Structure, Dynamics and Thermodynamics of Biomolecules

本项目将利用经验力场分析和预测生物分子的结构、动力学和热力学。特别是，将执行一个与联合国环境资源潜力的新接口，对其进行基准测试，并用于研究新系统。UNRES是一个粗粒度模型，以联合原子为特征，简化了景观并加速了采样。最初的应用将考虑与病毒感染相关的结构蛋白，例如来自SARS-CoV2的蛋白质E病毒孔蛋白五聚体。进一步的工作将把分析扩展到核酸的相应力场，以治疗RNA和DNA。然后就可以解决蛋白质与核酸的相互作用。这些粗粒度模型应该提供一种方便的方法来处理聚合或产生液-液相分离以产生无膜隔室的肽。这些能力将为聚合和相分离现象提供新的见解，并帮助我们理解替代肽序列产生不同涌现特性的倾向。

This project will analyse and predict the structure, dynamics and thermodynamics of biomolecules using empirical force fields. In particular, a new interface to the UNRES potential will be implemented, benchmarked, and employed to study new systems. UNRES is a coarse-grained model, featuring united atoms, which simplifies the landscape and accelerates sampling. Initial applications will consider structural proteins associated with viral infection, such as the protein E viroporin pentamer from SARS-CoV2. Further work will extend the analysis to the corresponding force field for nucleic acids, to treat RNA and DNA. Protein interactions with nucleic acids can then be addressed. These coarse-grained models should provide a convenient way to treat peptides that aggregate or produce liquid-liquid phase separation to produce membraneless compartments. These capabilities will provide new insight in the aggregation and phase separation phenomena, and help us to understand the propensity of alternative peptide sequences to produce different emergent properties.