Fast Computations for Structural Transitions in Proteins

描述（由申请人提供）：缺乏对蛋白质构象转变的可靠描述代表了结构生物学知识体系中的一个关键空白。从酶到运动蛋白，构象转变不仅是许多蛋白质功能的核心，而且结构中间体也作为过渡状态抑制剂药物的一类公认的靶标。因此，我们提出了一种新的计算方法来研究(a)钙调蛋白（CAM）和(b)肌凝蛋白（引起肌肉收缩的蛋白质马达）中戏剧性的构象转变。钙调蛋白介导从基因表达到肌肉收缩到有丝分裂的基本过程。新方案将建立在非常有希望的初步结果的基础上，这些结果展示了前所未有的生理时间尺度。结合残基水平建模和精细网格离散化，该方法已经被证明能够无偏动态模拟钙调蛋白的两个72残基结构域中的几十个构象转变。实际上，该协议每天在便宜的单处理器台式计算机上生成几个转换事件。这种高效率将使研究肌凝蛋白在有限的计算机资源。一个多层次的建模方法是这个建议的核心。从最初的“粗粒度”模型（例如，残留物水平）产生的结果将使用一系列逐渐更精确的力场进行细化。结合离散化实现的高质量采样，多层次建模将使计算数据具有高度的置信度。事实上，模拟结果——包括结构中间体模型和动力学临界残留物的特性——将用于设计实验（由合作者执行），旨在提高我们对结构事件的详细理解。由于其速度和简单性，新协议为专家和非专家都有价值的软件工具提供了理想的基础。提出了一个详细的分发用户友好软件包的计划，并且源代码将供专家用户修改。

DESCRIPTION (provided by applicant): The lack of reliable descriptions of conformational transitions in proteins represents a critical gap in the body of structural biology knowledge. Not only are conformational transitions at the heart of many proteins' functions --- from enzymes to motor proteins --- but structural intermediates also serve as a well-established class of targets for transition-state inhibitor drugs. We therefore propose a novel computational approach to study the dramatic conformational transitions in (a) calmodulin (CAM), which mediates essential processes from gene expression to muscle contraction to mitosis, and (b) myosin, the protein motor that causes muscle contraction. The new protocol will build on extremely promising preliminary results, which demonstrate unprecedented access to physiological timescales. Combining residue-level modeling and fine-grid discretization, the approach has already proven capable of unbiased dynamic simulation of dozens of conformational transitions in each of the two 72-residue domains of calmodulin. In fact, the protocol generates several transition events per day on an inexpensive, single-processor desktop computer. This high efficiency will enable the study of myosin with modest computer resources. A multi-level approach to modeling is central to this proposal. Results generated from initial "coarse grained" models (e.g., residue-level) will be refined using a series of progressively more accurate force fields. Combined with the high-quality sampling enabled by discretization, multi-level modeling will permit a high degree of confidence in the computational data. Indeed, the simulation results --- including models of structural intermediates and the identities of kinetically critical residues --- will be used to design experiments (to be performed by collaborators) aimed toward improving our detailed understanding of structural events. Because of its speed and simplicity, the new protocol forms an ideal basis for a software tool of value to expert and non-expert alike. A detailed plan for distributing user-friendly software packages is presented, and the source code will be available for modification by expert users.