CAREER: In Silico Single-Molecule Force Spectroscopy

该奖项部分由2021年美国救援计划法案（公法117-2）资助。其他资金由生物科学理事会分子和细胞生物科学部的分子生物物理学项目和刺激竞争性研究的既定项目（EPSCoR）提供。从石器时代起，人类就知道机械力可以用来弯曲和折断材料。年幼的孩子凭直觉塑造橡皮泥，在决定撕扯或捏捏材料时，他们没有意识到自己在控制剪切力，而施加的力的方向决定了它们的效果。然而，如果我们放大到生物分子，应用机械力的结果就变得不那么直观了。事实上，在剪切力作用下的化学反应非常有趣，相对较软的键会变得非常牢固，这取决于施加在它们身上的力。这种有趣的行为对所有细胞的内部运作至关重要，因为蛋白质经常受到机械力的影响。通常，这些力的方向性和振幅可以调节生物活动。在这个项目中，研究人员不仅研究了具有机械活性的蛋白质的有趣行为，也就是说，它们会根据施加在它们身上的力做出不同的反应，而且还开发了计算工具，使研究它们的原子细节成为可能。特别是，在好细菌和坏细菌表面发现的机械活性蛋白将被研究，以阐明它们如何对剪切力具有极强的弹性，并允许感染在我们体内发生。此外，将开发新的沉浸式技术来观察剪切力载荷下的这些蛋白质，为“道路上的沉浸式生物物理学”项目提供动力，在该项目中开发的工具和知识将被带到阿拉巴马州历史上STEM代表性不足的地区。然后，一个可充气的投影圆顶将被用来教授生命的分子机制。该项目的长期目标是用原子和亚原子分辨率来表征蛋白质：细胞外蛋白质复合物具有显著的机械稳定性的蛋白质相互作用。该项目的中心假设是，进化创造了几何结构，不同的蛋白质在机械压力下使用这些几何结构变得更强，在需要时也可以模块化和灵活。这一假设是基于初步的工作，该工作表明了一个简单的几何机制，负责机械稳定性，但在分子水平上实现这一假设是具有挑战性的。这里的基本原理是，理解起作用的分子细节将允许操纵机械稳定性；用于指导能够抑制粘附过程的分子的开发；并建议开发生物技术工具，这些工具可以从这些蛋白质的机械稳定性中获益。这些目标将通过以下方式实现：开发生物信息学工具来复活纤维素体蛋白的祖先，以了解机械稳定性是如何进化的；2. 研究葡萄球菌与人类细胞外基质形成高度稳定结合的机制。特别是，本项目将采用经典分子动力学、混合量子/经典计算和降维方法的结合，以表征蛋白质在机械应力下的亚原子性质。此外，通过将新的分子动力学方法实现到图形用户界面中，分析和可视化将变得更加容易。大多数新的实现将被纳入QwikMD，它将结合基于人工智能的结构预测新方法，以及新的沉浸式可视化渲染，这将允许使用便携式天文馆式圆顶和虚拟现实耳机进行科学推广。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This award is funded in part under the American Rescue Plan Act of 2021 (Public Law 117-2). Other funding was provided by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and by the Established Program to Stimulate Competitive Research (EPSCoR).Since the stone age, humans know that mechanical forces can be used to bend and break materials. Young children intuitively shape playdough, unaware that they are controlling shear-forces when deciding to tear or pinch the material, where the direction of applied force defines their effects. However, the outcomes of applied mechanical forces become much less intuitive if we zoom into biomolecules. In fact, chemistry at shear forces is quite intriguing, with relatively soft bonds becoming very strong depending on how force is applied to them. Such intriguing behavior is crucial for the inner workings of all cells, where proteins are often under the influence of mechanical forces. Frequently, the directionality and amplitude of these forces can regulate biological activities. In this project, the researchers are not only investigating the intriguing behavior of proteins that are mechanoactive, that is, that react differently depending on the forces applied on them, but also developing computational tools that make it possible to study them with atomic detail. Particularly, mechanoactive proteins that are found in the surface of both good and bad bacteria will be investigated to elucidate how they become extremally resilient to shear forces and allow infections to take place within our bodies. Additionally, new immersive technologies will be developed to observe these proteins under shear-force load, powering the “Immersive Biophysics on the Road” program, where tools and knowledge developed in this project will be taken to areas in Alabama that are historically underrepresented in STEM. An inflatable projection dome will then be used to teach the molecular mechanisms of life. The long-term goal of this project is to characterize, with atomic and sub-atomic resolution, the protein:protein interactions responsible for the remarkable mechanostability of extracellular protein complexes. The central hypothesis of this project is that evolution has created geometrical artifices that are used by different proteins to become stronger when under mechanical stress, and also modular and flexible when needed. This hypothesis is based on preliminary work that has shown a simple geometric mechanism responsible for mechanostability, but that is challenging to be achieved at the molecular level. Here, the rationale is that understanding the molecular details at play will allow for the manipulation of mechanostability; for guiding the development of molecules that can inhibit adhesion processes; and for proposing the development of biotechnology tools that could profit from the mechanostability of these proteins. These goals will be achieved by: 1. developing bioinformatic tools to resurrect cellulosomal proteins ancestors to understand how mechanostability evolved; 2. Investigating the mechanism by which staph bacteria form highly-stable bonds to the human extra-cellular matrix. Particularly, this project will employ a combination of classical molecular dynamics, hybrid quantum/classical calculations, and dimensionality reduction methods, in order to characterize sub-atomic properties of proteins under mechanical stress. Additionally, new molecular dynamics methods for analysis and visualization will be made easier by implementing them into graphical user interfaces. Most of the new implementations will be made into QwikMD, which will incorporate new methods for structure prediction based on artificial intelligence, as well as new immersive visualization renderings, which will allow for the use of portable planetarium-like domes and virtual reality headsets for science outreach.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.