Molecular Modeling of Ion Channel and Other Membrane Proteins

分子建模核心与细胞生物学实验室的罗伯特·盖斯博士部门有着长期的合作。我们采用进化的方法来研究离子通道蛋白，通过制作每个亚家族的代表性模型来研究K通道伴随着Na和Ca~(2+)通道的结构变化。为此，我们最近发表了原核生物NaChBac通道的模型，它是祖先K通道与后代Na和Ca~(2+)通道之间的进化联系。这些模型解释了决定特定离子选择性的孔隙中氨基酸残基类型的微妙平衡，以及电压传感器和活化门的耦合。我们现在正在利用这些结果作为垫脚石来模拟更复杂的真核细胞的钠和钙通道。在与实验小组的合作中，我们将使用这些模型来分析钙通道阻滞剂的分子药理学(在治疗人类高血压和心脏病以及潜在的抗真菌剂方面很重要)，并更好地了解与遗传疾病相关的突变如何改变钙通道的门控特性。最近，我们还回顾了我们过去的工作，模拟与阿尔茨海默病相关的淀粉样β蛋白多肽(ABP)形成的离子通道结构。虽然过去人们认为阿尔茨海默氏症是由大的纤维结构引起的，但最近的许多研究表明，导致短期记忆丧失的长时程增强抑制和导致细胞死亡的神经毒性是由于肽的较小寡聚体组装造成的。最近的研究也表明并证实了神经毒性涉及低聚物与膜的相互作用，并且ABP确实形成了跨膜离子通道。然而，不幸的是，ABP的水和膜结合的低聚结构对环境的特殊性非常敏感，并且随着时间的推移而变化，这一事实阻碍了直接的实验测定。因此，我们通过将所有最近的实验数据与计算分子建模技术相结合来更新我们的ABP结构模型。我们即将发表两篇论文，从水溶和膜结合的ABP的最小缔合追踪长纤维和离子通道结构的发展。我们现在将探索这些模型如何帮助设计修饰的多肽以形成更稳定的结构确定组件，以及它们如何作为药物设计的靶标。我们还一直在对Prion蛋白(PrP)的结构进行建模，PrP具有类似于ABP的氨基酸序列片段。这些模型旨在帮助药物开发，以对抗PrP引起的海绵状脑病。

The Molecular Modeling Core enjoys a long-standing collaboration with Dr. Robert Guys section in the Lab of Cell Biology. We have taken an evolutionary approach to the study of ion channel proteins, examining the structural changes that accompanied the development of Na+ and Ca2+ channels from K+ channels by making representative models of each subfamily. In this pursuit, we have recently published models of the prokaryotic NaChBac channel, which is an evolutionary link between the ancestor K+ channels and the descendent Na+ and Ca2+ channels. The models explain the delicate balance of amino acid residue types in the pore that determine the specific ion selectivity, and the coupling of the voltage-sensor and activation gate. We are now using these results as a stepping stone to model the more complex eukaryotic Na+ and Ca2+ channels. In collaboration with experimental groups, we will be using these models to analyze the molecular pharmacology of Ca2+ channel blockers (important in treating hypertension and heart disease in humans and potentially as antifungicides) and to better understand how mutations associated with genetic diseases alter the gating properties of Ca2+ channels. Recently, we have also revisited our past work modeling the ion channel structures formed by the Amyloid-Beta Peptide (ABP) associated with Alzheimers disease. While it used to be thought that Alzheimers was caused by large fibril structures, numerous recent studies now indicate that the inhibition of long-term potentiation responsible for short-term memory loss and the neurotoxicity responsible for cell death are due to smaller oligomeric assemblies of the peptides. Recent studies also indicate and confirm that the neurotoxity involves interactions of the oligomers with membranes and that ABP indeed forms transmembrane ion channels. Unfortunately, however, direct experimental determination has been hampered by the fact that both aqueous and membrane-bound oligomeric structures of ABP are very sensitive to the specifics of the environment, and change over time. Consequently, we have updated our modeling of ABP structures by combining all the recent experimental data with computational molecular modeling techniques. We are about ready to publish two papers that trace the development of both long fibrils and ion channel structures from the smallest associations of aqueous-soluble and membrane-bound ABP. We will now explore how these models can help design modified peptides to form more stable assemblies for structure determination, and how they can serve as targets for drug design. We have also been modeling structures of the Prion Protein (PrP), which has segments of amino acid sequence similar to ABP. These models are intended to help pharmaceutical development to combat the spongiform encephalopathies caused by PrP.