Theoretical and experimental investigation of multi-domain protein folding and conformational dynamics

项目总结 正确的折叠对于获得蛋白质独特的三维结构至关重要，而构象 蛋白质的动力学在其生物学功能中起着重要作用。尽管已经取得了重大进展 在理解单域蛋白质的折叠/展开和构象动力学方面取得了进展，这些 多结构域蛋白质的两个基本过程在很大程度上仍未被探索，这已经被提出。 占所有真核生物蛋白质的80%。因此，我们在认识上存在着很大的差距 大多数人类的折叠/展开和构象动力学的潜在机制 我们试图通过理论和实验研究来解决这些不确定性。在这 提议，我们制定了一项全面的战略来回答上述深入的机制上的未知 通过随后的实验验证的能量景观方法获得多结构域蛋白质。这个 能源格局方法通过建立 揭示潜在机制的理论模型。通过建立微观能源景观 和基于结构的模型，我们将阐明DPO4的折叠/去折叠机制，一个多结构域， Y家族DNA聚合酶在体外和体内对绕过未修复的DNA损伤至关重要(这里指的是 模拟体内条件)，并预测在不同条件下可能的中间状态和临界残留物 环境，包括核糖体(共翻译)和聚集剂(体内)的存在 作为不同的热和化学变性剂条件。通过我们的微观能源格局和 基于结构的模型，我们将揭示不同结构之间构象变化的潜在机制 定量研究DPO4与DNA或蛋白质复制因子--增殖细胞核抗原结合时的构象状态 对功能至关重要的稳定性、动力学和结构热点。理论模型预测将是 通过停流、圆二向色性、荧光能量转移等测试和验证 光谱实验。该提案产生的结果将推动DNA聚合酶领域的发展 虽然这里开发的方法是通用的，可以作为研究折叠/展开的框架 以及其他多结构域蛋白的构象动力学。此外，蛋白质的错综复杂 我们建议的研究揭示的折叠/展开和构象转变将有助于蛋白质的设计 和药物发现。

PROJECT SUMMARY Proper folding is crucial to achieving a protein’s unique three dimensional structure while the conformational dynamics of the protein play a major role in its biological function. Although significant progress has been made in understanding the folding/unfolding and conformational dynamics for single-domain proteins, these two fundamental processes remain largely unexplored for multi-domain proteins, which have been suggested to account for up to 80% of all eukaryotic proteins. Therefore, a significant disparity exists in our understanding of the underlying mechanisms of folding/unfolding and conformational dynamics for the majority of human proteins and we seek to address these uncertainties through theoretical and experimental investigation. In this proposal, we devise a comprehensive strategy to answer the above, in-depth mechanistic unknowns regarding multi-domain proteins through an energy landscape approach with subsequent experimental validation. The energy landscape approach significantly improves technical capabilities through the establishment of theoretical models for uncovering underlying mechanisms. By establishing the microscopic energy landscape and structure based models, we will elucidate the folding/unfolding mechanisms of DPO4, a multi-domain, model Y-family DNA polymerase critical for bypassing unrepaired DNA lesions, in vitro and in vivo (here means mimicking in vivo conditions), and predict possible intermediate states and critical residues under various environments, including the presence of the ribosome (co-translational) and a crowding agent (in vivo), as well as different thermal and chemical denaturant conditions. Through our microscopic energy landscape and structure based models, we will reveal the underlying mechanisms of conformational changes between various conformational states of DPO4 upon binding to DNA or a protein replication factor PCNA through quantifying the stability, kinetics, and structural hot spots critical for function. The theoretical model predictions will be tested and validated through stopped-flow, circular dichroism, fluorescence energy transfer, and other spectroscopic experiments. The results generated from the proposal will advance the DNA polymerase field while the methods developed here are general and can serve as a framework for studies of folding/unfolding and conformational dynamics of other multi-domain proteins. Moreover, the intricacies of protein folding/unfolding and conformational transitions revealed by our proposed studies will facilitate protein design and drug discovery.