A New Pradigm for the Rational Expression of Integral Membrane Proteins

摘要 整合膜蛋白（IMP）具有基本的科学和医学重要性，因为它们支配细胞膜， 营养和信息在细胞膜上的流动，因为它们构成了最大的一类治疗药物， 目标的然而，IMP的结构和生物物理特性远远落后于其他蛋白质类别，这是由于 无法可靠地生产大量的IMP用于实验研究。根本差距在于 目前还不存在理解氨基酸和核苷酸之间联系的框架 IMP的序列及其表达水平，技术上的根本差距在于， 没有成功的战略 用于一般预测和改善IMP表达水平。 目前的工作将消除这些根本差距 通过以下创新组合，在知识和技术方面发挥作用：（i）表征IMP表达的实验方法 水平，跨越多个蛋白质家族和表达系统，（ii）严格的数据驱动策略， 不同IMP序列特性对表达的作用，以及（iii）粗粒度分子动力学方法， 模拟-在无偏的生物时间尺度上-作为IMP表达瓶颈的关键机制步骤。 加州理工学院的米勒和克莱蒙斯实验室的拟议合作在这方面具有独特的优势 努力，创造一个新的范例，合理表达IMP的机会。拟议研究的成功 将通过提供强大且可访问的计算工具来增加IMP表达，从而产生变革性影响 对于研究界来说，通过推进这一庞大而重要的蛋白质类别的基本特征， 以及加速医疗和制药应用。

ABSTRACT Integral membrane proteins (IMPs) are of both fundamental scientific and medical importance, because they govern the flow of nutrients and information across cell membranes and because they comprise the largest class of therapeutic drug targets. However, the structural and biophysical characterization of IMPs lags far behind that of other protein classes, due to the inability to reliably produce significant quantities of IMPs for experimental studies. The fundamental gap in knowledge is that no framework currently exists for understanding the connection between the amino-acid and nucleotide sequence of an IMP and its expression level, and the fundamental gap in technology is that no successful strategies exist for the general prediction and improvement IMP expression levels. The current work will remove these fundamental gaps in knowledge and technology via the innovative combination of (i) experimental methods to characterize IMP expression levels, spanning across multiple protein families and expression systems, (ii) rigorous data-driven strategies to disentangle the role of diverse IMP sequence properties on expression, and (iii) coarse-grained molecular dynamics methods to enable the simulation - on unbiased biological timescales - of key mechanistic steps that act as bottlenecks to IMP expression. The proposed collaboration of the Miller and Clemons laboratories at Caltech is uniquely positioned to succeed in this effort, creating the opportunity for a new paradigm for the rational expression of IMPs. Success of the proposed research will have transformational impact by providing powerful and accessible computational tools for increased IMP expression to the research community, by advancing the fundamental characterization of this large and important class of proteins, and by accelerating medical and pharmaceutical applications.