IDBR Type A: Optimization of microsecond mixing devices for biological kinetics via simulation and experiment

马萨诸塞州大学医学院正在获得一项奖励，以开发微秒混合装置，使生物动力学研究成为可能。该奖项由生物基础设施部（生物科学理事会）的生物研究仪器开发部颁发，由化学，生物工程，环境和运输系统部（工程理事会）的流体动力学计划共同资助。 非技术摘要：蛋白质，RNA和蛋白质-RNA复合物在细胞中执行许多基本功能。生物化学反应在细胞内以微秒到毫秒的时间尺度发生，在此期间这些分子作为瞬时填充的中间结构存在，并且难以用常规方法观察。 蛋白质和RNA的折叠和组装是涉及瞬时中间体的生化反应的例子，科学家们研究这些中间体是为了更好地了解最终的功能构象是如何产生的。这些基础研究还有助于理解为什么一些较小的较少的构象可以导致异常功能，如聚集，如在一些人类疾病中。 研究这些部分或瞬时填充构象的一种方法是在瞬时构象仍以高群体存在时监测它们。 这需要非常快速地启动反应，通常在微秒内，并使用揭示结构信息的技术来观察它。本计画将提供研究生与本科生在生物物理与流体动力学的跨学科研究中实习的机会。研究人员希望与公司合作，一旦开发和测试完成，就将其商业化。技术摘要：在这个项目中，研究人员将开发由石英制成的微流体设备，可以通过在微秒内混合溶液来启动折叠和组装反应。 该设备的一个独特功能是它与小角度X射线散射测量（SAXS）和其他光学探头的兼容性。 SAXS是一种光谱工具，可以揭示大分子的大小，形状和低分辨率结构的信息。 最终目标是在反应期间的各个时间点生成大分子的结构快照（例如，RNA折叠）。 在这些微流体装置中，一旦溶液混合，距离就与时间成线性比例。 通过使微流体装置平移穿过光束，获得一系列时间测量。 与SAXS一起使用的微流体装置的先前实施方式受到时间分辨率或大量样品消耗的限制。 在该项目中，研究团队将使用计算流体动力学模拟来优化混合效率，以设计一种可以在时间范围内从微秒扩展到数百毫秒的设备。 该装置可以很容易地优化用于与其他探针的二级，三级和四级大分子结构。 该项目是实验生物物理学小组、计算流体动力学小组、致力于x射线物理学的国家实验室和专门从事石英加工的微细加工公司之间的跨学科合作。 由此产生的优化设备将提供给所有科学家研究生物大分子通过SAXS光束线在国家同步加速器。 将为对这一技术感兴趣的新用户举办讲习班，包括辅导和实验课程。

An award is being made to the University of Massachusetts Medical School, to develop microsecond mixing devices that will enable researh in biological kinetics. This award made by the Instrument Development for Biological Research, in the Division of Biological Infrastructure (Biological Sciences Directorate) is jointly funded by and the Fluid Dynamics program in the Division of Chemical, Bioengineering, Environmental and Transport Systems (Engineering Directorate). Non Technical Abstract:Proteins, RNA and protein-RNA complexes perform many essential functions in cells. Biochemcial reactions occur within a cell on the microsecond to millisecond timescale during which these molecules are present as transiently populated intermediate structures, and are difficult to observe with conventional methods. The folding and assembly of proteins and RNA are examples of biochemical reactions that involve transient intermediates, which scientists investigate in order to better understand how the final functional conformation is generated. Such fundamental studies also help to understand why some minor less populated conformations can result in aberrant function, such as aggregation, as in some human diseases. One approach to studying these partially or transiently populated conformations is to monitor them while the transient conformation is still present at a high population. This requires initiating a reaction very quickly, typically in microseconds, and observing it using a technique that reveals structural information. This project will provide opportunities for graduate students and undergraduates to be traiend in interdisciplinary research that straddles biophysics and fluid dynamics. The investigators hope to partner with companies to commercialize their device, once it is developed and tested. Technical Abstract:In this project, the researchers will develop microfluidic devices manufactured from quartz that can initiate folding and assembly reactions by mixing of solutions in microseconds. A unique feature of the device will be its compatibility with small-angle x-ray scattering measurements (SAXS) and other optical probes. SAXS is a spectroscopic tool that reveals information about the size, shape and low-resolution structure of macromolecules. The ultimate goal is to generate structural snapshots of macromolecules at various time points during a reaction (e.g., RNA folding). In these microfluidic devices, once the solutions are mixed, distance becomes linearly proportional to time. By translating the microfluidic device across the beam a series of time measurements is obtained. Previous implementations of microfluidic devices for use with SAXS have been limited by either time resolution or large sample consumption. In this project, the research team will optimize the mixing efficiency using computational fluid dynamics simulations to design a device that can extend from microseconds to hundreds of milliseconds in time range. The device can be easily optimized for use with other probes of secondary, tertiary and quaternary macromolecular structure. This project is an interdisciplinary collaboration between an experimental biophysics group, a computational fluid dynamics group, a national laboratory dedicated to x-ray physics and a microfabrication company specializing in quartz machining. The resulting optimized device will be available to all scientists studying biological macromolecules via SAXS beamlines at national synchrotrons. Workshops involving tutorial and experimental sessions will be provided to new users interested in this technology.