Virtually all processes in living organisms, from nutrient transport to the regulation of growth, are mediated by proteins. Gaining a detailed view of the biological processes occurring in plants requires understanding of the structure and function of the proteins involved in these processes. Sequence information is widely available for proteins across organisms, but structural information is still lacking, especially for plant proteins. Out of ~52 million protein sequences that are available on the UniProt databaseas of 2018, only 100000 (0.2%) have structures deposited in Protein Data Bank (PDB), and only~4000 (4%) of these structures are of plant proteins. Structural biology has provided valuable insights and high-resolution views of the bio-physical processes in plants, such as photosynthesis, hormone signaling, nutrient transport, and toxin efflux. However, structural biology only provides few “snapshots” of protein structure, whereas in vivo, protein function involves complex dynamical processes such as ligand binding and conformational changes that structures alone are unable to capture in full detail.
Here, we present molecular dynamics (MD) simulations as a “computational microscope” that can be used to capture detailed structural and dynamical information about the molecular machinery in plants and gain high-resolution insights into plant growth and function. In addition to the background information provided here, we have prepared a set of tutorials that allow students to run and explore MD simulations of plant proteins.