Accelerated Molecular Dynamics Simulations Of Phosphate Binding Proteins

Phosphorous, an essential element for life, is used in the agriculture for fertilizing and is necessary for sustaining the global food supply. Unfortunately it is a limited resource, and some estimates predict depletion within this century. To avoid future food scarcity it is crucial to recover the lost phosphorous. One potential approach for recovery is to employ suitable proteins in a biomimetic application. Phosphate binding proteins which are natively found in Escherichia coli have evolved for optimized binding of phosphate with a high affinity and selectivity. These proteins can potentially be engineered for phosphate recovery due to their ability to bind and release phosphates repeatedly without consuming other resources.Understanding the protein behavior at the molecular level is critical for implementing them in a phosphate scavenging application. This includes studying the protein configurations, motions, binding and release mechanism by computational methods. Molecular dynamics is a useful tool for studying protein-ligand interactions, however one needs sufficient sampling to discover the entire configuration space. This is achieved by running accelerated Molecular Dynamics using Graphics Processing Units with CUDA in the simulation software AMBER.Preliminary results shows how the protein closes, and makes a hydrogen bonded network to the phosphate anion, when it is in the vicinity of the binding site. Oppositely, if the phosphate anion is missing from the binding site, the protein opens up again, ready to receive a new ligand. Furthermore the binding energies, hydrogen bond mechanism and effects of binding site mutations are investigated.