Fast model systems for misfolding, binding and aggregation

用于错误折叠、绑定和聚合的快速模型系统

• 批准号: 9042853
• 负责人: MARTIN GRUEBELE
• 金额: $ 27.87万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2017-09-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9042853
• 关键词: Adult; Amyloid; Amyloidosis; Binding; Binding Proteins; Binding Sites; Biological Models; Chimera organism; Communities; Complement; Complex; Computers; Coupled; Data; Deglutition; Development; Device or Instrument Development; Diffusion; Disease; Dissociation; Elements; Engineering; Equilibrium; Event; Experimental Models; Eyelid structure; Feedback; Free Energy; Future; Generations; Goals; Grant; Health; Illinois; Kinetics; Knowledge; Lasers; Learning; Measures; Micelles; Mining; Modeling; Mutation; Nucleic Acids; Pathway interactions; Plant Roots; Population; Postdoctoral Fellow; Process; Proteins; RNA; RNA Binding; RNA-Binding Proteins; Reaction; Relaxation; Relaxation Techniques; Research; Resolution; Signal Transduction; Site; Sorting - Cell Movement; Speed; Structure; Students; System; Technology; Time; U1A protein; United States National Institutes of Health; Visit; Work; base; crosslink; improved; instrument; interest; intermolecular interaction; meetings; millisecond; molecular dynamics; monomer; next generation; protein aggregation; protein folding; prototype; research study; simulation; single molecule; success; supercomputer; temperature jump

DESCRIPTION (provided by applicant): Fast (microsecond) experiments and molecular dynamics simulation are finally working hand-in-hand to provide validated atomistic pictures of protein folding dynamics. Larger proteins and millisecond folders are around the corner, although empirical force fields need more improvement before mechanistic predictions become as reliable as average rate coefficients or native structures. It is time to extend this simulation experiment interplay to misfolding, aggregation and binding processes. The problem is that such processes are usually slow - seconds to days. In order to compare experiment and simulation directly during the next 4 years, when simulations will not reach far beyond the 1 ms regime yet, the solution is simple: create small and fast experimental model systems for misfolding, aggregation and binding. These are analogous to fast two-state and downhill folding studied during the last 10 years: certainly not all proteins fold that way, but much useful was learned from our ability to directly compare such model proteins with simulation. Here, we propose development of: 1) λ6-85 as a model system for sheet-containing misfolded traps (T denaturation and T-jumps) as well as excess helix-containing traps (P denaturation, P-jumps). The key is that all folding and misfolding events are completed in ~ 1 ms or faster. 2a) Fast-folding tethered proteins (WW and λ6-85) to facilitate the interplay between transient aggregation and folding. Oligomeric aggregates include chimeras with elements swapped among monomers, as well as less structured aggregates. Tethering allows high effective concentrations without going to high protein concentration (leading to uncontrollable aggregation), and also helps keep MD simulation by keeping reactants in close proximity. 2b) U1A-RNA binding to multiple sites on U1A protein will be a fast model system for binding at multiple sites. 3) For the next generation of misfolding/aggregation/binding research, we will develop a single molecule instrument capable of high throughput (106 molecules/day) and studying 2 or more molecules interacting without cross-linking them or confining them in a micelle. Five simulation groups have been brought on board (Schulten, Shaw, Cheung, Luthey-Schulten and Pande), and their students/postdocs are already working closely with mine so simulation can be developed in parallel with the experiments. The goal is to provide data in the few microsecond to few millisecond range, amenable to full atom simulation over the next 4 years, so misfolding/aggregation/binding processes can be studied at the atomistic level, but on systems small and fast enough for simulation to work. We build on our knowledge of λ6-85, WW domain and U1A, so much is known experimentally and computationally about the monomeric building blocks of our misfolding/aggregation/binding models.

描述（由适用提供）：快速（微秒）实验和分子动力学模拟最终与蛋白质折叠动力学的验证原子图片一起工作。较大的蛋白质和毫秒文件夹即将到来，尽管经验力场需要更多的改进，然后才能与平均速率系数或天然结构一样可靠。现在是时候扩展此模拟了 实验与错误折叠，聚集和结合过程的相互作用。问题在于，此类过程通常很慢 - 秒至几天。为了在接下来的4年中直接比较实验和仿真，当模拟尚未超出1 ms制度时，解决方案很简单：创建小而快速的实验模型系统，以用于错误折叠，聚集和结合。在过去的10年中，这些类似于快速两态和下坡折叠研究：当然，并非所有蛋白质都以这种方式折叠，但是从我们将这种模型蛋白质与模拟进行比较的能力中学到了很多有用的东西。在这里，我们提出：1）λ6-85作为含薄片的错误折叠陷阱（T变性和T-Jumps）的模型系统，以及超过含螺旋的陷阱（P变性，P-Jumps）。关键是所有折叠和错误折叠事件均在〜1 ms或更快地完成。 2A）快速折叠的束缚蛋白（WW和λ6-85），以促进瞬态聚集和折叠之间的相互作用。寡聚聚集体包括嵌合体，其中元素在单体之间交换，结构化骨料较少。束缚允许高效浓度无需高蛋白浓度（导致无法控制的聚集），还可以通过使反应物保持紧邻，有助于保持MD模拟。 2B）U1A-RNA与U1a蛋白上多个位点结合的结合将是在多个位点结合的快速模型系统。 3）对于下一代的失误/聚集/结合研究，我们将开发一种能够具有高吞吐量的单个分子仪器（106个分子/天），并研究2个或更多的分子相互作用而不交联或将它们限制在胶束中。已经将五个模拟小组（Schulten，Shaw，Cheung，Luthey-Schulten和Pande）带入了，他们的学生/PostDocs已经与我的学生密切合作，因此可以与实验并行开发模拟。目的是在未来4年内提供几微秒至几毫秒范围内的数据，因此可以在未来4年内进行完全原子模拟，因此可以在原子级上研究错误折叠/聚合/结合过程，但是在系统上很小且足够快，足以仿真可以工作。我们基于对λ6-85，WW域和U1A的知识，在实验和计算上众所周知，关于我们错误折叠/聚合/结合模型的单体构建块。