Characterization of flexible molecules in solution: the RGDW peptide

Molecular dynamics simulations with adaptive umbrella sampling of the potential energy are used to study conformations of the adhesion peptide RGDW. The peptide is simulated in a box of explicit water. It results in a combination of room temperature (300 K) simulations, in which conformations dominating the average properties of the system are sampled, with high temperature ( approximately 1000 K) simulations in which free energy barriers separating different local minima are crossed efficiently. The simulations with explicit water are compared to simulations of the isolated peptide using different treatments of the electrostatics, and to published experimental data. There is good agreement for data related to the backbone conformation of the peptide. Some discrepancies are evident for data related to side-chain conformations. Together the simulations and experiments provide a description of the RGDW system that is more detailed and reliable than what can be obtained by either simulations or experiments alone.