Computational analysis of protein/membrane interactions

描述（由申请人提供）：细胞生物学的一个基本问题是如何实现和调节细胞膜上的蛋白质募集。拟议研究的长期目标是表征外周膜蛋白与磷脂膜结合的结构和能量基础，进而更好地了解细胞中膜介导事件的生物物理基础。总体策略基于两种不同的计算方法：1)计算蛋白质和膜之间的物理相互作用，以及2)用于序列分析，结构比较和结构预测的生物信息学工具。通过平行研究不同的膜相互作用蛋白，将验证两个假设：1)两种物理因素-静电和疏水性-是膜结合的主要决定因素；2)这些物理因素表现为序列、结构和生物物理特征的模式，可用于预测膜靶向电位。第一个具体目标是描述非特异性静电和疏水相互作用如何介导分泌磷脂酶A2所表现出的广泛的膜结合行为。第二个具体目标是了解静电相互作用在钙依赖和独立的C2结构域膜结合中的作用。第三个具体目标是建立磷酸肌苷的结构模型，磷酸肌苷是一类重要的信号脂类。第四个具体目标是确定普莱克斯汀同源（PH）结构域与含磷酸肌苷的膜的特异性和非特异性相互作用的能量基础。通过与实验组的合作，计算结果将用于实验的设计和解释，并将导致可用于检测蛋白质中膜靶向基元的规则。分泌的磷脂酶A2与炎症有关，含有C2和PH结构域的蛋白参与磷酸肌苷信号传导与肿瘤发生有关；这些蛋白质需要膜结合才能发挥作用。因此，对控制膜结合的分子机制的详细了解将有助于合理设计抑制膜结合的药物。

DESCRIPTION (provided by applicant): A fundamental question in cell biology is how the recruitment of proteins to cellular membranes is achieved and regulated. The long term objective of the proposed research is to characterize the structural and energetic basis for the binding of peripheral membrane proteins to phospholipid membranes and, in turn, to better understand the biophysical basis of membrane-mediated events in cells. The overall strategy is based on two distinct computational approaches: 1) the calculation of the physical interactions between proteins and membranes, and 2) bioinformatics tools for sequence analysis, structure comparison and structure prediction. By studying different membrane-interacting proteins in parallel, two hypotheses will be tested: 1) that two physical factors-electrostatics and hydrophobicity-are the major determinants of membrane binding, and 2) that these physical factors are manifested as patterns in sequence, structure and biophysical characteristics that can be used to predict membrane targeting potential. The first specific aim is to describe how nonspecific electrostatic and hydrophobic interactions mediate the wide range of membrane binding behaviors exhibited by secreted phospholipases A2. The second specific aim is to understand the role of electrostatic interactions in the calcium-dependent and independent membrane binding of C2 domains. The third specific aim is to develop structural models for phosphoinositides, an important class of signaling lipids. The fourth specific aim is to determine the energetic basis of both the specific and non-specific interactions of pleckstrin homology (PH) domains with membranes containing phosphoinositides. The computational results will be used in the design and interpretation of experiments through collaborations with experimental groups and will lead to rules that can be used to detect membrane targeting motifs in proteins. Secreted phospholipases A2 have been implicated in inflammation, and C2 and PH domain-containing proteins involved in phosphoinositide signaling have been implicated in oncogenesis; these proteins require membrane association for their function. Thus, a detailed understanding of the molecular mechanisms underlying the control of membrane association would facilitate the rational design of drugs that inhibit membrane binding.