From Ion Channel Structure to Function: Better Tools to Annotate Membrane Protein Structures

我们思考和移动的方式，以及我们与周围环境相互作用和感知的方式，只是由离子通道和膜转运蛋白控制的一些重要过程。实际上，身体中的几乎每一个过程都需要带电离子（如氯化钠等盐）或其他分子（如葡萄糖）进出我们的细胞。如果没有这些膜蛋白形成的微孔，细胞就只是一个不透气的塑料袋，无法与环境相互作用。因此，这些膜蛋白不仅对所有形式的“生物电”和细胞信号至关重要，而且对生命本身也至关重要。因此，目前50%的药物靶点被认为位于细胞膜内，这也许并不奇怪。这些蛋白质的重要性也推动了许多最新的进展，现在使我们能够以精致的细节可视化它们的3D结构。然而，这些图像仅仅代表了理解离子通道如何工作的漫长旅程的开始。这种理解的核心不仅是能够可视化离子通过这些蛋白质的跨膜途径，而且还能够识别这些孔内存在的任何障碍。这是重要的，因为控制这些障碍，使细胞电信号被打开或关闭。离子通常移动通过通道在他们的“水合”状态，即溶解在水中，因此以前的方法识别障碍主要集中在比较溶解的离子的相对大小，通过它移动的路径的大小。这种方法在过去被证明是非常有用的。然而，我们和其他人的研究现在清楚地表明，这些狭窄通道的相对油脂性或“疏水性”对离子的运动也有深远的影响，即它不仅仅是孔有多宽的问题。这是因为水的行为非常不同，在一个狭窄的油腻毛孔相比，一个表面很容易润湿或“湿”。因此，如果孔隙的一部分不容易充满水，那么离子就不能通过，并形成屏障。这一过程背后的科学原理也解释了为什么油和水不能混合，细胞膜和生物分子如何组装，以及为什么水对几乎所有形式的生命都是必不可少的。不幸的是，不可能直接可视化水在这种纳米尺寸的孔隙中的行为。然而，我们最近发现，被称为“分子动力学模拟”的强大计算方法可以准确地模拟这些过程，因此可以作为一个“计算显微镜”来可视化这种行为。使用这种方法，我们已经预测了疏水性障碍的存在，在几个新的通道结构。重要的是，我们已经用各种实验方法验证了这些预测，包括直接改变通道本身的“润湿性”。这些结果对我们理解这些离子通道的功能产生了重大影响。在这个项目中，我们将开发新的工具来模拟和预测水在膜孔和运输途径中的行为。这将使广泛的科学家，从普通用户到专业的结构生物学家，能够准确地预测任何新的或现有的蛋白质结构中的疏水屏障。为了支持这一点，我们将进一步完善和实验验证我们的计算方法在几个模型通道系统，以提高我们对这些过程的机械理解。这些预测工具的设计将考虑到最终用户的要求，并易于在从台式PC到超级计算机的许多不同平台上实施。该工具包旨在满足快速增长的功能注释需求，并将对理解离子通道和膜转运蛋白如何工作产生深远影响。

The way we think and move, as well as the way we interact with and perceive our surroundings are just a few of the important processes controlled by ion channels and membrane transport proteins. In effect, almost every process in the body requires the movement of charged ions (like salts such as sodium chloride), or other molecules (like glucose), into and out of our cells. Without the tiny pores created by these membrane proteins a cell would just be an impermeable plastic bag incapable of interacting with its environment.These membrane proteins are therefore not only essential for all forms of 'bioelectrical' and cellular signalling, but also for life itself. It is therefore perhaps not surprising that 50% of current drug targets are thought to reside within cell membranes. The importance of these proteins has also driven many recent advances that now allow us to visualise their 3-D structure in exquisite detail. However, these images represent only the beginning of a long journey to understand how an ion channel works.Central to this understanding is not only the ability to visualise the transmembrane pathways which ions take through these proteins, but also to identify any barriers which exist within these pores. This is important because controlling these barriers enables cellular electrical signals to be switched on or off.Ions generally move through channels in their 'hydrated' state i.e. dissolved in water, and so previous methods for identification of barriers have mostly focussed on comparing the relative size of a dissolved ion to the size of the pathway through which it moves. This approach has proven extremely useful in the past. However, studies by us and others, now clearly demonstrate that the relative greasiness or 'hydrophobicity' of these narrow pathways also has a profound influence on the movement of ions, i.e. it is not just a matter of how wide the holes are. This is because water behaves very differently in a narrow greasy pore compared to one where the surface is easily wetted or 'hydrophilic'. As a result, if a section of a pore does not easily fill with water then ions cannot pass through, and a barrier is created. The scientific principles underlying this process also explain why oil and water do not mix, how cell membranes and biomolecules assemble, and why water is so essential for nearly all forms of life.Unfortunately, it is not possible to directly visualise the behaviour of water in such nanometre-sized pores. However, we have recently shown that powerful computational methods known as 'Molecular Dynamics Simulations' can accurately model these processes and therefore act as a 'computational microscope' to visualise this behaviour. Using this approach we have predicted the existence of hydrophobic barriers in several novel channel structures. Importantly, we have validated these predictions with a variety of experimental approaches, including direct changes to the 'wettability' of the channel itself. These results have had a major impact on our understanding of how these ion channels function.In this project we will develop new tools to simulate and predict the behaviour of water in membrane pores and transport pathways. This will enable a wide range of scientists, from the casual user to expert structural biologist, to accurately predict these hydrophobic barriers in any new or existing protein structure. To underpin this we will improve our mechanistic understanding of these processes by further refining and experimentally validating our computational methods in several model channel systems. These predictive tools will be designed with the requirements of the end-user in mind and for easy implementation on a number of different platforms, ranging from desktop PCs to supercomputers. The toolkit aims to meet a rapidly increasing demand for functional annotation and will have a far reaching impact on understanding how ion channels and membrane transport proteins work.