Proteins at Work: Computational Biopolymer Science of Energy, Electron, Proton Transfer and Ligand Migration

Molecular functions of folded proteins are investigated in the light of biophysical computations. In particular, we have focused on the molecular mechanism of photoreceptor proteins. Using theoretical/computational techniques, I study what happens in these photoreceptor proteins after light illumination and how these proteins convert light energy into conformational changes. Vibrational relaxations and molecular dynamics play crucial roles in heat, energy and signal transfer processes. I introduced a new concept of site-site energy conductivity and successfully characterized the intramolecular communication chart of the photoactive yellow protein. Analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans revealed the active role of the protein environment in the electron transfer. I observed busy trafficking of electron-tunneling currents at the methionine residue, Met-353. Interestingly, the amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyase.