Collaborative Research: Energy Landscapes of Designed Cold Unfolding Proteins

合作研究：设计的冷展开蛋白质的能量景观

• 批准号: 2319819
• 负责人: Brian Kuhlman
• 金额: $ 20.69万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2319819&HistoricalAwards=false
• 关键词: Collaborative; Research; Energy; Landscapes; Designed

Proteins are very large biological molecules synthesized in living organisms by linking hundreds or even thousands of amino acids to form a linear chain. Proteins are required for life and they are thus important targets for fundamental and biomedical research, including drug development, and biotechnology. Enzymes catalyzing biochemical reactions, protein drugs such as insulin, and antibodies conveying immunity are well-known examples. Importantly, the biological function of proteins is intimately linked to the many different three-dimensional shapes the linear chains can adopt, and these shapes depend critically on both temperature and pressure. The objective of this project is to enhance the understanding of the distinct shapes which proteins adopt at extreme conditions, that is, at very low temperatures below the freezing point of water and/or at very high pressures of several hundreds of atmospheres. This is required to understand life in the vast ecosystems existing under these conditions (e.g. in oceans and the polar regions), to understand how these shapes relate to protein function, protein related diseases, protein vaccine development, and protein drug formulation, and to enhance the engineering of bio-technologically and bio-medically important ‘cold adapted proteins’. The research contributes to develop rules to predict protein shapes and their energetic properties under such extreme conditions, and newly developed methodologies and computational tools will be made available to the broader scientific community. The project enables cross-interdisciplinary training of researchers, including scientists from underrepresented groups. To pursue this goal and to increase interest in STEM in general, Drs. Kuhlman and Szyperski, participate in well-established, major initiatives at their schools which are dedicated to promote inclusive communities, to retain underrepresented students in STEM and to mentor students. They also participate in NSF-funded research opportunities for undergraduates, and offer webinars on ‘linchpins’ for the understanding of (bio)physical chemistry and (bio)physics. Programming workshops focusing on methods for molecular modeling will also be offered.The relationship between the different three-dimensional molecular shapes of proteins dominating at different temperatures / pressures is related to their molecular energies and entropies, which are represented by so called ‘energy landscapes’. Proteins which tend to lose a well-defined shape at low temperatures have been named ‘cold unfolding proteins’. Research focuses on exploring and understanding the energy landscapes of such proteins. This includes the structural and thermodynamic properties of the ‘cold’ low energy / low entropy states, their transitions to other states and, in general, a more advanced understanding of protein pressure-temperature ‘phase diagrams’. A unique approach combining computational de novo protein design, cutting-edge biophysical techniques and molecular dynamics (MD) simulations is employed in order to specifically test central structural and thermodynamic hypotheses, namely that (i) a mixed hydrophobic / hydrophilic protein core results in a partially cold unfolded cold state in which water molecules form an integral part, (ii) this is manifested in complex energy landscapes, (iii) this results in a distinct thermodynamic signature for the formation of such cold states, and (iv) the co-operativity of the formation of the cold states decreases with an increasing hydrophilic content of the folded core. Moreover, the research lays the foundation to tackle the hypothesis that cold states can be functionally important, even at ambient conditions when they are lowly populated. Finally, new computational design protocols are developed which facilitate or enable the design of beta-sheet containing cold unfolding proteins, and the redesign of folded, naturally occurring proteins to congeners which unfold under extreme conditions in order to validate newly established principles. This project is supported by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences.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.

蛋白质是通过将数百甚至数千种氨基酸连接以形成线性链来合成的生物分子。蛋白质是生命所必需的，因此它们是基础和生物医学研究（包括药物开发和生物技术）的重要目标。催化生化反应的酶，胰岛素等蛋白质药物和输送免疫力的抗体是众所周知的例子。重要的是，蛋白质的生物学功能与线性链可以采用的许多不同的三维形状密切相关，并且这些形状批评温度和压力都取决于温度和压力。该项目的目的是增强对蛋白质在极端条件下采用的不同形状的理解，也就是说，在低于水的冰点和/或数百种气氛的极高压力下，在非常低的温度下。这是在这些条件下（例如在海洋和极地地区）中存在的巨大生态系统中的生活，以了解这些形状如何与蛋白质功能，蛋白质相关疾病，蛋白质疫苗的发育和蛋白质药物配方奶粉以及增强生物技术和生物学重要性的“冷适应蛋白”的工程。该研究有助于制定规则，以预测这种极端条件下的蛋白质形状及其能量性能，新开发的方法和计算工具将提供给更广泛的科学界。该项目可以对研究人员进行跨学科培训，包括来自代表性不足的群体的科学家。追求这一目标并增加对STEM的兴趣，Drs。库尔曼（Kuhlman）和西普斯基（Szyperski）参加了他们的学校良好的主要举措，这些举措致力于促进包容性社区，保留代表性不足的学生在STEM和精神学生中。他们还为本科生提供了NSF资助的研究机会，并为“ Linchpins”的网络研讨会提供了了解（BIO）物理化学和（BIO）物理学的理解。还将提供关注分子建模方法的编程研讨会。在不同温度 /压力下统治的蛋白质的不同三维分子形状之间的关系与它们的分子能量和熵有关，这些蛋白质由所谓的“能量景观”所代表的。在低温下倾向于失去明确形状的蛋白质被称为“冷展开蛋白质”。研究重点是探索和了解此类蛋白质的能量景观。这包括“冷”低能 /低熵状态的结构和热力学特性，它们向其他状态的过渡，并且通常对蛋白质压力温度“相位图”有更先进的理解。采用一种独特的方法，结合了从头蛋白质设计，尖端的生物物理技术和分子动力学（MD）模拟，以特异性测试中心的结构和热力学假设，即（i）（i）（i）（i）混合疏水 /亲水性蛋白质核心在一个部分冷的状态中形成了一个冷冷的状态，即在该状态下造成的摩尔群落（II）II II II II II II II II构成了II的集成（景观，（iii）这会导致形成这种冷态的独特热力学特征，以及（iv）冷态形成的合作性随着折叠核的亲水性含量的增加而降低。此外，该研究奠定了基础，以解决以下假设：即使在人口较低的环境条件下，冷状态在功能上也很重要。最后，开发了新的计算设计方案，这些方案有助于或实现包含冷蛋白的beta表的设计，以及在极端条件下展开的折叠式，自然发生的蛋白质的重新设计，以验证新确定的原则。该项目得到了分子和细胞生物科学划分的分子生物物理学群集的支持。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响审查标准，通过评估被认为是宝贵的支持。