Bridging molecular studies of model and real biological systems with biophysics experiments on complex samples

将模型和真实生物系统的分子研究与复杂样品的生物物理学实验联系起来

• 批准号: RGPIN-2018-05154
• 负责人: Booth, Valerie
• 金额: $ 2.62万
• 依托单位: Memorial University of Newfoundland
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=744066
• 关键词: Bridging; molecular; studies; model; real

The theme of the NSERC-based research in our lab is bridging model and real biological systems. The rationale for this approach is that detailed, molecular level, structural and dynamics research on biological molecules is generally done with systems of very simple composition, e.g. with one type of lipid and one type of protein. However, it's not always clear how the results from these simple systems compare to what goes on in the real, much more complex biological systems. Thus, our approach is to build bridges between the biophysical methods that have been developed for simple systems and extend them to much more complex biological systems in order to gain important insights into real life molecular structure and dynamics. With this Discovery Grant renewal, I am planning two main foci. Objective 1 will build on our already successful NSERC research into how antimicrobial peptides (AMPs) interact with intact bacteria. AMPs are a crucial component of the innate immune system of many organisms and can protect against a variety of invading pathogens including bacteria, viruses, and microbial eukaryotes. However, our understanding of how AMPs work does not extend much past how they interact with one component of pathogens: the lipids. With Objective 2, we will apply our expertise in performing biophysics with complex biological samples into a new area to us, soft interactions in molecular crowding, initially as applied to Intrinsically Disordered Proteins (IDPs). Molecular crowding, i.e. the effect of the very high concentration of biomolecules inside cells, is important because it can modify the structure and function of biological molecules compared to what is observed in dilute conditions via traditional biochemistry experiments.The potential impact of Objective 1 relates to the enormous disparity between conditions used for studies of AMP molecular mechanisms, versus experiments where biological functional is actually observed; it takes an AMP to lipid ratio of ~10,000 greater to see inhibition of cell growth as compared to the ratio needed to see lipid bilayer disruption with a model lipid system. Thus, it is of high interest to find out with which components, besides the lipids, the AMP is interacting and how the non-lipid interactions modify the AMP-induced membrane disruption. There has been a high level of interest in the earlier phase of our work in this area, as evidenced by three invited reviews on the topic, and we expect this high interest to continue.Our results from Objective 2 will impact the field via building a much needed and novel bridge to better understand how the large body of work performed on simple crowding systems can be applied to real cells. Conversely, our results should also help explain observations gleaned from in-cell experiments. Additionally, our work will provide valuable insights into parameters of interest in getting quality data with any kind of protein via in-cell NMR.

我们实验室基于 NSERC 的研究主题是桥接模型和真实生物系统。这种方法的基本原理是，对生物分子的详细、分子水平、结构和动力学研究通常是使用非常简单组成的系统来完成的，例如具有一种类型的脂质和一种类型的蛋白质。然而，我们并不总是清楚这些简单系统的结果与真实的、更复杂的生物系统中发生的结果相比如何。因此，我们的方法是在为简单系统开发的生物物理方法之间建立桥梁，并将其扩展到更复杂的生物系统，以获得对现实生活分子结构和动力学的重要见解。通过续签发现补助金，我计划了两个主要重点。 目标 1 将建立在我们已经成功的 NSERC 关于抗菌肽 (AMP) 如何与完整细菌相互作用的研究的基础上。 AMP 是许多生物体先天免疫系统的重要组成部分，可以防御多种入侵的病原体，包括细菌、病毒和微生物真核生物。 然而，我们对 AMP 工作原理的理解并没有超出它们如何与病原体的一种成分（脂质）相互作用。通过目标 2，我们将利用复杂生物样品进行生物物理学方面的专业知识，将其应用到一个新领域，即分子拥挤中的软相互作用，最初应用于本质无序蛋白质 (IDP)。分子拥挤，即细胞内生物分子浓度非常高的影响，非常重要，因为与传统生物化学实验在稀释条件下观察到的结果相比，它可以改变生物分子的结构和功能。目标 1 的潜在影响涉及用于 AMP 分子机制研究的条件与实际观察生物功能的实验之间的巨大差异；与使用模型脂质系统观察脂质双层破坏所需的比率相比，AMP 与脂质的比率要高出约 10,000 倍才能看到对细胞生长的抑制。 因此，找出除脂质之外 AMP 与哪些成分相互作用以及非脂质相互作用如何改变 AMP 诱导的膜破坏是非常有意义的。正如该主题的三篇受邀评论所证明的那样，人们对我们在这一领域的早期阶段的工作表现出高度的兴趣，并且我们预计这种高度兴趣将继续下去。我们的目标 2 的结果将通过建立一个急需的新颖桥梁来影响该领域，以更好地理解如何将在简单拥挤系统上进行的大量工作应用于真实细胞。相反，我们的结果也应该有助于解释从细胞内实验中收集到的观察结果。此外，我们的工作将为通过细胞内 NMR 获取任何类型蛋白质的质量数据的相关参数提供有价值的见解。