配体识别。域显示出更高的多样性，在合作伙伴比预测，访问范围广泛的亲和力，并可能从事以前未知的变构信号。随着我们对PDZ结构域结合偏好的了解的增加，关于PDZ结构域特异性的想法证明是不完整的。这是因为蛋白质不是可以立即衍生功能的静态结构。相反，折叠的蛋白质是动态的平均结构周围产生的天然状态构象的合奏。越来越多的证据表明，自然状态的运动或动力学对功能至关重要。像蛋白质结构的其他方面一样，蛋白质动力学可能处于进化压力下，以优化或微调特定任务。在这个建议中，我们的目标是扩大传统的概念的结构功能轴，包括动态。我们提出了以下假设：PDZ结构域配体识别是由其结构的侧链动力学（SCD）的特定分布，即其“动力学基序”调制。我们用三个目标来检验我们的假设。在目标#1中，我们将访问SCD的进化压力，并将其与在PDZ结构域家族中观察到的功能差异联系起来。在目标#2中，我们寻求找到相关运动，因为它们是蛋白质长距离通讯而无需构象变化的合理机制。最后，在目标#3中，我们设计了一个“混合”PDZ结构域，并测试了长距离动态变化可能会改变界面结合偏好。在这个提议中，我们希望确定SCD是否在确定PDZ结构域特异性中起作用，以及动力学传递特异性的机制。我们是由更好地理解PDZ结构域结合允许合理的药物设计和蛋白质设计的基本原理驱动的。此外，PDZ结构域相互作用可以作为许多混杂蛋白质-蛋白质相互作用的模型系统。

PDZ domains are one of the most abundant proteins in the human proteome and are essential to normal cellular physiology. Not surprisingly, errors in either sequence or expression lead to a number of disease states ranging from the rare Usher's Syndrome to Colon Cancer. Yet, we struggle to understand the promiscuous protein-protein interactions which PDZ domains drive and there remains no clear molecular mechanism which details PDZ domain ligand recognition. Domains show a higher diversity in partners than predicted, access a wide range of affinities, and might engage in previously unknown allosteric signaling. As our knowledge of PDZ domain binding preferences increases, ideas about PDZ domains specificity from x-ray structure prove incomplete. This is because proteins are not static structures from which function might be immediately derived. Instead, folded proteins are dynamic around an average structure producing an ensemble of native state conformations. Increasing evidence demonstrates that the motions, or dynamics, of the native state are essential for function. Like other facets of protein architecture, protein dynamics may be under evolutionary pressure to optimize or fine tune a specific task. In this proposal, we have the objective of expanding the traditional notion of a structure-function axis to include dynamics. We put forth the following hypothesis: PDZ domain ligand recognition is modulated by the specific distribution of side-chain dynamics (SCD) of its structure, i.e. its 'dynamics motif'. We test our hypothesis with three aims. In Aim #1, we will access the evolutionary pressure on SCD and relate this to functional differences observed across the PDZ domain family. In Aim #2, we seek to find correlated motions as they are a plausible mechanism for long distance communication in proteins without the need for conformational change. And finally, in Aim #3, we design a 'hybrid' PDZ domain and test how long distance alterations in dynamics may alter the interface binding preferences. In this proposal, we expect to determine if SCD have a role in determining PDZ domain specificity, and further, the mechanism with which dynamics convey specificity. We are driven by the rationale that better understanding of PDZ domain binding allows for rational drug design and protein design. And further, PDZ domain interaction may serve as a model system for many promiscuous protein-protein interactions.