Molecular dynamics (MD) simulations have become an essential tool for studying the structure-function relationships of proteins with known crystal structures. We are committed to developing the application of MD simulations in photosynthesis research to achieve structural insights into the complex photosynthetic processes in thylakoid membranes.

Introduction of molecular dynamics simulations services in photosynthesis

Photosynthesis is a complex physiological process regulated by dynamic interactions between proteins, pigments, lipids, enzymes and cofactors. With the rapid development of high-performance computer clusters and efficient parallel molecular modeling software, MD simulations provide a powerful toolkit to study the dynamics of (bio)molecular ensembles at different scales. Thus, MD simulations are well suited to solve various problems arising in the field of photosynthesis research.

Photosynthetic systems contain a variety of large photoactive pigment-protein complexes (PPCs) that convert the energy of absorbed light into electronic excitations and electrochemical potential gradients in photosynthetic organisms. PPCs have been the subject of numerous experimental and theoretical studies, however, understanding the function of PPCs at the atomic level is still a challenge to be overcome. The development of MD simulation techniques enables the characterization of energy transfer and electron transfer processes, which provide potential strategies for researchers in the field of photosynthesis.

Fig.1 Schematic of the thylakoid membrane and of the light reactions. (Liguori, 2020)