IDBR: Phase Diagram Visualizer (PDV) for Biomacromolecules

IDBR：生物大分子相图可视化工具 (PDV)

• 批准号: 0552084
• 负责人: Victor Barocas
• 金额: $ 27.69万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2009-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0552084&HistoricalAwards=false
• 关键词: IDBR; Phase; Diagram; Visualizer; PDV

This award is for the development of a new instrument called the Phase Diagram Visualizer (PDV). The PDV will be used to optimize the conditions for crystallizing proteins. This has a large potential value, because the ability to crystallize proteins is currently a bottleneck in efforts to determine protein structures. The PDV is a novel microfluidic device for creating overlapping concentration gradients of protein, precipitant, and buffer. Crystal formation will be visualized, and software will determine the phase diagram of the system, based on the diffusion constants for the protein and other solutes. The PDV's microfluidic device will have a chamber with a wide, shallow central platform region and four surrounding wells. Two wells will be filled with buffer, one with protein solution, and one with a potential precipitant (e.g., sodium chloride). Diffusion from the wells into the platform region will create stable concentration gradients of protein and precipitant, and crystals will form only in regions where the two concentrations are above the saturation level. A three-dimensional microfluidic feed system will be constructed to allow multiple working units to operate in parallel. Once the crystallization is complete, the user will construct a light micrograph of the results, and the software component of the PDV be used. The software will solve the diffusion problem to determine the solution composition in the platform region, and then each pixel will be converted from (x,y) values to concentrations of protein and precipitant, and the corresponding points will be used to construct a phase diagram for the protein-precipitant system. Thus, a single experiment will generate the entire solution phase diagram. The phase diagram will then be available for use in a variety of phase-diagram-based methods for crystal growth. The broad impact of the Phase Diagram Visualizer will be considerable. A conservative estimate of the human proteome is 100,000 proteins, and only a few thousand have been structurally characterized. Given that the major obstacle to protein structure characterization is growing a large, high quality crystal, access to phase diagram information will be a boon to structural biologists. Structural biology has impact not only on basic cell science but also on public health through understanding of disease and design of new drugs. The project will also contribute to Education and Human Resources through the training of a graduate student and an undergraduate who will work together, to their mutual benefit. A modified version of the PDV will make an excellent demonstration for use in undergraduate or secondary teaching, illustrating fundamental scientific concepts such as diffusion and solubility.

该奖项是为了开发一种名为相图可视化仪（PDV）的新仪器。 PDV将用于优化蛋白质结晶的条件。这具有很大的潜在价值，因为结晶蛋白质的能力目前是确定蛋白质结构的瓶颈。PDV是一种新型的微流体装置，用于产生蛋白质、沉淀剂和缓冲液的重叠浓度梯度。晶体形成将被可视化，软件将根据蛋白质和其他溶质的扩散常数确定系统的相图。PDV的微流体装置将具有一个腔室，该腔室具有宽而浅的中心平台区域和四个周围的威尔斯。两个威尔斯孔将填充缓冲液，一个填充蛋白质溶液，一个填充潜在沉淀剂（例如，氯化钠）。从威尔斯孔扩散到平台区域将产生蛋白质和沉淀剂的稳定浓度梯度，并且晶体将仅在两种浓度高于饱和水平的区域中形成。一个三维的微流体进料系统将被构建，以允许多个工作单元并行操作。一旦结晶完成，用户将构建结果的光学显微照片，并使用PDV的软件组件。该软件将解决扩散问题，以确定平台区域中的溶液组成，然后将每个像素从（x，y）值转换为蛋白质和沉淀剂的浓度，并将相应的点用于构建蛋白质-沉淀剂系统的相图。因此，一个单一的实验将产生整个溶液相图。然后，相图将可用于各种基于相图的晶体生长方法。相图可视化工具的广泛影响将是相当大的。人类蛋白质组的保守估计是10万种蛋白质，只有几千种蛋白质具有结构特征。鉴于蛋白质结构表征的主要障碍是生长大的、高质量的晶体，获得相图信息将是结构生物学家的布恩。结构生物学不仅对基础细胞科学产生影响，而且通过对疾病的理解和新药的设计对公共卫生产生影响。该项目还将通过培训一名研究生和一名本科生，为教育和人力资源做出贡献，他们将共同努力，互惠互利。PDV的修改版本将为本科或中学教学提供很好的演示，说明基本的科学概念，如扩散和溶解度。