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.

蛋白质是在生物体中通过连接数百甚至数千个氨基酸形成线性链而合成的非常大的生物分子，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、蛋白质药物（例如胰岛素）和传递免疫力的抗体都是众所周知的例子。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，而这些形状关键取决于。两种温度该项目的目的是增强对蛋白质在极端条件下（即低于水冰点的极低温度和/或数百个大气压的极高压力下）所呈现的不同形状的理解。这需要了解这些条件下（例如海洋和极地）存在的广阔生态系统中的生命，了解这些形状与蛋白质功能、蛋白质相关疾病、蛋白质疫苗开发和蛋白质药物配方的关系，并增强生物技术工程和该研究有助于制定在这种极端条件下预测蛋白质形状及其能量特性的规则，并且新开​​发的方法和计算工具将提供给更广泛的科学界。 - 对研究人员（包括来自代表性不足群体的科学家）进行跨学科培训，为了实现这一目标并提高对 STEM 的整体兴趣，Kuhlman 和 Szyperski 博士参与了学校致力于促进包容性社区的成熟重大举措，保留他们还参与 NSF 资助的本科生研究机会，并提供有关“关键”的网络研讨会，以了解（生物）物理化学和（生物）物理编程研讨会，重点关注分子方法。还将提供建模。在不同温度/压力下占主导地位的蛋白质的不同三维分子形状之间的关系与其分子能量和熵有关，这由所谓的“能量景观”表示。在低温下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，其中包括“冷”低能/低熵状态的结构和热力学特性。为了了解它们向其他状态的转变，以及对蛋白质压力-温度“相图”的更深入的理解，我们采用了一种结合计算从头蛋白质设计、尖端生物物理技术和分子动力学 (MD) 模拟的独特方法。专门测试中央结构和热力学假设，即（i）混合疏水/亲水蛋白质核心导致部分冷的展开冷状态，其中水分子形成一个组成部分，（ii）这在复杂的能量景观中得到体现，（iii）这个结果这种冷态形成的独特热力学特征，以及（iv）冷态形成的协同性随着折叠核心亲水含量的增加而降低。此外，该研究为解决这一假设奠定了基础。寒冷的国家可以即使在细胞数量很少的环境条件下，其功能也很重要。最后，开发了新的计算设计方案，该方案促进或实现了包含冷未折叠蛋白质的β折叠的设计，以及将折叠的天然存在的蛋白质重新设计为未折叠的同系物。该项目得到了分子和细胞生物科学部分子生物物理学集群的支持。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准。