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，这是结构生物学知识体系中的一个严重缺口。构象转变不仅是许多蛋白质功能的核心-从酶到马达蛋白质-而且结构中间体也是过渡状态抑制剂药物的一类公认的靶点。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)肌球蛋白的戏剧性构象转变，钙调蛋白参与从基因表达到肌肉收缩再到有丝分裂的重要过程，而肌球蛋白是导致肌肉收缩的蛋白质马达。新的协议将建立在非常有希望的初步结果的基础上，这些结果证明了前所未有的获得生理时间尺度的机会。结合残基水平的建模和精细网格离散，该方法已经被证明能够无偏地动态模拟钙调蛋白的两个72个残基结构域中的数十个构象转变。事实上，该协议每天在一台廉价的单处理器台式计算机上生成几个转换事件。这种高效率将使肌球蛋白的研究能够用最少的计算机资源。多层次的建模方法是这一提议的核心。从初始的“粗粒”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改进。与离散化实现的高质量采样相结合，多水平建模将允许计算数据具有高度的置信度。事实上，模拟结果-包括结构中间体的模型和动力学关键残基的身份--将被用于设计旨在改善我们对结构事件的详细理解的实验(将由合作者执行)。由于其速度和简单性，新协议形成了对专家和非专家都有价值的软件工具的理想基础。提出了分发用户友好的软件包的详细计划，并将提供源代码供专家用户修改。

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.