Structure, Disorder and Dynamics in Crambin Crystals at Resolution

这项提议的目标是获得蛋白质及其溶剂的原子分辨率图像，并测试分子动力学计算对结构中原子的平均位置和迁移率的模拟情况。这可以通过使用衍射法确定蛋白质的振动和平衡结构以及通过使用经验力场从理论上来实现。Crambin是一种疏水性的植物蛋白(MW=4720)，它的独特之处在于它的衍射率超过0.83A，在这个分辨率极限下可以观察到99%的衍射数据。这意味着它的结构可以被确定，而不受蛋白质提纯的通常限制。虽然目前尚不清楚Crambin的功能，但它作为一种局部麻醉剂具有活性。上述目标将通过以下具体手段使用CRAMBIN来实现：针对0.83A、130K和0.945 A、300K X射线数据对CRAMBIN模型进行不受限制的改进；300K时中子和X射线数据的共同改进；多种温度下CRAMBIN X射线数据的改进；全晶体分子动力学模拟和与X射线结构的比较；对蛋白质水结构预测方法进行了分析。这个项目提供了一个独特的机会，利用单晶X射线衍射获得蛋白质分子及其周围溶剂的实验图像，以及它的动态运动的极其清晰的细节。所揭示的精细特征可以对照目前用于预测和改进蛋白质结构的理论进行测试。事实上，克拉姆宾的晶体非常有序，这使得这些细节的确定和测试成为可能。

The goal of this proposal is to obtain a picture of a protein and its solvent at atomic resolution and to test how well the average position and mobility of atoms in the structure are modeled by molecular dynamics calculations. This can be accomplished experimentally by determining the protein's vibration and equilibrium structure using diffraction methods and theoretically by using empirical force fields. Crambin is a hydrophobic, plant protein (MW = 4720) that is unique because it diffracts beyond 0.83 A and has 99% of its diffraction data observed at this resolution limit. This means its structure can be determined free of the usual restraints of protein refinement. Although crambin's function is not yet known, it has activity as a local anesthetic. The above goal will be addressed using crambin by the following specific means: unrestrained refinement of the crambin model against the 0.83 A, 130 K and the 0.945 A, 300 K X-ray data; corefinement of neutron and X-ray data at 300 K; refinement of crambin X-ray data at multiple temperatures; full-crystal molecular dynamics simulations and comparison with the X-ray structure; and analysis of the methods to predict protein water structure. %%% This project provides a unique opportunity to obtain an experimental picture of a protein molecule, its surrounding solvent, and its dynamic movement in extremely sharp detail using single crystal X-ray diffraction. The fine features that are revealed can be tested against theories that are currently being used to predict and refine the architecture of proteins. The fact that crystals of crambin are extremely well ordered make possible the determination and testing of these details.