Structure, Dynamics and Thermodynamics of Biomolecules

点击翻译按钮获取中文摘要

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.