Concerted membrane diffraction and simulation studies

描述（申请人提供）：准确定量描述膜活性蛋白和肽与膜界面的相互作用对于理解许多重要问题是重要的，包括膜结合结构域如何与膜相互作用以将信号转导蛋白靶向到各种亚细胞区室，白喉毒素T结构域的膜上的pH诱导的重折叠如何引起高电荷螺旋穿过脂质双层，以及更简单的毒素和抗菌肽如何渗透膜。发展定量描述的最具挑战性的方面之一是缺乏用于观察流体脂质膜中分子相互作用的结构方法。本研究项目的总体目标是开发和利用这种方法来解释在分子水平上的肽-双层相互作用能的测量。这些新的方法涉及协同使用的分子动力学模拟和x射线和中子衍射测量，以获得动态结构图像的肽双层相互作用的热无序膜。我们的具体目标是（1）推进一种新的衍射方法的发展-分子动力学/绝对尺度（MoDAS）精修-以获得在原子水平上与热无序脂质双层相互作用的肽的动态结构图像，（2）阐明疏水和静电相互作用如何在膜界面共同作用以介导蛋白质-脂质相互作用，（3）通过建立肽在膜界面的结构背景，改进预测肽在膜界面结合和折叠的物理化学规则，以及（4）使用中子衍射实验，量子化学计算和MD模拟来深入了解色氨酸侧链对膜界面的偏好。

DESCRIPTION (provided by applicant): Accurate quantitative descriptions of the interactions of membrane-active proteins and peptides with membrane interfaces is important for understanding many important problems, including how membrane binding domains interact with membranes to target signal transduction proteins to various subcellular compartments, how pH-induced refolding on membranes of the diphtheria toxin T-domain cause highly charged helices to cross lipid bilayers, and how simpler toxins and antimicrobial peptides permeabilize membranes. One of the most challenging aspects of the development of quantitative descriptions is the shortage of structural methods for observing molecular interactions in fluid lipid membranes. The general goal of this research project is the development and exploitation of such methods for interpreting measurements of peptide-bilayer interaction energies at the molecular level. These new methods involve the concerted use of molecular dynamics simulations and x-ray & neutron diffraction measurements to obtain dynamic structural images of peptide-bilayer interactions in thermally disordered membranes. Our specific aims are to (1) advance the development of a novel diffraction method--Molecular Dynamics/Absolute Scale (MoDAS) refinement--in order to gain dynamic structural images of peptides interacting at the atomic level with thermally disordered lipid bilayers, (2) clarify how hydrophobic and electrostatic interactions work together at membrane interfaces to mediate protein-lipid interactions, (3) improve physicochemical rules for predicting the binding and folding of peptides at membrane interfaces by establishing a structural context for them, and (4) use neutron diffraction experiments, quantum chemical calculations, and MD simulations to gain insights into the preference of tryptophan side chains for the membrane interface.