Multi-scale modeling of gas transport through channels in living cells

DESCRIPTION (provided by applicant): The transport of gases across cell membranes is one of the most fundamental of physiological processes-O2 for oxidative metabolism, CO2 for acid-base balance, and NH3 for waste disposal. CO2 retention and hyperammonemia are key components of diseases that are major public health concerns. The traditional dogma had been that all gases cross all cell membranes by diffusing through membrane lipid. However, some membranes are gas impermeable and require protein 'gas channels' such as the aquaporins AQP1 (abundant in red blood cells) and AQP5 (abundant in airway epithelia) to conduct gases such as CO2 and NH3. Movement of these gases through AQPs results in a disturbance of pH in microdomains around the channels that we can measure using a pH microelectrode. However, the mechanism of gas conduction is poorly understood. Molecular dynamic simulations, measurements of the pH beneath an electrode touching the surface (pHS) of a model spherical cell (Xenopus oocytes), as well as a mathematical model addressing these pHS changes have provided the first insights into CO2 and NH3 movement through channels. However, a fundamental understanding of such movements across cell membranes requires more advanced multi-scale mathematical models (microscopic, mesoscopic, sub-macroscopic and macroscopic) in order to elucidate mechanisms of gas permeation in normal and pathological states. The PIs (Drs. Boron, Somersalo, and Tajkhorshid) propose to combine state-of-the-art molecular dynamic simulations and computational modeling with novel experimental studies to develop a predictive mathematical model for permeation of various gases across diverse cell membranes of different protein composition, based on integration of data from complementary methodologies across a range of spatial and temporal scales. We will run molecular dynamic simulations of NH3 and CO2 passage through wild-type, mutant, chemically modified, and metal-bound aquaporins in Aim 1 to predict single channel permeabilities (microscopic scale) that will inform the modeling in Aim 2 and cell physiology in Aim 3. In Aim 2, we will create new computational models of gas transport through single and multiple aquaporins in a lipid bilayer (mesoscopic scale), beneath the pHS electrode (sub-macroscopic scale) and in the whole cell (macroscopic scale). Finally in Aim 3, informed by Aims 1 and 2, we will validate the simulations and models in oocytes using electrophysiological and optical methods.

描述（由申请人提供）：气体跨细胞膜的运输是用于氧化代谢的生理过程中最基本的一项，酸碱平衡的二氧化碳和用于废物处理的NH3。二氧化碳保留和高氨比是主要公共卫生问题的疾病的关键组成部分。传统的教条是所有气体通过通过膜脂质扩散而穿越所有细胞膜。但是，某些膜是不渗透的，需要蛋白质的“气通道”，例如水通道蛋白AQP1（红细胞丰富）和AQP5（在气道上皮中丰富）以进行CO2和NH3等气体。这些气体通过AQP的运动导致在通道周围微区域中pH的干扰，我们可以使用pH微电极进行测量。但是，气体传导的机制知之甚少。分子动力学模拟，在电极下的pH值接触球形细胞（Xenopus卵母细胞）的表面（pHS）的测量，以及解决这些pHS变化的数学模型，为CO2和NH3通过通道运动提供了第一个洞察力。但是，对整个细胞膜运动的基本理解需要更先进的多规模数学模型（显微镜，介观，亚宏观和宏观镜），以阐明正常和病理状态中气体渗透机制。 PIS（Boron博士，Somersalo和Tajkhorshid）提议将最新的分子动力学模拟和计算模型与新型实验研究结合起来，以开发一种预测性数学模型，以渗透到不同蛋白质组成的各种细胞膜中的各种气体的渗透性，该模型是基于互补方法的整合范围跨互补方法的整合范围跨互补方法组成的。我们将通过AIM 1中的野生型，突变体，化学修饰和金属结合的水通道蛋白来进行NH3和CO2通过的分子动态模拟，以预测单个通道渗透率（微观尺度），该模型将在AIM 3中为AIM 2和细胞生理中的建模提供了AIM 3中的模型。在pHS电极（亚宏观尺度）和整个细胞（宏观尺度）之下。最后，在AIM 3中，通过AIMS 1和2告知，我们将使用电生理和光学方法验证卵母细胞中的模拟和模型。