第160回 第2部

X-ray crystallography has been the most important experimental method to obtain the structural information of biomolecules. However, there are some limitations on it. For example, using X-ray crystallography, it is difficult to capture the conformational dynamics of bio-macromolecules in solution, which is closely related with their functions. In addition, this technique requires molecules to be crystallized. So it is difficult to apply to insoluble molecules or intrinsically disordered proteins. Limitations of crystallography are being complemented by alternative methods in both experimental and computational methods. In this presentation, I will show two kind of computational studies to capture biological molecular structures and dynamics.
First topic is "Thermodynamic properties of water molecules around DNA". DNA strands can adopt many structures in addition to Watson-Crick duplex, which depend on the solvent conditions. To understand how cosolute molecules such as ethylene glycol affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around the different DNA structures using grid inhomogeneous solvation theory (GIST). I will discuss free energy of water molecules dependence on DNA structures in the presence of cosolutes.
Second topic is "Three-dimensional reconstruction from diffraction images obtained by X-ray free electron laser experiment". Single particle analysis using X-ray free electron laser (XFEL) enables us to observe hard-to-crystallize biomolecules in a state close to nature. In order to restore 3D structures of the molecule from the diffraction images obtained by XFEL experiments, estimation of laser beam incidence angles to the molecule for each image and phase retrieval are required. For this purpose, we are developing an algorithm, “slice matching”. I will show the results of simulation study of slice matching for large biomolecule, ribosome, and the trials for applying our slice matching protocol for two experimental data. Also, I will discuss the requirements for the experimental conditions to obtain the diffraction images to restore the molecular structure at certain resolution.